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_1541177.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1541177.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1541177.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.41, per 1000 atoms: 0.42 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: 0.30 Conformation dependent library (CDL) restraints added in 114.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.92: 575 0.92 - 1.17: 1067 1.17 - 1.42: 625 1.42 - 1.66: 843 1.66 - 1.91: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" N BGLN A 80 " pdb=" CA BGLN A 80 " ideal model delta sigma weight residual 1.459 1.694 -0.235 1.19e-02 7.06e+03 3.88e+02 bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.692 -0.233 1.19e-02 7.06e+03 3.82e+02 bond pdb=" CA ALA A 61 " pdb=" C ALA A 61 " ideal model delta sigma weight residual 1.523 1.284 0.239 1.35e-02 5.49e+03 3.13e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.518 -0.192 1.10e-02 8.26e+03 3.03e+02 bond pdb=" C ALA A 36 " pdb=" O ALA A 36 " ideal model delta sigma weight residual 1.236 1.436 -0.200 1.22e-02 6.72e+03 2.70e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3146 4.72 - 9.44: 1861 9.44 - 14.16: 655 14.16 - 18.88: 105 18.88 - 23.60: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 140.59 -19.36 8.10e-01 1.52e+00 5.71e+02 angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 123.10 142.90 -19.80 1.17e+00 7.31e-01 2.86e+02 angle pdb=" O ILE A 91 " pdb=" C ILE A 91 " pdb=" N LEU A 92 " ideal model delta sigma weight residual 121.83 138.06 -16.23 1.03e+00 9.43e-01 2.48e+02 angle pdb=" C ACYS A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 120.03 104.54 15.49 9.90e-01 1.02e+00 2.45e+02 angle pdb=" CA BLEU A 153 " pdb=" C BLEU A 153 " pdb=" O BLEU A 153 " ideal model delta sigma weight residual 120.30 105.59 14.71 1.07e+00 8.73e-01 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 1291 16.51 - 33.01: 125 33.01 - 49.52: 49 49.52 - 66.03: 12 66.03 - 82.53: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 105 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual -122.00 -144.65 22.65 0 2.50e+00 1.60e-01 8.20e+01 dihedral pdb=" N ILE A 105 " pdb=" C ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual 123.40 143.79 -20.39 0 2.50e+00 1.60e-01 6.65e+01 dihedral pdb=" C VAL A 186 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta harmonic sigma weight residual -122.00 -141.95 19.95 0 2.50e+00 1.60e-01 6.37e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.019 - 0.214: 92 0.214 - 0.410: 75 0.410 - 0.605: 43 0.605 - 0.800: 23 0.800 - 0.996: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG BLEU A 153 " pdb=" CB BLEU A 153 " pdb=" CD1BLEU A 153 " pdb=" CD2BLEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -3.59 1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.64 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ALA A 79 " pdb=" N ALA A 79 " pdb=" C ALA A 79 " pdb=" CB ALA A 79 " both_signs ideal model delta sigma weight residual False 2.48 1.56 0.93 2.00e-01 2.50e+01 2.14e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.029 2.00e-02 2.50e+03 7.00e-02 1.47e+02 pdb=" CG PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.121 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.121 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.123 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.025 2.00e-02 2.50e+03 5.95e-02 1.06e+02 pdb=" CG TYR A 139 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.118 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.078 