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_8666014.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_8666014.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8666014.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: 1.46, per 1000 atoms: 0.43 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: 0.34 Conformation dependent library (CDL) restraints added in 144.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 430 0.90 - 1.16: 1197 1.16 - 1.43: 670 1.43 - 1.69: 835 1.69 - 1.96: 21 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.244 1.430 -0.186 1.00e-02 1.00e+04 3.46e+02 bond pdb=" C LEU A 77 " pdb=" N GLY A 78 " ideal model delta sigma weight residual 1.334 1.544 -0.211 1.14e-02 7.69e+03 3.42e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.447 1.251 0.196 1.08e-02 8.57e+03 3.29e+02 bond pdb=" C ASP A 60 " pdb=" O ASP A 60 " ideal model delta sigma weight residual 1.236 1.451 -0.215 1.19e-02 7.06e+03 3.26e+02 bond pdb=" CD ARG A 145 " pdb=" NE ARG A 145 " ideal model delta sigma weight residual 1.458 1.209 0.249 1.40e-02 5.10e+03 3.15e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 2961 4.39 - 8.79: 1912 8.79 - 13.18: 728 13.18 - 17.57: 152 17.57 - 21.97: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 119.71 106.85 12.86 8.10e-01 1.52e+00 2.52e+02 angle pdb=" CA GLY A 137 " pdb=" C GLY A 137 " pdb=" O GLY A 137 " ideal model delta sigma weight residual 119.82 103.97 15.85 1.14e+00 7.69e-01 1.93e+02 angle pdb=" C LEU A 82 " pdb=" N SER A 83 " pdb=" CA SER A 83 " ideal model delta sigma weight residual 120.28 139.74 -19.46 1.44e+00 4.82e-01 1.83e+02 angle pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 108.40 95.27 13.13 1.00e+00 1.00e+00 1.72e+02 angle pdb=" ND1 HIS A 126 " pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 106.10 118.65 -12.55 1.00e+00 1.00e+00 1.57e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 1291 16.76 - 33.53: 135 33.53 - 50.29: 34 50.29 - 67.05: 16 67.05 - 83.81: 5 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BGLU A 90 " pdb=" N BGLU A 90 " pdb=" CA BGLU A 90 " pdb=" CB BGLU A 90 " ideal model delta harmonic sigma weight residual -122.60 -146.96 24.36 0 2.50e+00 1.60e-01 9.50e+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 6.20e+01 dihedral pdb=" N BGLU A 90 " pdb=" C BGLU A 90 " pdb=" CA BGLU A 90 " pdb=" CB BGLU A 90 " ideal model delta harmonic sigma weight residual 122.80 142.46 -19.66 0 2.50e+00 1.60e-01 6.18e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.240: 108 0.240 - 0.472: 75 0.472 - 0.705: 36 0.705 - 0.937: 19 0.937 - 1.170: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.42 -1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.52 -1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" CA BGLU A 90 " pdb=" N BGLU A 90 " pdb=" C BGLU A 90 " pdb=" CB BGLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.072 2.00e-02 2.50e+03 6.70e-02 1.35e+02 pdb=" CG TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.110 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.107 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.097 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.107 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.058 2.00e-02 2.50e+03 6.22e-02 1.16e+02 pdb=" CG BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.128 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.053 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.074 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.046 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.061 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.041 