Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6109584.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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_6109584.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6109584.pdb" } 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: 1.78, per 1000 atoms: 0.53 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 130.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.88: 354 0.88 - 1.14: 1254 1.14 - 1.41: 606 1.41 - 1.67: 899 1.67 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.074 0.252 1.10e-02 8.26e+03 5.25e+02 bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 0.978 0.258 1.14e-02 7.69e+03 5.13e+02 bond pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " ideal model delta sigma weight residual 1.326 1.539 -0.213 1.10e-02 8.26e+03 3.75e+02 bond pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta sigma weight residual 1.459 1.682 -0.223 1.23e-02 6.61e+03 3.28e+02 bond pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta sigma weight residual 1.540 1.330 0.209 1.17e-02 7.31e+03 3.19e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 3134 4.50 - 9.00: 1817 9.00 - 13.51: 653 13.51 - 18.01: 154 18.01 - 22.51: 19 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 77 " pdb=" C LEU A 77 " pdb=" O LEU A 77 " ideal model delta sigma weight residual 120.42 134.22 -13.80 1.06e+00 8.90e-01 1.70e+02 angle pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" O SER A 85 " ideal model delta sigma weight residual 120.32 134.53 -14.21 1.10e+00 8.26e-01 1.67e+02 angle pdb=" O SER A 3 " pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 123.10 108.37 14.73 1.15e+00 7.56e-01 1.64e+02 angle pdb=" O SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " ideal model delta sigma weight residual 122.96 137.30 -14.34 1.13e+00 7.83e-01 1.61e+02 angle pdb=" O ASP A 131 " pdb=" C ASP A 131 " pdb=" N BLYS A 132 " ideal model delta sigma weight residual 122.15 136.13 -13.98 1.14e+00 7.69e-01 1.50e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.80: 1290 16.80 - 33.60: 133 33.60 - 50.40: 37 50.40 - 67.20: 17 67.20 - 83.99: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -146.39 23.79 0 2.50e+00 1.60e-01 9.06e+01 dihedral pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual 122.80 141.79 -18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" N LEU A 77 " pdb=" C LEU A 77 " pdb=" CA LEU A 77 " pdb=" CB LEU A 77 " ideal model delta harmonic sigma weight residual 122.80 141.70 -18.90 0 2.50e+00 1.60e-01 5.72e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.233: 104 0.233 - 0.459: 75 0.459 - 0.685: 39 0.685 - 0.910: 21 0.910 - 1.136: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.45 -1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -3.72 1.10 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.52e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.053 2.00e-02 2.50e+03 7.11e-02 1.52e+02 pdb=" CG ATYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.102 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.083 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.090 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.091 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.051 2.00e-02 2.50e+03 7.37e-02 1.22e+02 pdb=" CG HIS A 126 " 0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.145 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.063 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.085 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.050 2.00e-02 2.50e+03 6.22e-02 1.16e+02 pdb=" CG BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.087 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.008 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.082 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.020 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.070 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1294 2.36 - 2.92: 8315 2.92 - 3.48: 10443 3.48 - 4.04: 15052 4.04 - 4.60: 21546 Nonbonded interactions: 56650 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.794 