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.107 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.059 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.060 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.027 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 583 2.24 - 2.83: 7551 2.83 - 3.42: 10765 3.42 - 4.01: 15326 4.01 - 4.60: 22349 Nonbonded interactions: 56574 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.655 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.770 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.797 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.847 2.100 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.849 2.270 ... (remaining 56569 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_1541177_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= 0.3631 r_free= 0.2015 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472330 | | target function (ml) not normalized (work): 22048.587450 | | target function (ml) not normalized (free): 1150.209547 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3818 0.2177 4.8569 4.8917| | 2: 3.78 - 3.00 1.00 2430 110 0.3402 0.1741 4.0766 4.1417| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.93 0.83 0.13 6618.71| | 2: 3.78 - 3.00 2430 110 0.93 11.51 1.48 0.26 458.90| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 392.22 max = 12083.73 mean = 3582.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.49| |phase err.(test): min = 0.00 max = 89.99 mean = 33.19| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.239 1557 Z= 5.520 Angle : 5.413 19.796 2118 Z= 3.892 Chirality : 0.397 0.996 243 Planarity : 0.032 0.090 284 Dihedral : 14.027 82.534 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 34.59 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.51), residues: 224 helix: -3.09 (0.37), residues: 108 sheet: -0.73 (0.78), residues: 38 loop : 0.17 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.089 0.020 ARG A 98 TYR 0.087 0.038 TYR A 139 PHE 0.138 0.046 PHE A 164 HIS 0.088 0.044 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= 0.3631 r_free= 0.2015 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472330 | | target function (ml) not normalized (work): 22048.587450 | | target function (ml) not normalized (free): 1150.209547 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3587 0.3665 0.2119 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3587 0.3665 0.2119 n_refl.: 5182 remove outliers: r(all,work,free)=0.2532 0.2559 0.2119 n_refl.: 5178 overall B=-2.87 to atoms: r(all,work,free)=0.2425 0.2448 0.2070 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1583 0.1582 0.1598 n_refl.: 5178 remove outliers: r(all,work,free)=0.1579 0.1577 0.1598 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 0.3894 449.586 406.553 0.656 1.063 0.398 11.894-9.307 99.02 97 4 0.1943 714.204 691.564 0.940 1.059 0.372 9.237-7.194 100.00 213 7 0.2174 584.077 576.911 0.981 1.053 0.348 7.162-5.571 100.00 427 22 0.2358 438.279 424.861 0.940 1.041 0.294 5.546-4.326 100.00 867 58 0.1401 601.695 595.346 0.988 1.022 0.258 4.315-3.360 100.00 1859 96 0.1314 572.218 566.190 1.052 0.990 0.202 3.356-3.002 100.00 1373 60 0.1628 440.746 431.874 1.065 0.959 0.032 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6692 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1577 r_free=0.1598 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1584 r_free=0.1611 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.577833 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.559129 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 