2.00e-02 2.50e+03 5.42e-02 8.82e+01 pdb=" CG TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.085 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.079 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1084 2.32 - 2.89: 8132 2.89 - 3.46: 10475 3.46 - 4.03: 15267 4.03 - 4.60: 21704 Nonbonded interactions: 56662 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.755 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.775 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.779 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.814 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.827 2.450 ... (remaining 56657 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_8666014_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= 0.3613 r_free= 0.2073 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469761 | | target function (ml) not normalized (work): 22035.922254 | | target function (ml) not normalized (free): 1151.760605 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3798 0.2323 4.8539 4.9188| | 2: 3.78 - 3.00 1.00 2430 110 0.3387 0.1650 4.0746 4.1208| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.77 0.83 0.13 6606.70| | 2: 3.78 - 3.00 2430 110 0.94 11.36 1.48 0.26 451.50| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 384.48 max = 12068.45 mean = 3572.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.33| |phase err.(test): min = 0.00 max = 89.94 mean = 33.58| |-----------------------------------------------------------------------------| ----------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 0.249 1557 Z= 5.435 Angle : 5.396 19.459 2118 Z= 3.758 Chirality : 0.408 1.170 243 Planarity : 0.030 0.091 284 Dihedral : 13.832 83.813 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 32.43 % 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: -3.35 (0.45), residues: 224 helix: -3.25 (0.33), residues: 105 sheet: -0.98 (0.72), residues: 38 loop : -0.95 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.023 ARG A 98 TYR 0.085 0.037 TYR A 139 PHE 0.090 0.027 PHE A 164 HIS 0.047 0.017 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3613 r_free= 0.2073 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469761 | | target function (ml) not normalized (work): 22035.922254 | | target function (ml) not normalized (free): 1151.760605 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3573 0.3649 0.2183 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3573 0.3649 0.2183 n_refl.: 5182 remove outliers: r(all,work,free)=0.2530 0.2552 0.2183 n_refl.: 5178 overall B=-2.37 to atoms: r(all,work,free)=0.2437 0.2456 0.2145 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1565 0.1560 0.1663 n_refl.: 5178 remove outliers: r(all,work,free)=0.1560 0.1555 0.1663 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 0.3877 449.620 405.838 0.612 1.090 0.400 11.894-9.307 99.02 97 4 0.1872 714.257 694.592 0.882 1.085 0.372 9.237-7.194 100.00 213 7 0.2224 584.121 574.173 0.921 1.076 0.358 7.162-5.571 100.00 427 22 0.2241 438.312 425.482 0.886 1.059 0.310 5.546-4.326 100.00 867 58 0.1398 601.740 595.696 0.943 1.032 0.272 4.315-3.360 100.00 1859 96 0.1300 572.261 566.497 1.024 0.986 0.198 3.356-3.002 100.00 1373 60 0.1598 440.779 432.958 1.053 0.941 0.074 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9174 b_overall=-4.1077 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1663 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1558 r_free=0.1666 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.279860 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.791395 