2.450 nonbonded pdb=" O LEU A 58 " pdb=" H LYS A 62 " model vdw 1.837 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.844 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.845 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.846 2.270 ... (remaining 56645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_6109584_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3623 r_free= 0.2065 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464147 | | target function (ml) not normalized (work): 22008.244966 | | target function (ml) not normalized (free): 1144.683600 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3803 0.2356 4.8516 4.92| | 2: 3.78 - 3.00 1.00 2430 110 0.3403 0.1572 4.0655 4.0549| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.79 0.83 0.13 6616.69| | 2: 3.78 - 3.00 2430 110 0.93 11.39 1.48 0.26 443.21| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 374.59 max = 12080.20 mean = 3573.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.35| |phase err.(test): min = 0.00 max = 89.94 mean = 33.65| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.258 1557 Z= 5.426 Angle : 5.213 16.162 2118 Z= 3.693 Chirality : 0.407 1.136 243 Planarity : 0.032 0.103 284 Dihedral : 14.506 83.994 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.11 % 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: -1.34 (0.53), residues: 224 helix: -2.39 (0.40), residues: 102 sheet: -0.59 (0.89), residues: 30 loop : 1.29 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.105 0.019 ARG A 28 TYR 0.101 0.031 TYR A 139 PHE 0.071 0.025 PHE A 164 HIS 0.099 0.048 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3623 r_free= 0.2065 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464147 | | target function (ml) not normalized (work): 22008.244966 | | target function (ml) not normalized (free): 1144.683600 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3577 0.3653 0.2148 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3577 0.3653 0.2148 n_refl.: 5182 remove outliers: r(all,work,free)=0.2524 0.2547 0.2148 n_refl.: 5178 overall B=-2.82 to atoms: r(all,work,free)=0.2416 0.2436 0.2107 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1562 0.1559 0.1618 n_refl.: 5178 remove outliers: r(all,work,free)=0.1557 0.1554 0.1618 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3850 449.783 410.978 0.671 1.062 0.407 11.894-9.307 99.02 97 4 0.1874 714.517 696.172 0.947 1.058 0.393 9.237-7.194 100.00 213 7 0.2184 584.333 576.889 0.979 1.051 0.364 7.162-5.571 100.00 427 22 0.2306 438.471 425.087 0.939 1.040 0.303 5.546-4.326 100.00 867 58 0.1365 601.958 595.187 0.986 1.022 0.247 4.315-3.360 100.00 1859 96 0.1295 572.469 565.936 1.049 0.991 0.192 3.356-3.002 100.00 1373 60 0.1622 440.940 433.052 1.063 0.960 0.043 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6034 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1554 r_free=0.1618 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1554 r_free=0.1618 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.628630 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.894328 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1783 0.0624 0.010 1.0 2.6 0.5 0.0 0 9.814 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 17.83 6.24 3.013 16.041 1.894 0.018 10.23 17.91 7.68 4.816 16.179 1.894 0.015 Individual atomic B min max mean iso aniso Overall: 2.21 111.85 17.33 5.26 1785 0 Protein: 2.21 111.85 14.63 5.25 1519 0 Water: 4.05 111.48 33.05 N/A 258 0 Other: 15.75 35.50 23.76 N/A 8 0 Chain A: 2.21 111.85 17.33 N/A 1785 0 Histogram: Values Number of atoms 2.21 - 13.17 928 13.17 - 24.14 474 24.14 - 35.10 187 35.10 - 46.07 111 46.07 - 57.03 55 57.03 - 67.99 14 67.99 - 78.96 7 78.96 - 89.92 5 89.92 - 100.89 1 100.89 - 111.85 3 =========================== Idealize ADP of riding H ========================== r_work=0.1023 r_free=0.1791 r_work=0.1017 r_free=0.1793 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1793 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1014 r_free = 0.1793 