0.1155 0.1811 0.0656 0.010 1.0 3.2 0.5 0.0 0 9.789 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.55 18.11 6.56 3.013 15.988 1.559 0.018 10.23 18.11 7.88 4.526 16.130 1.559 0.014 Individual atomic B min max mean iso aniso Overall: 2.24 111.43 17.28 4.95 1785 0 Protein: 2.24 111.25 14.58 4.95 1519 0 Water: 3.99 111.43 33.01 N/A 258 0 Other: 17.21 33.52 23.35 N/A 8 0 Chain A: 2.24 111.43 17.28 N/A 1785 0 Histogram: Values Number of atoms 2.24 - 13.16 938 13.16 - 24.08 472 24.08 - 35.00 184 35.00 - 45.92 105 45.92 - 56.83 56 56.83 - 67.75 13 67.75 - 78.67 8 78.67 - 89.59 5 89.59 - 100.51 1 100.51 - 111.43 3 =========================== Idealize ADP of riding H ========================== r_work=0.1023 r_free=0.1811 r_work=0.1017 r_free=0.1813 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1813 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 = 0.1820 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 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= 0.1820 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013929 | | target function (ls_wunit_k1) not normalized (work): 68.586667 | | target function (ls_wunit_k1) not normalized (free): 10.795690 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1055 0.1014 0.1820 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2089 0.2088 0.2233 n_refl.: 5176 remove outliers: r(all,work,free)=0.2089 0.2088 0.2233 n_refl.: 5176 overall B=-0.94 to atoms: r(all,work,free)=0.2050 0.2047 0.2221 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1056 0.1015 0.1809 n_refl.: 5176 remove outliers: r(all,work,free)=0.1056 0.1015 0.1809 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 0.3337 330.484 312.736 0.669 1.022 0.381 11.894-9.307 99.02 97 4 0.1494 525.000 516.536 0.974 1.022 0.361 9.237-7.194 100.00 213 7 0.1618 429.346 430.241 1.011 1.020 0.320 7.162-5.571 100.00 427 22 0.1609 322.172 318.502 0.972 1.015 0.302 5.546-4.326 100.00 867 58 0.0912 442.296 438.889 0.994 1.008 0.216 4.315-3.360 100.00 1859 96 0.0773 420.629 420.603 1.042 0.996 0.193 3.356-3.002 100.00 1373 60 0.1015 323.986 322.312 1.026 0.984 0.031 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3837 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1015 r_free=0.1809 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1015 r_free=0.1809 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1015 r_free=0.1809 | n_water=258 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1032 r_free=0.1789 | n_water=250 | time (s): 19.440 (total time: 20.040) Filter (q & B) r_work=0.1033 r_free=0.1794 | n_water=248 | time (s): 1.550 (total time: 21.590) Compute maps r_work=0.1033 r_free=0.1794 | n_water=248 | time (s): 0.570 (total time: 22.160) Filter (map) r_work=0.1344 r_free=0.1834 | n_water=146 | time (s): 1.920 (total time: 24.080) Find peaks r_work=0.1344 r_free=0.1834 | n_water=146 | time (s): 0.550 (total time: 24.630) Add new water r_work=0.1686 r_free=0.2153 | n_water=229 | time (s): 1.420 (total time: 26.050) Refine new water occ: r_work=0.1160 r_free=0.1693 adp: r_work=0.1142 r_free=0.1714 occ: r_work=0.1137 r_free=0.1675 adp: r_work=0.1126 r_free=0.1694 occ: r_work=0.1124 r_free=0.1675 adp: r_work=0.1122 r_free=0.1681 ADP+occupancy (water only), MIN, final r_work=0.1122 r_free=0.1681 r_work=0.1122 r_free=0.1681 | n_water=229 | time (s): 4.560 (total time: 30.610) Filter (q & B) r_work=0.1124 r_free=0.1688 | n_water=228 | time (s): 1.920 (total time: 32.530) Filter (dist only) r_work=0.1124 r_free=0.1685 | n_water=227 | time (s): 17.950 (total time: 50.