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 0.1157 0.1789 0.0632 0.010 1.0 2.9 0.5 0.0 0 9.140 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 17.89 6.32 3.013 16.489 1.791 0.018 10.19 17.84 7.65 4.791 16.651 1.791 0.014 Individual atomic B min max mean iso aniso Overall: 2.53 111.93 17.82 5.20 1785 0 Protein: 2.53 111.44 15.13 5.18 1519 0 Water: 4.50 111.93 33.49 N/A 258 0 Other: 16.61 38.58 23.94 N/A 8 0 Chain A: 2.53 111.93 17.82 N/A 1785 0 Histogram: Values Number of atoms 2.53 - 13.47 913 13.47 - 24.41 485 24.41 - 35.35 188 35.35 - 46.29 114 46.29 - 57.23 56 57.23 - 68.17 12 68.17 - 79.11 8 79.11 - 90.05 5 90.05 - 100.99 1 100.99 - 111.93 3 =========================== Idealize ADP of riding H ========================== r_work=0.1019 r_free=0.1784 r_work=0.1012 r_free=0.1790 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1012 r_free = 0.1790 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 = 0.1012 r_free = 0.1781 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.14 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= 0.1012 r_free= 0.1781 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013903 | | target function (ls_wunit_k1) not normalized (work): 68.459187 | | target function (ls_wunit_k1) not normalized (free): 10.320580 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1051 0.1012 0.1781 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2116 0.2115 0.2223 n_refl.: 5176 remove outliers: r(all,work,free)=0.2116 0.2115 0.2223 n_refl.: 5176 overall B=-1.02 to atoms: r(all,work,free)=0.2072 0.2070 0.2210 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1054 0.1015 0.1776 n_refl.: 5176 remove outliers: r(all,work,free)=0.1054 0.1015 0.1776 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 0.3270 317.068 299.990 0.654 1.035 0.376 11.894-9.307 99.02 97 4 0.1532 503.688 496.682 0.957 1.034 0.351 9.237-7.194 100.00 213 7 0.1658 411.917 411.495 1.000 1.030 0.331 7.162-5.571 100.00 427 22 0.1628 309.093 306.290 0.968 1.024 0.302 5.546-4.326 100.00 867 58 0.0924 424.341 421.467 0.993 1.012 0.233 4.315-3.360 100.00 1859 96 0.0765 403.553 403.272 1.051 0.994 0.183 3.356-3.002 100.00 1373 60 0.1003 310.834 309.344 1.041 0.975 0.071 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.6709 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1015 r_free=0.1776 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1018 r_free=0.1782 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1018 r_free=0.1782 | n_water=258 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1048 r_free=0.1762 | n_water=246 | time (s): 20.420 (total time: 21.030) Filter (q & B) r_work=0.1046 r_free=0.1762 | n_water=243 | time (s): 1.570 (total time: 22.600) Compute maps r_work=0.1046 r_free=0.1762 | n_water=243 | time (s): 0.660 (total time: 23.260) Filter (map) r_work=0.1355 r_free=0.1853 | n_water=139 | time (s): 1.790 (total time: 25.050) Find peaks r_work=0.1355 r_free=0.1853 | n_water=139 | time (s): 0.520 (total time: 25.570) Add new water r_work=0.1710 r_free=0.2160 | n_water=228 | time (s): 1.840 (total time: 27.410) Refine new water occ: r_work=0.1161 r_free=0.1670 adp: r_work=0.1139 r_free=0.1672 occ: r_work=0.1135 r_free=0.1649 adp: r_work=0.1125 r_free=0.1655 occ: r_work=0.1123 r_free=0.1646 adp: r_work=0.1121 r_free=0.1646 ADP+occupancy (water only), MIN, final r_work=0.1121 r_free=0.1646 r_work=0.1121 r_free=0.1646 | n_water=228 | time (s): 5.540 (total time: 32.950) Filter (q & B) r_work=0.1122 r_free=0.1649 | n_water=227 | time (s): 1.760 (total time: 34.710) Filter (dist only) r_work=0.1121 r_free=0.1645 | n_water=225 | time (s): 19.720 (total time: 54.