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1014 r_free= 0.1793 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014024 | | target function (ls_wunit_k1) not normalized (work): 69.052845 | | target function (ls_wunit_k1) not normalized (free): 10.726331 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1054 0.1014 0.1793 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2088 0.2087 0.2229 n_refl.: 5176 remove outliers: r(all,work,free)=0.2088 0.2087 0.2229 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2049 0.2046 0.2219 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1057 0.1017 0.1788 n_refl.: 5176 remove outliers: r(all,work,free)=0.1057 0.1017 0.1788 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3317 330.393 311.482 0.679 1.008 0.381 11.894-9.307 99.02 97 4 0.1521 524.855 518.003 0.988 1.008 0.361 9.237-7.194 100.00 213 7 0.1677 429.228 429.633 1.026 1.008 0.331 7.162-5.571 100.00 427 22 0.1641 322.083 318.287 0.981 1.006 0.302 5.546-4.326 100.00 867 58 0.0908 442.174 439.487 1.000 1.003 0.222 4.315-3.360 100.00 1859 96 0.0769 420.513 420.447 1.040 0.998 0.193 3.356-3.002 100.00 1373 60 0.1011 323.897 322.035 1.016 0.993 0.047 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3902 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1017 r_free=0.1788 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1017 r_free=0.1788 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1788 | n_water=258 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.1041 r_free=0.1772 | n_water=248 | time (s): 20.200 (total time: 20.760) Filter (q & B) r_work=0.1040 r_free=0.1776 | n_water=245 | time (s): 1.830 (total time: 22.590) Compute maps r_work=0.1040 r_free=0.1776 | n_water=245 | time (s): 0.610 (total time: 23.200) Filter (map) r_work=0.1341 r_free=0.1851 | n_water=146 | time (s): 1.590 (total time: 24.790) Find peaks r_work=0.1341 r_free=0.1851 | n_water=146 | time (s): 0.420 (total time: 25.210) Add new water r_work=0.1682 r_free=0.2110 | n_water=231 | time (s): 1.260 (total time: 26.470) Refine new water occ: r_work=0.1143 r_free=0.1707 adp: r_work=0.1121 r_free=0.1696 occ: r_work=0.1119 r_free=0.1686 adp: r_work=0.1109 r_free=0.1683 occ: r_work=0.1108 r_free=0.1679 adp: r_work=0.1106 r_free=0.1674 ADP+occupancy (water only), MIN, final r_work=0.1106 r_free=0.1674 r_work=0.1106 r_free=0.1674 | n_water=231 | time (s): 3.740 (total time: 30.210) Filter (q & B) r_work=0.1106 r_free=0.1674 | n_water=231 | time (s): 1.000 (total time: 31.210) Filter (dist only) r_work=0.1109 r_free=0.1660 | n_water=229 | time (s): 17.840 (total time: 49.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.698603 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.842234 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1004 0.1791 0.0787 0.009 1.0 4.2 0.5 0.6 0 11.349 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.04 17.91 7.87 4.635 16.695 2.842 0.014 9.41 18.28 8.87 5.359 17.069 2.842 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.77 16.48 6.41 1756 0 Protein: 0.00 108.77 14.86 6.38 1519 0 Water: 0.00 63.27 26.88 N/A 229 0 Other: 14.05 39.39 26.27 N/A 8 0 Chain A: 0.00 108.77 15.67 N/A 1671 0 Chain S: 4.30 60.16 32.44 N/A 85 0 Histogram: Values Number of atoms 0.00 - 10.88 693 10.88 - 21.75 665 21.75 - 32.63 204 32.63 - 43.51 114 43.51 - 54.38 42 54.38 - 65.26 26 65.26 - 76.14 5 76.14 - 87.02 4 87.02 - 97.89 1 97.89 - 108.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.0941 r_free=0.1828 r_work=0.0938 r_free=0.1829 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0938 r_free = 0.1829 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0936 r_free = 0.1820 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0936 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011883 | | target function (ls_wunit_k1) not normalized (work): 58.513548 | | target function (ls_wunit_k1) not normalized (free): 10.089918 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0981 0.0936 0.1820 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2111 0.2115 0.2187 n_refl.: 5176 remove