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.269243 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.788538 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 0.1018 0.1793 0.0774 0.009 1.0 4.5 0.5 0.6 0 11.635 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.18 17.93 7.74 4.452 16.635 2.789 0.014 9.40 18.19 8.79 5.635 17.083 2.789 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.66 16.60 6.71 1754 0 Protein: 0.00 108.66 15.02 6.69 1519 0 Water: 0.00 63.91 26.93 N/A 227 0 Other: 13.14 33.28 22.94 N/A 8 0 Chain A: 0.00 108.66 15.80 N/A 1672 0 Chain S: 3.17 59.52 32.86 N/A 82 0 Histogram: Values Number of atoms 0.00 - 10.87 707 10.87 - 21.73 647 21.73 - 32.60 199 32.60 - 43.46 123 43.46 - 54.33 37 54.33 - 65.19 27 65.19 - 76.06 7 76.06 - 86.93 3 86.93 - 97.79 2 97.79 - 108.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.0940 r_free=0.1819 r_work=0.0936 r_free=0.1819 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0936 r_free = 0.1819 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0934 r_free = 0.1823 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 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= 0.0934 r_free= 0.1823 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011879 | | target function (ls_wunit_k1) not normalized (work): 58.491193 | | target function (ls_wunit_k1) not normalized (free): 9.902322 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0979 0.0934 0.1823 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2123 0.2127 0.2207 n_refl.: 5176 remove outliers: r(all,work,free)=0.2123 0.2127 0.2207 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2123 0.2127 0.2207 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0982 0.0937 0.1834 n_refl.: 5176 remove outliers: r(all,work,free)=0.0982 0.0937 0.1834 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 0.3206 330.484 315.678 0.699 0.998 0.381 11.894-9.307 99.02 97 4 0.1455 525.000 517.093 0.988 1.001 0.360 9.237-7.194 100.00 213 7 0.1473 429.346 429.304 1.025 1.001 0.305 7.162-5.571 100.00 427 22 0.1399 322.172 318.762 0.997 1.001 0.300 5.546-4.326 100.00 867 58 0.0788 442.296 439.005 1.012 1.001 0.230 4.315-3.360 100.00 1859 96 0.0732 420.629 420.693 1.055 1.001 0.200 3.356-3.002 100.00 1373 60 0.0967 323.986 324.289 1.031 1.000 0.044 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.3256 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0937 r_free=0.1834 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.0941 r_free=0.1833 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0941 r_free=0.1833 | n_water=227 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0956 r_free=0.1838 | n_water=222 | time (s): 19.160 (total time: 19.730) Filter (q & B) r_work=0.1015 r_free=0.1867 | n_water=220 | time (s): 1.450 (total time: 21.180) Compute maps r_work=0.1015 r_free=0.1867 | n_water=220 | time (s): 0.450 (total time: 21.630) Filter (map) r_work=0.1288 r_free=0.1889 | n_water=148 | time (s): 1.310 (total time: 22.940) Find peaks r_work=0.1288 r_free=0.1889 | n_water=148 | time (s): 0.380 (total time: 23.320) Add new water r_work=0.1685 r_free=0.2258 | n_water=239 | time (s): 1.390 (total time: 24.710) Refine new water occ: r_work=0.1062 r_free=0.1806 adp: r_work=0.1057 r_free=0.1820 occ: r_work=0.1045 r_free=0.1792 adp: r_work=0.1045 r_free=0.1805 occ: r_work=0.1035 r_free=0.1776 adp: r_work=0.1034 r_free=0.1789 ADP+occupancy (water only), MIN, final r_work=0.1034 r_free=0.1789 r_work=0.1034 r_free=0.1789 | n_water=239 | time (s): 11.780 (total time: 36.490) Filter (q & B) r_work=0.1034 r_free=0.1787 | n_water=237 | time (s): 1.630 (total time: 38.120) Filter (dist only) r_work=0.1044 r_free=0.1796 | n_water=235 | time (s): 18.790 (total time: 56.