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.006134 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.618633 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 0.1023 0.1731 0.0708 0.009 1.0 4.2 0.5 0.6 0 11.003 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.23 17.31 7.08 4.634 17.137 2.619 0.014 9.53 17.51 7.98 5.353 17.389 2.619 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 108.11 16.60 6.25 1752 0 Protein: 0.00 108.11 15.04 6.24 1519 0 Water: 0.00 63.43 26.83 N/A 225 0 Other: 11.44 38.18 24.66 N/A 8 0 Chain A: 0.00 108.11 15.76 N/A 1665 0 Chain S: 1.68 61.20 32.64 N/A 87 0 Histogram: Values Number of atoms 0.00 - 10.81 678 10.81 - 21.62 668 21.62 - 32.43 215 32.43 - 43.24 109 43.24 - 54.05 45 54.05 - 64.86 24 64.86 - 75.67 6 75.67 - 86.49 4 86.49 - 97.30 1 97.30 - 108.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.0953 r_free=0.1751 r_work=0.0951 r_free=0.1751 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0951 r_free = 0.1751 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0949 r_free = 0.1747 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.21 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= 0.0949 r_free= 0.1747 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ls_wunit_k1) (work): 0.012245 | | target function (ls_wunit_k1) not normalized (work): 60.294751 | | target function (ls_wunit_k1) not normalized (free): 9.147280 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0989 0.0949 0.1747 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2143 0.2151 0.2141 n_refl.: 5176 remove outliers: r(all,work,free)=0.2143 0.2151 0.2141 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2143 0.2151 0.2141 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0994 0.0953 0.1761 n_refl.: 5176 remove outliers: r(all,work,free)=0.0990 0.0949 0.1761 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 0.3237 316.489 296.724 0.646 1.024 0.360 11.894-9.307 99.02 97 4 0.1483 503.688 496.786 0.966 1.024 0.360 9.237-7.194 100.00 213 7 0.1496 411.917 412.487 1.007 1.022 0.320 7.162-5.571 100.00 427 22 0.1441 309.093 307.337 0.988 1.018 0.300 5.546-4.326 100.00 867 58 0.0798 424.341 421.923 1.005 1.010 0.250 4.315-3.360 100.00 1859 96 0.0730 403.553 403.333 1.061 0.997 0.190 3.356-3.002 100.00 1373 60 0.0989 310.834 309.608 1.048 0.984 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9557 b_overall=-4.3559 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0949 r_free=0.1761 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=0.0950 r_free=0.1760 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0950 r_free=0.1760 | n_water=225 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0963 r_free=0.1739 | n_water=218 | time (s): 17.980 (total time: 18.670) Filter (q & B) r_work=0.1020 r_free=0.1760 | n_water=216 | time (s): 1.410 (total time: 20.080) Compute maps r_work=0.1020 r_free=0.1760 | n_water=216 | time (s): 0.470 (total time: 20.550) Filter (map) r_work=0.1276 r_free=0.1848 | n_water=148 | time (s): 1.300 (total time: 21.850) Find peaks r_work=0.1276 r_free=0.1848 | n_water=148 | time (s): 0.560 (total time: 22.410) Add new water r_work=0.1660 r_free=0.2245 | n_water=233 | time (s): 1.800 (total time: 24.210) Refine new water occ: r_work=0.1066 r_free=0.1779 adp: r_work=0.1061 r_free=0.1792 occ: r_work=0.1048 r_free=0.1771 adp: r_work=0.1048 r_free=0.1779 occ: r_work=0.1037 r_free=0.1757 adp: r_work=0.1037 r_free=0.1767 ADP+occupancy (water only), MIN, final r_work=0.1037 r_free=0.1767 r_work=0.1037 r_free=0.1767 | n_water=233 | time (s): 10.280 (total time: 34.490) Filter (q & B) r_work=0.1037 r_free=0.1767 | n_water=233 | time (s): 0.900 (total time: 35.390) Filter (dist only) r_work=0.1053 r_free=0.1787 | n_water=230 | time (s): 18.760 (total time: 54.