outliers: r(all,work,free)=0.2111 0.2115 0.2187 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2111 0.2115 0.2187 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0980 0.0935 0.1833 n_refl.: 5176 remove outliers: r(all,work,free)=0.0979 0.0933 0.1833 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3128 327.610 318.523 0.692 1.012 0.382 11.894-9.307 99.02 97 4 0.1447 524.855 518.781 0.979 1.013 0.370 9.237-7.194 100.00 213 7 0.1464 429.228 431.205 1.014 1.012 0.300 7.162-5.571 100.00 427 22 0.1420 322.083 319.251 0.984 1.010 0.290 5.546-4.326 100.00 867 58 0.0785 442.174 439.707 1.001 1.006 0.240 4.315-3.360 100.00 1859 96 0.0719 420.513 420.266 1.046 0.999 0.190 3.356-3.002 100.00 1373 60 0.0975 323.897 322.852 1.027 0.992 0.068 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.7637 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0933 r_free=0.1833 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0934 r_free=0.1834 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0934 r_free=0.1834 | n_water=229 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.0946 r_free=0.1811 | n_water=225 | time (s): 18.950 (total time: 19.630) Filter (q & B) r_work=0.1027 r_free=0.1803 | n_water=222 | time (s): 1.810 (total time: 21.440) Compute maps r_work=0.1027 r_free=0.1803 | n_water=222 | time (s): 0.650 (total time: 22.090) Filter (map) r_work=0.1294 r_free=0.1875 | n_water=150 | time (s): 1.780 (total time: 23.870) Find peaks r_work=0.1294 r_free=0.1875 | n_water=150 | time (s): 0.510 (total time: 24.380) Add new water r_work=0.1665 r_free=0.2185 | n_water=235 | time (s): 1.550 (total time: 25.930) Refine new water occ: r_work=0.1050 r_free=0.1747 adp: r_work=0.1044 r_free=0.1765 occ: r_work=0.1032 r_free=0.1747 adp: r_work=0.1033 r_free=0.1753 occ: r_work=0.1022 r_free=0.1734 adp: r_work=0.1023 r_free=0.1741 ADP+occupancy (water only), MIN, final r_work=0.1023 r_free=0.1741 r_work=0.1023 r_free=0.1741 | n_water=235 | time (s): 10.230 (total time: 36.160) Filter (q & B) r_work=0.1023 r_free=0.1744 | n_water=234 | time (s): 1.920 (total time: 38.080) Filter (dist only) r_work=0.1022 r_free=0.1738 | n_water=233 | time (s): 17.920 (total time: 56.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.074816 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.265140 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0928 0.1812 0.0884 0.011 1.1 4.8 0.5 0.6 0 0.537 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.28 18.12 8.84 5.358 17.685 0.265 5.149 8.88 18.00 9.11 7.373 17.702 0.265 5.059 Individual atomic B min max mean iso aniso Overall: 0.00 108.26 16.34 9.13 1760 0 Protein: 0.00 108.26 15.01 9.11 1519 0 Water: 0.00 58.27 24.69 N/A 233 0 Other: 10.61 40.49 26.00 N/A 8 0 Chain A: 0.00 108.26 15.78 N/A 1659 0 Chain S: 0.00 57.03 25.59 N/A 101 0 Histogram: Values Number of atoms 0.00 - 10.83 686 10.83 - 21.65 660 21.65 - 32.48 226 32.48 - 43.30 118 43.30 - 54.13 36 54.13 - 64.95 16 64.95 - 75.78 10 75.78 - 86.60 4 86.60 - 97.43 3 97.43 - 108.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.0888 r_free=0.1800 r_work=0.0894 r_free=0.1808 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0894 r_free = 0.1808 target_work(ml) = 5.064 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0882 r_free = 0.1790 target_work(ml) = 5.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0882 r_free= 0.1790 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.056875 | | target function (ml) not normalized (work): 24894.996402 | | target function (ml) not normalized (free): 1840.400845 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0929 0.0882 0.1790 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2116 0.2131 0.2011 n_refl.: 5175 remove outliers: r(all,work,free)=0.2116 0.2131 0.2011 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2116 0.2131 0.2011 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0922 0.0877 0.1786 n_refl.: 5175 remove outliers: r(all,work,free)=0.0920 0.0875 0.1786 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3515 329.789 301.546 0.618 