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.135296 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.204152 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 0.0945 0.1813 0.0868 0.011 1.1 4.5 0.5 0.0 0 0.568 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.45 18.13 8.68 5.551 17.858 0.204 5.171 9.02 17.97 8.95 7.209 17.883 0.204 5.079 Individual atomic B min max mean iso aniso Overall: 0.00 108.39 16.52 8.94 1762 0 Protein: 0.00 108.39 15.20 8.93 1519 0 Water: 0.11 58.91 24.74 N/A 235 0 Other: 10.73 38.65 24.00 N/A 8 0 Chain A: 0.00 108.39 15.89 N/A 1655 0 Chain S: 0.11 56.77 26.21 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.84 699 10.84 - 21.68 639 21.68 - 32.52 234 32.52 - 43.36 120 43.36 - 54.20 34 54.20 - 65.03 19 65.03 - 75.87 9 75.87 - 86.71 3 86.71 - 97.55 4 97.55 - 108.39 1 =========================== Idealize ADP of riding H ========================== r_work=0.0902 r_free=0.1797 r_work=0.0907 r_free=0.1801 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0907 r_free = 0.1801 target_work(ml) = 5.082 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0894 r_free = 0.1780 target_work(ml) = 5.074 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0894 r_free= 0.1780 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.074047 | | target function (ml) not normalized (work): 24984.607377 | | target function (ml) not normalized (free): 1808.989447 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0938 0.0894 0.1780 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2147 0.2157 0.2147 n_refl.: 5176 remove outliers: r(all,work,free)=0.2147 0.2157 0.2147 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2147 0.2157 0.2147 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0935 0.0892 0.1773 n_refl.: 5176 remove outliers: r(all,work,free)=0.0932 0.0888 0.1773 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 0.3557 329.880 302.268 0.628 0.997 0.354 11.894-9.307 99.02 97 4 0.1732 525.000 514.106 0.946 1.000 0.350 9.237-7.194 100.00 213 7 0.1897 429.346 425.932 0.987 1.001 0.295 7.162-5.571 100.00 427 22 0.1792 322.172 313.968 0.969 1.002 0.278 5.546-4.326 100.00 867 58 0.0919 442.296 437.352 0.996 1.002 0.245 4.315-3.360 100.00 1859 96 0.0597 420.629 420.116 1.045 1.002 0.210 3.356-3.002 100.00 1373 60 0.0617 323.986 323.371 1.022 1.001 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-5.8407 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0887 r_free=0.1773 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=0.0888 r_free=0.1777 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0888 r_free=0.1777 | n_water=235 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0907 r_free=0.1752 | n_water=232 | time (s): 18.110 (total time: 18.680) Filter (q & B) r_work=0.0935 r_free=0.1763 | n_water=229 | time (s): 1.620 (total time: 20.300) Compute maps r_work=0.0935 r_free=0.1763 | n_water=229 | time (s): 0.450 (total time: 20.750) Filter (map) r_work=0.1159 r_free=0.1810 | n_water=169 | time (s): 1.380 (total time: 22.130) Find peaks r_work=0.1159 r_free=0.1810 | n_water=169 | time (s): 0.470 (total time: 22.600) Add new water r_work=0.1486 r_free=0.2164 | n_water=245 | time (s): 1.320 (total time: 23.920) Refine new water occ: r_work=0.0988 r_free=0.1810 adp: r_work=0.0987 r_free=0.1820 occ: r_work=0.0977 r_free=0.1797 adp: r_work=0.0977 r_free=0.1807 occ: r_work=0.0968 r_free=0.1783 adp: r_work=0.0967 r_free=0.1793 ADP+occupancy (water only), MIN, final r_work=0.0967 r_free=0.1793 r_work=0.0967 r_free=0.1793 | n_water=245 | time (s): 7.930 (total time: 31.850) Filter (q & B) r_work=0.0968 r_free=0.1796 | n_water=244 | time (s): 1.310 (total time: 33.160) Filter (dist only) r_work=0.0968 r_free=0.1796 | n_water=244 | time (s): 17.880 (total time: 51.