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.116025 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.211746 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 0.0953 0.1841 0.0888 0.011 1.0 3.8 0.5 0.6 0 0.558 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.53 18.41 8.88 5.269 17.820 0.212 5.136 9.08 18.32 9.24 7.153 17.821 0.212 5.036 Individual atomic B min max mean iso aniso Overall: 0.00 106.77 16.43 8.75 1757 0 Protein: 0.00 106.77 15.16 8.73 1519 0 Water: 0.00 58.43 24.44 N/A 230 0 Other: 8.50 45.07 27.02 N/A 8 0 Chain A: 0.00 106.77 15.81 N/A 1650 0 Chain S: 0.00 55.00 25.99 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.68 664 10.68 - 21.35 671 21.35 - 32.03 228 32.03 - 42.71 123 42.71 - 53.39 38 53.39 - 64.06 15 64.06 - 74.74 10 74.74 - 85.42 3 85.42 - 96.09 4 96.09 - 106.77 1 =========================== Idealize ADP of riding H ========================== r_work=0.0908 r_free=0.1832 r_work=0.0914 r_free=0.1843 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0914 r_free = 0.1843 target_work(ml) = 5.040 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0903 r_free = 0.1820 target_work(ml) = 5.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0903 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.032184 | | target function (ml) not normalized (work): 24768.409314 | | target function (ml) not normalized (free): 1869.198752 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0950 0.0903 0.1820 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2052 0.2051 0.2179 n_refl.: 5174 remove outliers: r(all,work,free)=0.2052 0.2051 0.2179 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2052 0.2051 0.2179 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0944 0.0898 0.1817 n_refl.: 5174 remove outliers: r(all,work,free)=0.0944 0.0898 0.1817 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 0.3735 316.489 287.130 0.607 0.992 0.344 11.894-9.307 99.02 97 4 0.1852 503.688 487.137 0.950 0.996 0.340 9.237-7.194 100.00 213 7 0.1891 411.917 406.422 0.997 0.998 0.315 7.162-5.571 100.00 427 22 0.1892 309.093 300.619 0.982 0.999 0.310 5.546-4.326 100.00 867 58 0.0915 424.341 419.606 1.001 1.000 0.240 4.315-3.360 100.00 1859 96 0.0594 403.553 403.069 1.056 1.002 0.210 3.356-3.002 100.00 1373 60 0.0619 310.834 310.823 1.036 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.4817 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0898 r_free=0.1818 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0900 r_free=0.1817 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0900 r_free=0.1817 | n_water=230 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0922 r_free=0.1825 | n_water=227 | time (s): 19.900 (total time: 20.540) Filter (q & B) r_work=0.0987 r_free=0.1859 | n_water=224 | time (s): 2.030 (total time: 22.570) Compute maps r_work=0.0987 r_free=0.1859 | n_water=224 | time (s): 0.610 (total time: 23.180) Filter (map) r_work=0.1253 r_free=0.1956 | n_water=152 | time (s): 1.640 (total time: 24.820) Find peaks r_work=0.1253 r_free=0.1956 | n_water=152 | time (s): 0.400 (total time: 25.220) Add new water r_work=0.1609 r_free=0.2275 | n_water=233 | time (s): 1.260 (total time: 26.480) Refine new water occ: r_work=0.1033 r_free=0.1848 adp: r_work=0.1027 r_free=0.1861 occ: r_work=0.1019 r_free=0.1840 adp: r_work=0.1017 r_free=0.1853 occ: r_work=0.1010 r_free=0.1829 adp: r_work=0.1008 r_free=0.1842 ADP+occupancy (water only), MIN, final r_work=0.1008 r_free=0.1842 r_work=0.1008 r_free=0.1842 | n_water=233 | time (s): 11.320 (total time: 37.800) Filter (q & B) r_work=0.1008 r_free=0.1846 | n_water=231 | time (s): 1.490 (total time: 39.290) Filter (dist only) r_work=0.1007 r_free=0.1853 | n_water=230 | time (s): 17.570 (total time: 56.