0.996 0.348 11.894-9.307 99.02 97 4 0.1744 524.855 511.305 0.954 0.998 0.340 9.237-7.194 100.00 213 7 0.1840 429.228 424.496 0.995 1.000 0.295 7.162-5.571 100.00 427 22 0.1798 322.083 313.599 0.974 1.000 0.290 5.546-4.326 100.00 867 58 0.0908 442.174 437.544 0.994 1.001 0.240 4.315-3.360 100.00 1859 96 0.0588 420.513 420.180 1.043 1.002 0.200 3.356-3.002 100.00 1373 60 0.0598 323.897 323.274 1.024 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-5.8910 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0875 r_free=0.1786 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0876 r_free=0.1781 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0876 r_free=0.1781 | n_water=233 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0880 r_free=0.1792 | n_water=232 | time (s): 19.670 (total time: 20.330) Filter (q & B) r_work=0.0928 r_free=0.1805 | n_water=230 | time (s): 1.260 (total time: 21.590) Compute maps r_work=0.0928 r_free=0.1805 | n_water=230 | time (s): 0.440 (total time: 22.030) Filter (map) r_work=0.1235 r_free=0.1824 | n_water=155 | time (s): 1.500 (total time: 23.530) Find peaks r_work=0.1235 r_free=0.1824 | n_water=155 | time (s): 0.530 (total time: 24.060) Add new water r_work=0.1562 r_free=0.2100 | n_water=234 | time (s): 1.760 (total time: 25.820) Refine new water occ: r_work=0.1000 r_free=0.1792 adp: r_work=0.0997 r_free=0.1805 occ: r_work=0.0988 r_free=0.1783 adp: r_work=0.0988 r_free=0.1793 occ: r_work=0.0980 r_free=0.1768 adp: r_work=0.0979 r_free=0.1779 ADP+occupancy (water only), MIN, final r_work=0.0979 r_free=0.1779 r_work=0.0979 r_free=0.1779 | n_water=234 | time (s): 13.280 (total time: 39.100) Filter (q & B) r_work=0.0980 r_free=0.1786 | n_water=232 | time (s): 1.380 (total time: 40.480) Filter (dist only) r_work=0.0996 r_free=0.1778 | n_water=228 | time (s): 19.050 (total time: 59.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.029803 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.211624 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0911 0.1866 0.0955 0.011 1.0 4.5 0.5 0.0 0 0.515 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.11 18.66 9.55 7.085 17.869 0.212 5.056 8.91 18.84 9.93 8.225 18.005 0.212 4.996 Individual atomic B min max mean iso aniso Overall: 0.00 108.48 16.67 10.72 1755 0 Protein: 0.00 108.48 15.44 10.71 1519 0 Water: 0.00 56.89 24.48 N/A 228 0 Other: 14.38 44.81 26.67 N/A 8 0 Chain A: 0.00 108.48 16.11 N/A 1647 0 Chain S: 0.00 56.89 25.08 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.85 660 10.85 - 21.70 676 21.70 - 32.54 228 32.54 - 43.39 107 43.39 - 54.24 47 54.24 - 65.09 16 65.09 - 75.93 10 75.93 - 86.78 8 86.78 - 97.63 1 97.63 - 108.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.0891 r_free=0.1884 r_work=0.0896 r_free=0.1885 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0896 r_free = 0.1885 target_work(ml) = 5.001 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0886 r_free = 0.1866 target_work(ml) = 4.994 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0886 r_free= 0.1866 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.994229 | | target function (ml) not normalized (work): 24581.594853 | | target function (ml) not normalized (free): 2041.024699 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0886 0.1866 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2095 0.2100 0.2159 n_refl.: 5174 remove outliers: r(all,work,free)=0.2095 0.2100 0.2159 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2095 0.2100 0.2159 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0884 0.1869 n_refl.: 5174 remove outliers: r(all,work,free)=0.0934 0.0884 0.1869 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3723 329.789 301.741 0.632 0.989 0.350 11.894-9.307 99.02 97 4 0.1859 524.855 507.298 0.949 0.993 0.330 9.237-7.194 100.00 213 7 0.2065 429.228 422.222 1.000 0.996 0.300 7.162-5.571 100.00 427 22 0.2048 322.083 310.947 0.983 0.997 0.290 5.546-4.326 100.00 867 58 0.0967 442.174 436.642 1.006 0.999 0.224 4.315-3.360 100.00 1859 96 0.0565 420.513 420.652 1.068 1.002 0.210 3.356-3.002 100.00 