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.970743 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.217396 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 0.0895 0.1862 0.0967 0.011 1.1 3.8 0.5 0.0 0 0.485 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.95 18.62 9.67 6.963 18.046 0.217 5.005 8.75 18.78 10.03 8.245 18.153 0.217 4.945 Individual atomic B min max mean iso aniso Overall: 0.00 110.01 16.86 10.80 1771 0 Protein: 0.00 110.01 15.61 10.79 1519 0 Water: 0.00 57.61 24.37 N/A 244 0 Other: 12.08 41.66 24.00 N/A 8 0 Chain A: 0.00 110.01 16.22 N/A 1650 0 Chain S: 0.00 52.30 25.54 N/A 121 0 Histogram: Values Number of atoms 0.00 - 11.00 703 11.00 - 22.00 642 22.00 - 33.00 235 33.00 - 44.00 121 44.00 - 55.01 36 55.01 - 66.01 16 66.01 - 77.01 8 77.01 - 88.01 6 88.01 - 99.01 3 99.01 - 110.01 1 =========================== Idealize ADP of riding H ========================== r_work=0.0875 r_free=0.1878 r_work=0.0879 r_free=0.1883 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0879 r_free = 0.1883 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0866 r_free = 0.1868 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.23 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= 0.0866 r_free= 0.1868 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.941826 | | target function (ml) not normalized (work): 24323.666674 | | target function (ml) not normalized (free): 2253.367862 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0917 0.0866 0.1868 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2058 0.2059 0.2185 n_refl.: 5174 remove outliers: r(all,work,free)=0.2058 0.2059 0.2185 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2058 0.2059 0.2185 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0914 0.0864 0.1847 n_refl.: 5174 remove outliers: r(all,work,free)=0.0914 0.0864 0.1847 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 0.3811 329.880 299.730 0.582 0.986 0.316 11.894-9.307 99.02 97 4 0.1912 525.000 510.980 0.948 0.991 0.313 9.237-7.194 100.00 213 7 0.2139 429.346 421.598 0.996 0.994 0.280 7.162-5.571 100.00 427 22 0.2067 322.172 311.946 0.990 0.996 0.270 5.546-4.326 100.00 867 58 0.0962 442.296 437.045 1.018 0.999 0.230 4.315-3.360 100.00 1859 96 0.0531 420.629 420.317 1.074 1.003 0.210 3.356-3.002 100.00 1373 60 0.0426 323.986 324.365 1.050 1.007 0.066 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.3100 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0864 r_free=0.1847 After: r_work=0.0867 r_free=0.1844 ================================== NQH flips ================================== r_work=0.0867 r_free=0.1844 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=0.0868 r_free=0.1842 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0868 r_free=0.1842 | n_water=244 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.0905 r_free=0.1821 | n_water=238 | time (s): 19.510 (total time: 20.180) Filter (q & B) r_work=0.0971 r_free=0.1863 | n_water=236 | time (s): 1.280 (total time: 21.460) Compute maps r_work=0.0971 r_free=0.1863 | n_water=236 | time (s): 0.450 (total time: 21.910) Filter (map) r_work=0.1235 r_free=0.1936 | n_water=169 | time (s): 1.500 (total time: 23.410) Find peaks r_work=0.1235 r_free=0.1936 | n_water=169 | time (s): 