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.053663 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.253881 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 0.0907 0.1883 0.0976 0.011 1.0 5.1 0.5 0.6 0 0.527 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.07 18.83 9.76 6.837 17.944 0.254 4.989 8.88 18.92 10.04 8.320 18.074 0.254 4.925 Individual atomic B min max mean iso aniso Overall: 0.00 106.08 16.77 10.88 1757 0 Protein: 0.00 106.08 15.63 10.88 1519 0 Water: 0.00 65.66 23.85 N/A 230 0 Other: 11.71 45.27 29.97 N/A 8 0 Chain A: 0.00 106.08 16.18 N/A 1639 0 Chain S: 0.00 53.18 24.99 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.61 650 10.61 - 21.22 652 21.22 - 31.82 250 31.82 - 42.43 128 42.43 - 53.04 39 53.04 - 63.65 17 63.65 - 74.26 8 74.26 - 84.87 6 84.87 - 95.47 5 95.47 - 106.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.0888 r_free=0.1892 r_work=0.0893 r_free=0.1895 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0893 r_free = 0.1895 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0883 r_free = 0.1872 target_work(ml) = 4.924 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0883 r_free= 0.1872 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.923728 | | target function (ml) not normalized (work): 24234.589244 | | target function (ml) not normalized (free): 2214.601326 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0933 0.0883 0.1872 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2091 0.2088 0.2256 n_refl.: 5174 remove outliers: r(all,work,free)=0.2091 0.2088 0.2256 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2091 0.2088 0.2256 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0931 0.0881 0.1877 n_refl.: 5174 remove outliers: r(all,work,free)=0.0931 0.0881 0.1877 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 0.3915 316.489 285.054 0.577 0.988 0.314 11.894-9.307 99.02 97 4 0.1939 503.688 487.387 0.952 0.994 0.310 9.237-7.194 100.00 213 7 0.2169 411.917 402.435 0.998 0.997 0.288 7.162-5.571 100.00 427 22 0.2065 309.093 299.776 0.993 0.998 0.273 5.546-4.326 100.00 867 58 0.0976 424.341 419.212 1.021 1.000 0.240 4.315-3.360 100.00 1859 96 0.0550 403.553 403.082 1.084 1.002 0.210 3.356-3.002 100.00 1373 60 0.0438 310.834 310.839 1.066 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.7739 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0881 r_free=0.1877 After: r_work=0.0884 r_free=0.1876 ================================== NQH flips ================================== r_work=0.0884 r_free=0.1876 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0884 r_free=0.1876 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0884 r_free=0.1876 | n_water=230 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0902 r_free=0.1867 | n_water=224 | time (s): 20.080 (total time: 20.650) Filter (q & B) r_work=0.1013 r_free=0.1922 | n_water=220 | time (s): 1.600 (total time: 22.250) Compute maps r_work=0.1013 r_free=0.1922 | n_water=220 | time (s): 0.500 (total time: 22.750) Filter (map) r_work=0.1268 r_free=0.2006 | n_water=158 | time (s): 1.650 (total time: 24.400) Find peaks r_work=0.1268 r_free=0.2006 | n_water=158 | time (s): 0.480 (total time: 