1373 60 0.0480 323.897 323.775 1.052 1.005 0.076 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1128 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0884 r_free=0.1869 After: r_work=0.0887 r_free=0.1867 ================================== NQH flips ================================== r_work=0.0887 r_free=0.1867 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0887 r_free=0.1870 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0887 r_free=0.1870 | n_water=228 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0897 r_free=0.1877 | n_water=225 | time (s): 17.710 (total time: 18.310) Filter (q & B) r_work=0.1004 r_free=0.1895 | n_water=221 | time (s): 1.400 (total time: 19.710) Compute maps r_work=0.1004 r_free=0.1895 | n_water=221 | time (s): 0.540 (total time: 20.250) Filter (map) r_work=0.1252 r_free=0.1939 | n_water=158 | time (s): 1.560 (total time: 21.810) Find peaks r_work=0.1252 r_free=0.1939 | n_water=158 | time (s): 0.580 (total time: 22.390) Add new water r_work=0.1547 r_free=0.2131 | n_water=230 | time (s): 1.250 (total time: 23.640) Refine new water occ: r_work=0.0999 r_free=0.1862 adp: r_work=0.0989 r_free=0.1867 occ: r_work=0.0981 r_free=0.1860 adp: r_work=0.0981 r_free=0.1860 occ: r_work=0.0974 r_free=0.1855 adp: r_work=0.0974 r_free=0.1855 ADP+occupancy (water only), MIN, final r_work=0.0974 r_free=0.1855 r_work=0.0974 r_free=0.1855 | n_water=230 | time (s): 11.800 (total time: 35.440) Filter (q & B) r_work=0.0974 r_free=0.1856 | n_water=228 | time (s): 1.590 (total time: 37.030) Filter (dist only) r_work=0.0975 r_free=0.1850 | n_water=226 | time (s): 17.710 (total time: 54.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.947572 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.256494 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0929 0.1840 0.0911 0.011 1.1 6.7 0.5 0.6 0 0.474 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.29 18.40 9.11 8.146 18.203 0.256 5.030 9.09 18.56 9.47 8.955 18.325 0.256 4.974 Individual atomic B min max mean iso aniso Overall: 0.00 110.63 16.92 11.91 1753 0 Protein: 0.00 110.63 15.81 11.90 1519 0 Water: 0.00 58.81 23.97 N/A 226 0 Other: 14.46 44.72 27.53 N/A 8 0 Chain A: 0.00 110.63 16.36 N/A 1638 0 Chain S: 0.00 58.81 24.86 N/A 115 0 Histogram: Values Number of atoms 0.00 - 11.06 675 11.06 - 22.13 643 22.13 - 33.19 243 33.19 - 44.25 114 44.25 - 55.31 40 55.31 - 66.38 15 66.38 - 77.44 11 77.44 - 88.50 7 88.50 - 99.56 3 99.56 - 110.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.0909 r_free=0.1856 r_work=0.0913 r_free=0.1860 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0913 r_free = 0.1860 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0905 r_free = 0.1857 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0905 r_free= 0.1857 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.973054 | | target function (ml) not normalized (work): 24477.370488 | | target function (ml) not normalized (free): 2124.237192 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1292 0.1870 5.5504 6.1702| | 2: 3.78 - 3.00 1.00 2430 110 0.0435 0.1837 4.3809 11.346| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.37 1.00 0.98 13526.81| | 2: 3.78 - 3.00 2430 110 0.99 1.84 1.00 1.00 934.60| |alpha: min = 0.97 max = 1.01 mean = 0.99| |beta: min = 594.92 max = 22601.92 mean = 7310.01| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 88.82 mean = 7.17| |phase err.(test): min = 0.00 max = 83.29 mean = 7.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0953 0.0905 0.1857 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2143 0.2147 0.2209 n_refl.: 5174 remove outliers: r(all,work,free)=0.2143 0.2147 0.2209 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2143 0.2147 0.2209 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0951 0.0903 0.1857 n_refl.: 5174 remove outliers: r(all,work,free)=0.0951 0.0903 0.1857 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3763 329.789 303.730 0.620 0.992 0.336 11.894-9.307 99.02 97 4 0.1942 524.855 509.051 0.949 0.997 0.320 9.237-7.194 100.00 213 7 0.2194 429.228 