0.500 (total time: 23.910) Add new water r_work=0.1494 r_free=0.2206 | n_water=236 | time (s): 1.590 (total time: 25.500) Refine new water occ: r_work=0.0992 r_free=0.1829 adp: r_work=0.0986 r_free=0.1831 occ: r_work=0.0982 r_free=0.1818 adp: r_work=0.0981 r_free=0.1824 occ: r_work=0.0977 r_free=0.1811 adp: r_work=0.0977 r_free=0.1811 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1811 r_work=0.0977 r_free=0.1811 | n_water=236 | time (s): 8.270 (total time: 33.770) Filter (q & B) r_work=0.0978 r_free=0.1813 | n_water=233 | time (s): 1.580 (total time: 35.350) Filter (dist only) r_work=0.0978 r_free=0.1813 | n_water=232 | time (s): 19.410 (total time: 54.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.948920 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.233806 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 0.0925 0.1820 0.0895 0.011 1.1 7.0 0.5 0.0 0 0.474 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.25 18.20 8.95 8.199 18.275 0.234 5.030 9.01 18.43 9.43 8.881 18.362 0.234 4.969 Individual atomic B min max mean iso aniso Overall: 0.00 113.11 16.90 11.66 1759 0 Protein: 0.00 113.11 15.92 11.64 1519 0 Water: 0.64 56.22 23.01 N/A 232 0 Other: 10.05 43.03 24.23 N/A 8 0 Chain A: 0.00 113.11 16.36 N/A 1637 0 Chain S: 2.42 48.80 24.03 N/A 122 0 Histogram: Values Number of atoms 0.00 - 11.31 710 11.31 - 22.62 634 22.62 - 33.93 239 33.93 - 45.24 111 45.24 - 56.55 35 56.55 - 67.86 10 67.86 - 79.18 10 79.18 - 90.49 6 90.49 - 101.80 3 101.80 - 113.11 1 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1843 r_work=0.0903 r_free=0.1847 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0903 r_free = 0.1847 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0898 r_free = 0.1832 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0898 r_free= 0.1832 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.970079 | | target function (ml) not normalized (work): 24462.727084 | | target function (ml) not normalized (free): 2269.734153 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1283 0.1761 5.553 6.1421| | 2: 3.78 - 3.00 1.00 2430 110 0.0429 0.1951 4.3723 12.705| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.47 1.00 0.98 14150.01| | 2: 3.78 - 3.00 2430 110 0.99 1.88 1.00 1.00 937.54| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 606.94 max = 24040.86 mean = 7626.99| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.47 mean = 7.24| |phase err.(test): min = 0.00 max = 79.56 mean = 7.27| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0945 0.0898 0.1832 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2121 0.2117 0.2307 n_refl.: 5174 remove outliers: r(all,work,free)=0.2121 0.2117 0.2307 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2121 0.2117 0.2307 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0944 0.0897 0.1834 n_refl.: 5174 remove outliers: r(all,work,free)=0.0944 0.0897 0.1834 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 0.3919 329.880 298.245 0.613 0.985 0.320 11.894-9.307 99.02 97 4 0.2003 525.000 508.037 0.989 0.991 0.305 9.237-7.194 100.00 213 7 0.2195 429.346 419.853 1.042 0.995 0.290 7.162-5.571 100.00 427 22 0.2105 322.172 312.116 1.038 0.997 0.290 5.546-4.326 100.00 867 58 0.1041 442.296 436.807 1.066 0.999 0.224 4.315-3.360 100.00 1859 96 0.0559 420.629 420.266 1.140 1.002 0.210 3.356-3.002 100.00 1373 60 0.0412 323.986 324.425 1.120 1.005 0.073 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.1861 ================= 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 : 0.3631 0.2015 0.082 5.413 8.8 119.3 19.9 258 0.000 1_bss: 0.1577 