24.880) Add new water r_work=0.1546 r_free=0.2200 | n_water=223 | time (s): 1.260 (total time: 26.140) Refine new water occ: r_work=0.1004 r_free=0.1884 adp: r_work=0.0996 r_free=0.1886 occ: r_work=0.0991 r_free=0.1876 adp: r_work=0.0991 r_free=0.1886 occ: r_work=0.0985 r_free=0.1873 adp: r_work=0.0985 r_free=0.1881 ADP+occupancy (water only), MIN, final r_work=0.0985 r_free=0.1881 r_work=0.0985 r_free=0.1881 | n_water=223 | time (s): 9.730 (total time: 35.870) Filter (q & B) r_work=0.0981 r_free=0.1881 | n_water=221 | time (s): 1.340 (total time: 37.210) Filter (dist only) r_work=0.0982 r_free=0.1892 | n_water=219 | time (s): 16.770 (total time: 53.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.936849 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.228309 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 0.0924 0.1872 0.0948 0.010 1.1 9.6 0.5 0.0 0 0.468 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.24 18.72 9.48 8.257 18.300 0.228 4.990 9.05 18.79 9.74 9.149 18.384 0.228 4.934 Individual atomic B min max mean iso aniso Overall: 0.00 107.18 16.90 12.05 1746 0 Protein: 0.00 107.18 15.97 12.05 1519 0 Water: 0.00 60.94 22.97 N/A 219 0 Other: 10.12 44.10 28.42 N/A 8 0 Chain A: 0.00 107.18 16.44 N/A 1632 0 Chain S: 0.00 52.05 23.49 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.72 656 10.72 - 21.44 625 21.44 - 32.15 270 32.15 - 42.87 109 42.87 - 53.59 45 53.59 - 64.31 19 64.31 - 75.02 8 75.02 - 85.74 7 85.74 - 96.46 3 96.46 - 107.18 4 =========================== Idealize ADP of riding H ========================== r_work=0.0905 r_free=0.1879 r_work=0.0910 r_free=0.1881 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0910 r_free = 0.1881 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0904 r_free = 0.1871 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0904 r_free= 0.1871 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.936233 | | target function (ml) not normalized (work): 24296.138004 | | target function (ml) not normalized (free): 2203.868623 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1288 0.1826 5.5155 6.07| | 2: 3.78 - 3.00 1.00 2430 110 0.0436 0.1946 4.3422 12.199| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.42 1.00 0.93 12722.38| | 2: 3.78 - 3.00 2430 110 0.99 1.94 1.00 0.96 878.49| |alpha: min = 0.92 max = 0.96 mean = 0.94| |beta: min = 560.33 max = 21312.19 mean = 6875.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.98 mean = 7.24| |phase err.(test): min = 0.00 max = 88.79 mean = 7.76| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0953 0.0904 0.1871 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2144 0.2146 0.2227 n_refl.: 5174 remove outliers: r(all,work,free)=0.2144 0.2146 0.2227 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2144 0.2146 0.2227 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0951 0.0903 0.1871 n_refl.: 5174 remove outliers: r(all,work,free)=0.0951 0.0903 0.1871 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 0.4005 316.489 282.239 0.606 0.986 0.320 11.894-9.307 99.02 97 4 0.1989 503.688 485.030 1.003 0.992 0.320 9.237-7.194 100.00 213 7 0.2198 411.917 401.146 1.043 0.996 0.315 7.162-5.571 100.00 427 22 0.2065 309.093 299.809 1.041 0.998 0.310 5.546-4.326 100.00 867 58 0.1034 424.341 418.573 1.069 1.000 0.234 4.315-3.360 100.00 1859 96 0.0580 403.553 403.558 1.150 1.003 0.220 3.356-3.002 100.00 1373 60 0.0413 310.834 311.308 1.133 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.6637 ================= 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 : 0.3613 0.2073 0.081 5.396 