422.552 1.002 1.000 0.290 7.162-5.571 100.00 427 22 0.2158 322.083 310.974 0.980 1.001 0.280 5.546-4.326 100.00 867 58 0.1043 442.174 436.313 1.017 1.002 0.240 4.315-3.360 100.00 1859 96 0.0571 420.513 420.370 1.091 1.002 0.217 3.356-3.002 100.00 1373 60 0.0416 323.897 323.432 1.079 1.002 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0871 ================= 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 : 0.3623 0.2065 0.081 5.213 8.8 119.3 19.9 258 0.000 1_bss: 0.1554 0.1618 0.081 5.213 6.0 116.5 17.1 258 0.000 1_settarget: 0.1554 0.1618 0.081 5.213 6.0 116.5 17.1 258 0.000 1_nqh: 0.1554 0.1618 0.081 5.213 6.0 116.5 17.1 258 0.000 1_weight: 0.1554 0.1618 0.081 5.213 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1159 0.1783 0.010 0.998 6.0 116.5 17.1 258 0.202 1_adp: 0.1023 0.1791 0.010 0.998 2.2 111.9 17.3 258 0.202 1_regHadp: 0.1017 0.1793 0.010 0.998 2.2 111.9 17.3 258 0.202 1_occ: 0.1014 0.1793 0.010 0.998 2.2 111.9 17.3 258 0.202 2_bss: 0.1017 0.1788 0.010 0.998 1.3 110.9 16.4 258 0.202 2_settarget: 0.1017 0.1788 0.010 0.998 1.3 110.9 16.4 258 0.202 2_updatecdl: 0.1017 0.1788 0.010 1.015 1.3 110.9 16.4 258 0.202 2_nqh: 0.1017 0.1788 0.010 1.015 1.3 110.9 16.4 258 0.202 2_sol: 0.1109 0.1660 0.010 1.015 1.0 110.9 15.8 229 n/a 2_weight: 0.1109 0.1660 0.010 1.015 1.0 110.9 15.8 229 n/a 2_xyzrec: 0.1004 0.1791 0.009 0.962 1.0 110.9 15.8 229 n/a 2_adp: 0.0941 0.1828 0.009 0.962 0.0 108.8 16.5 229 n/a 2_regHadp: 0.0938 0.1829 0.009 0.962 0.0 108.8 16.5 229 n/a 2_occ: 0.0936 0.1820 0.009 0.962 0.0 108.8 16.5 229 n/a 3_bss: 0.0933 0.1833 0.009 0.962 0.0 108.8 16.5 229 n/a 3_settarget: 0.0933 0.1833 0.009 0.962 0.0 108.8 16.5 229 n/a 3_updatecdl: 0.0933 0.1833 0.009 0.968 0.0 108.8 16.5 229 n/a 3_nqh: 0.0934 0.1834 0.009 0.968 0.0 108.8 16.5 229 n/a 3_sol: 0.1022 0.1738 0.009 0.968 0.0 108.8 16.3 233 n/a 3_weight: 0.1022 0.1738 0.009 0.968 0.0 108.8 16.3 233 n/a 3_xyzrec: 0.0928 0.1812 0.011 1.060 0.0 108.8 16.3 233 n/a 3_adp: 0.0888 0.1800 0.011 1.060 0.0 108.3 16.3 233 n/a 3_regHadp: 0.0894 0.1808 0.011 1.060 0.0 108.3 16.3 233 n/a 3_occ: 0.0882 0.1790 0.011 1.060 0.0 108.3 16.3 233 n/a 4_bss: 0.0875 0.1786 0.011 1.060 0.0 108.3 16.3 233 n/a 4_settarget: 0.0875 0.1786 0.011 1.060 0.0 108.3 16.3 233 n/a 4_updatecdl: 0.0875 0.1786 0.011 1.075 0.0 108.3 16.3 233 n/a 4_nqh: 0.0876 0.1781 0.011 1.075 0.0 108.3 16.3 233 n/a 4_sol: 0.0996 0.1778 0.011 1.075 0.0 108.3 16.4 228 n/a 4_weight: 0.0996 0.1778 0.011 1.075 0.0 108.3 16.4 228 n/a 4_xyzrec: 0.0911 0.1866 0.011 1.041 0.0 108.3 16.4 228 n/a 4_adp: 0.0891 0.1884 0.011 1.041 0.0 108.5 16.7 228 n/a 4_regHadp: 0.0896 0.1885 0.011 1.041 0.0 108.5 16.7 228 n/a 4_occ: 0.0886 0.1866 0.011 1.041 0.0 108.5 16.7 228 n/a 5_bss: 0.0884 0.1869 0.011 1.041 0.0 108.5 16.7 228 n/a 5_settarget: 0.0884 0.1869 0.011 1.041 0.0 108.5 16.7 228 n/a 5_updatecdl: 0.0884 0.1869 0.011 1.047 0.0 108.5 16.7 228 n/a 5_setrh: 0.0887 0.1867 0.011 1.047 0.0 108.5 16.7 228 n/a 5_nqh: 0.0887 0.1870 0.011 1.047 0.0 108.5 16.7 228 n/a 5_sol: 0.0975 0.1850 0.011 1.047 0.0 108.5 16.7 226 n/a 5_weight: 0.0975 0.1850 0.011 1.047 0.0 108.5 16.7 226 n/a 5_xyzrec: 0.0929 0.1840 0.011 1.106 0.0 108.5 16.7 226 n/a 5_adp: 0.0909 0.1856 0.011 1.106 0.0 110.6 16.9 226 n/a 5_regHadp: 0.0913 0.1860 0.011 1.106 0.0 110.6 16.9 226 n/a 5_occ: 0.0905 0.1857 0.011 1.106 0.0 110.6 16.9 226 n/a end: 0.0903 0.1857 0.011 1.106 0.0 110.6 16.9 226 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6109584_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6109584_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2900 Refinement macro-cycles (run) : 491.4000 Write final files (write_after_run_outputs) : 9.7200 Total : 504.4100 Total CPU time: 8.75 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:05 PST -0800 (1735492745.83 s) Start R-work = 0.1554, R-free = 0.1618 Final R-work = 0.0903, R-free = 0.1857 =============================================================================== Job complete usr+sys time: 532.58 seconds wall clock time: 9 minutes 14.27 seconds (554.27 seconds total)