0.1598 0.082 5.413 6.0 116.4 17.0 258 0.000 1_settarget: 0.1577 0.1598 0.082 5.413 6.0 116.4 17.0 258 0.000 1_nqh: 0.1584 0.1611 0.082 5.413 6.0 116.4 17.0 258 0.003 1_weight: 0.1584 0.1611 0.082 5.413 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1155 0.1811 0.010 0.986 6.0 116.4 17.0 258 0.212 1_adp: 0.1023 0.1811 0.010 0.986 2.2 111.4 17.3 258 0.212 1_regHadp: 0.1017 0.1813 0.010 0.986 2.2 111.4 17.3 258 0.212 1_occ: 0.1014 0.1820 0.010 0.986 2.2 111.4 17.3 258 0.212 2_bss: 0.1015 0.1809 0.010 0.986 1.3 110.5 16.3 258 0.212 2_settarget: 0.1015 0.1809 0.010 0.986 1.3 110.5 16.3 258 0.212 2_updatecdl: 0.1015 0.1809 0.010 1.006 1.3 110.5 16.3 258 0.212 2_nqh: 0.1015 0.1809 0.010 1.006 1.3 110.5 16.3 258 0.212 2_sol: 0.1124 0.1685 0.010 1.006 1.3 110.3 15.7 227 n/a 2_weight: 0.1124 0.1685 0.010 1.006 1.3 110.3 15.7 227 n/a 2_xyzrec: 0.1018 0.1793 0.009 1.005 1.3 110.3 15.7 227 n/a 2_adp: 0.0940 0.1819 0.009 1.005 0.0 108.7 16.6 227 n/a 2_regHadp: 0.0936 0.1819 0.009 1.005 0.0 108.7 16.6 227 n/a 2_occ: 0.0934 0.1823 0.009 1.005 0.0 108.7 16.6 227 n/a 3_bss: 0.0937 0.1834 0.009 1.005 0.0 108.7 16.6 227 n/a 3_settarget: 0.0937 0.1834 0.009 1.005 0.0 108.7 16.6 227 n/a 3_updatecdl: 0.0937 0.1834 0.009 1.002 0.0 108.7 16.6 227 n/a 3_nqh: 0.0941 0.1833 0.009 1.002 0.0 108.7 16.6 227 n/a 3_sol: 0.1044 0.1796 0.009 1.002 0.0 108.7 16.5 235 n/a 3_weight: 0.1044 0.1796 0.009 1.002 0.0 108.7 16.5 235 n/a 3_xyzrec: 0.0945 0.1813 0.011 1.079 0.0 108.7 16.5 235 n/a 3_adp: 0.0902 0.1797 0.011 1.079 0.0 108.4 16.5 235 n/a 3_regHadp: 0.0907 0.1801 0.011 1.079 0.0 108.4 16.5 235 n/a 3_occ: 0.0894 0.1780 0.011 1.079 0.0 108.4 16.5 235 n/a 4_bss: 0.0887 0.1773 0.011 1.079 0.0 108.4 16.5 235 n/a 4_settarget: 0.0887 0.1773 0.011 1.079 0.0 108.4 16.5 235 n/a 4_updatecdl: 0.0887 0.1773 0.011 1.091 0.0 108.4 16.5 235 n/a 4_nqh: 0.0888 0.1777 0.011 1.091 0.0 108.4 16.5 235 n/a 4_sol: 0.0968 0.1796 0.011 1.091 0.0 108.4 16.7 244 n/a 4_weight: 0.0968 0.1796 0.011 1.091 0.0 108.4 16.7 244 n/a 4_xyzrec: 0.0895 0.1862 0.011 1.060 0.0 108.4 16.7 244 n/a 4_adp: 0.0875 0.1878 0.011 1.060 0.0 110.0 16.9 244 n/a 4_regHadp: 0.0879 0.1883 0.011 1.060 0.0 110.0 16.9 244 n/a 4_occ: 0.0866 0.1868 0.011 1.060 0.0 110.0 16.9 244 n/a 5_bss: 0.0864 0.1847 0.011 1.060 0.0 110.0 16.9 244 n/a 5_settarget: 0.0864 0.1847 0.011 1.060 0.0 110.0 16.9 244 n/a 5_updatecdl: 0.0864 0.1847 0.011 1.069 0.0 110.0 16.9 244 n/a 5_setrh: 0.0867 0.1844 0.011 1.069 0.0 110.0 16.9 244 n/a 5_nqh: 0.0868 0.1842 0.011 1.069 0.0 110.0 16.9 244 n/a 5_sol: 0.0978 0.1813 0.011 1.069 0.0 110.0 16.7 232 n/a 5_weight: 0.0978 0.1813 0.011 1.069 0.0 110.0 16.7 232 n/a 5_xyzrec: 0.0925 0.1820 0.011 1.125 0.0 110.0 16.7 232 n/a 5_adp: 0.0901 0.1843 0.011 1.125 0.0 113.1 16.9 232 n/a 5_regHadp: 0.0903 0.1847 0.011 1.125 0.0 113.1 16.9 232 n/a 5_occ: 0.0898 0.1832 0.011 1.125 0.0 113.1 16.9 232 n/a end: 0.0897 0.1834 0.011 1.125 0.0 113.1 16.9 232 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1541177_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1541177_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9400 Refinement macro-cycles (run) : 472.8800 Write final files (write_after_run_outputs) : 11.5500 Total : 487.3700 Total CPU time: 8.44 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:48 PST -0800 (1735492728.13 s) Start R-work = 0.1577, R-free = 0.1598 Final R-work = 0.0897, R-free = 0.1834 =============================================================================== Job complete usr+sys time: 514.68 seconds wall clock time: 8 minutes 57.30 seconds (537.30 seconds total)