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1663 0.081 5.396 6.5 116.9 17.5 258 0.000 1_settarget: 0.1555 0.1663 0.081 5.396 6.5 116.9 17.5 258 0.000 1_nqh: 0.1558 0.1666 0.081 5.396 6.5 116.9 17.5 258 0.006 1_weight: 0.1558 0.1666 0.081 5.396 6.5 116.9 17.5 258 0.006 1_xyzrec: 0.1157 0.1789 0.010 0.953 6.5 116.9 17.5 258 0.215 1_adp: 0.1019 0.1784 0.010 0.953 2.5 111.9 17.8 258 0.215 1_regHadp: 0.1012 0.1790 0.010 0.953 2.5 111.9 17.8 258 0.215 1_occ: 0.1012 0.1781 0.010 0.953 2.5 111.9 17.8 258 0.215 2_bss: 0.1015 0.1776 0.010 0.953 1.5 110.9 16.8 258 0.215 2_settarget: 0.1015 0.1776 0.010 0.953 1.5 110.9 16.8 258 0.215 2_updatecdl: 0.1015 0.1776 0.010 0.971 1.5 110.9 16.8 258 0.215 2_nqh: 0.1018 0.1782 0.010 0.971 1.5 110.9 16.8 258 0.214 2_sol: 0.1121 0.1645 0.010 0.971 1.0 110.4 16.1 225 n/a 2_weight: 0.1121 0.1645 0.010 0.971 1.0 110.4 16.1 225 n/a 2_xyzrec: 0.1023 0.1731 0.009 0.962 1.0 110.4 16.1 225 n/a 2_adp: 0.0953 0.1751 0.009 0.962 0.0 108.1 16.6 225 n/a 2_regHadp: 0.0951 0.1751 0.009 0.962 0.0 108.1 16.6 225 n/a 2_occ: 0.0949 0.1747 0.009 0.962 0.0 108.1 16.6 225 n/a 3_bss: 0.0949 0.1761 0.009 0.962 0.0 108.1 16.6 225 n/a 3_settarget: 0.0949 0.1761 0.009 0.962 0.0 108.1 16.6 225 n/a 3_updatecdl: 0.0949 0.1761 0.009 0.969 0.0 108.1 16.6 225 n/a 3_nqh: 0.0950 0.1760 0.009 0.969 0.0 108.1 16.6 225 n/a 3_sol: 0.1053 0.1787 0.009 0.969 0.0 108.1 16.4 230 n/a 3_weight: 0.1053 0.1787 0.009 0.969 0.0 108.1 16.4 230 n/a 3_xyzrec: 0.0953 0.1841 0.011 1.044 0.0 108.1 16.4 230 n/a 3_adp: 0.0908 0.1832 0.011 1.044 0.0 106.8 16.4 230 n/a 3_regHadp: 0.0914 0.1843 0.011 1.044 0.0 106.8 16.4 230 n/a 3_occ: 0.0903 0.1820 0.011 1.044 0.0 106.8 16.4 230 n/a 4_bss: 0.0898 0.1818 0.011 1.044 0.0 106.8 16.4 230 n/a 4_settarget: 0.0898 0.1818 0.011 1.044 0.0 106.8 16.4 230 n/a 4_updatecdl: 0.0898 0.1818 0.011 1.056 0.0 106.8 16.4 230 n/a 4_nqh: 0.0900 0.1817 0.011 1.056 0.0 106.8 16.4 230 n/a 4_sol: 0.1007 0.1853 0.011 1.056 0.0 106.8 16.5 230 n/a 4_weight: 0.1007 0.1853 0.011 1.056 0.0 106.8 16.5 230 n/a 4_xyzrec: 0.0907 0.1883 0.011 1.041 0.0 106.8 16.5 230 n/a 4_adp: 0.0888 0.1892 0.011 1.041 0.0 106.1 16.8 230 n/a 4_regHadp: 0.0893 0.1895 0.011 1.041 0.0 106.1 16.8 230 n/a 4_occ: 0.0883 0.1872 0.011 1.041 0.0 106.1 16.8 230 n/a 5_bss: 0.0881 0.1877 0.011 1.041 0.0 106.1 16.8 230 n/a 5_settarget: 0.0881 0.1877 0.011 1.041 0.0 106.1 16.8 230 n/a 5_updatecdl: 0.0881 0.1877 0.011 1.050 0.0 106.1 16.8 230 n/a 5_setrh: 0.0884 0.1876 0.011 1.050 0.0 106.1 16.8 230 n/a 5_nqh: 0.0884 0.1876 0.011 1.050 0.0 106.1 16.8 230 n/a 5_sol: 0.0982 0.1892 0.011 1.050 0.0 106.1 16.7 219 n/a 5_weight: 0.0982 0.1892 0.011 1.050 0.0 106.1 16.7 219 n/a 5_xyzrec: 0.0924 0.1872 0.010 1.085 0.0 106.1 16.7 219 n/a 5_adp: 0.0905 0.1879 0.010 1.085 0.0 107.2 16.9 219 n/a 5_regHadp: 0.0910 0.1881 0.010 1.085 0.0 107.2 16.9 219 n/a 5_occ: 0.0904 0.1871 0.010 1.085 0.0 107.2 16.9 219 n/a end: 0.0903 0.1871 0.010 1.085 0.0 107.2 16.9 219 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8666014_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8666014_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.5000 Refinement macro-cycles (run) : 495.2600 Write final files (write_after_run_outputs) : 10.1300 Total : 509.8900 Total CPU time: 8.86 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:12 PST -0800 (1735492752.76 s) Start R-work = 0.1555, R-free = 0.1663 Final R-work = 0.0903, R-free = 0.1871 =============================================================================== Job complete usr+sys time: 539.20 seconds wall clock time: 9 minutes 21.29 seconds (561.29 seconds total)