Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.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" } 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 =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.06, per 1000 atoms: 0.61 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 140.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 530 0.91 - 1.19: 1154 1.19 - 1.47: 771 1.47 - 1.74: 684 1.74 - 2.02: 14 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.332 1.512 -0.180 6.60e-03 2.30e+04 7.43e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.335 1.581 -0.246 1.20e-02 6.94e+03 4.22e+02 bond pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 1.230 0.984 0.246 1.22e-02 6.72e+03 4.07e+02 bond pdb=" C GLY A 37 " pdb=" O GLY A 37 " ideal model delta sigma weight residual 1.234 1.027 0.207 1.05e-02 9.07e+03 3.88e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.025 0.212 1.15e-02 7.56e+03 3.40e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 3327 4.98 - 9.97: 1831 9.97 - 14.95: 525 14.95 - 19.94: 86 19.94 - 24.92: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 136.19 -14.69 1.00e+00 1.00e+00 2.16e+02 angle pdb=" CA ALYS A 132 " pdb=" C ALYS A 132 " pdb=" O ALYS A 132 " ideal model delta sigma weight residual 120.70 135.34 -14.64 1.03e+00 9.43e-01 2.02e+02 angle pdb=" CA GLY A 37 " pdb=" C GLY A 37 " pdb=" O GLY A 37 " ideal model delta sigma weight residual 120.76 132.10 -11.34 8.10e-01 1.52e+00 1.96e+02 angle pdb=" CA GLY A 37 " pdb=" C GLY A 37 " pdb=" N LEU A 38 " ideal model delta sigma weight residual 115.86 100.57 15.29 1.13e+00 7.83e-01 1.83e+02 angle pdb=" CA PHE A 164 " pdb=" C PHE A 164 " pdb=" O PHE A 164 " ideal model delta sigma weight residual 120.42 107.20 13.22 1.06e+00 8.90e-01 1.56e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1286 16.75 - 33.49: 138 33.49 - 50.24: 40 50.24 - 66.99: 16 66.99 - 83.73: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C CYS A 106 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " pdb=" CB CYS A 106 " ideal model delta harmonic sigma weight residual -122.60 -143.53 20.93 0 2.50e+00 1.60e-01 7.01e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.19 19.59 0 2.50e+00 1.60e-01 6.14e+01 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 140.60 -17.80 0 2.50e+00 1.60e-01 5.07e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.207: 93 0.207 - 0.411: 73 0.411 - 0.615: 46 0.615 - 0.818: 24 0.818 - 1.022: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 3.53 -1.02 2.00e-01 2.50e+01 2.61e+01 chirality pdb=" CA GLN A 180 " pdb=" N GLN A 180 " pdb=" C GLN A 180 " pdb=" CB GLN A 180 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.69 -0.94 2.00e-01 2.50e+01 2.20e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.000 2.00e-02 2.50e+03 6.53e-02 1.28e+02 pdb=" CG PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.040 9.50e-02 1.11e+02 6.74e-02 9.83e+01 pdb=" NE ARG A 145 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.147 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.044 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " -0.081 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.043 2.00e-02 2.50e+03 5.45e-02 8.90e+01 pdb=" CG TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.106 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.063 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.059 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.035 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 951 2.31 - 2.88: 8124 2.88 - 3.46: 10582 3.46 - 4.03: 15177 4.03 - 4.60: 21855 Nonbonded interactions: 56689 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.742 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.807 2.270 nonbonded pdb="HE21 GLN A 45 " pdb=" OD1 ASP A 49 " model vdw 1.809 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.820 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.844 2.100 ... (remaining 56684 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_8569971_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= 0.3616 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462468 | | target function (ml) not normalized (work): 21999.966667 | | target function (ml) not normalized (free): 1150.572121 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3797 0.2159 4.8457 4.89| | 2: 3.78 - 3.00 1.00 2430 110 0.3395 0.1682 4.0682 4.1472| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 6601.11| | 2: 3.78 - 3.00 2430 110 0.94 11.36 1.48 0.26 446.27| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 382.04 max = 12075.13 mean = 3567.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.97 mean = 30.33| |phase err.(test): min = 0.00 max = 89.90 mean = 33.09| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.266 1557 Z= 5.641 Angle : 5.182 20.690 2118 Z= 3.682 Chirality : 0.386 1.022 243 Planarity : 0.032 0.094 284 Dihedral : 14.037 83.732 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 0.54 % Favored : 98.92 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 30.27 % 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: -2.63 (0.45), residues: 224 helix: -2.81 (0.33), residues: 109 sheet: -0.30 (0.68), residues: 38 loop : -0.38 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.087 0.025 ARG A 28 TYR 0.080 0.032 TYR A 141 PHE 0.098 0.039 PHE A 119 HIS 0.026 0.012 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= 0.3616 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462468 | | target function (ml) not normalized (work): 21999.966667 | | target function (ml) not normalized (free): 1150.572121 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3571 0.3649 0.2083 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3571 0.3649 0.2083 n_refl.: 5182 remove outliers: r(all,work,free)=0.2522 0.2548 0.2083 n_refl.: 5178 overall B=-2.85 to atoms: r(all,work,free)=0.2413 0.2435 0.2030 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1563 0.1564 0.1552 n_refl.: 5178 remove outliers: r(all,work,free)=0.1559 0.1559 0.1552 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 0.3887 449.682 404.810 0.667 1.057 0.394 11.894-9.307 99.02 97 4 0.1894 714.355 694.293 0.946 1.054 0.383 9.237-7.194 100.00 213 7 0.2187 584.201 575.753 0.986 1.048 0.358 7.162-5.571 100.00 427 22 0.2334 438.372 424.607 0.945 1.038 0.297 5.546-4.326 100.00 867 58 0.1396 601.822 594.486 0.984 1.021 0.255 4.315-3.360 100.00 1859 96 0.1298 572.339 565.936 1.051 0.992 0.205 3.356-3.002 100.00 1373 60 0.1597 440.840 432.763 1.058 0.963 0.107 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6444 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1559 r_free=0.1552 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=0.1561 r_free=0.1553 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.271234 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.819097 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 0.1163 0.1769 0.0606 0.010 1.0 2.6 0.5 0.0 0 9.636 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 17.69 6.06 3.013 16.009 1.819 0.018 10.21 17.56 7.35 4.887 16.206 1.819 0.015 Individual atomic B min max mean iso aniso Overall: 2.23 111.45 17.41 5.22 1785 0 Protein: 2.23 110.97 14.74 5.21 1519 0 Water: 4.01 111.45 32.92 N/A 258 0 Other: 15.86 36.59 23.72 N/A 8 0 Chain A: 2.23 111.45 17.41 N/A 1785 0 Histogram: Values Number of atoms 2.23 - 13.15 926 13.15 - 24.07 474 24.07 - 35.00 189 35.00 - 45.92 110 45.92 - 56.84 53 56.84 - 67.76 16 67.76 - 78.68 8 78.68 - 89.61 5 89.61 - 100.53 1 100.53 - 111.45 3 =========================== Idealize ADP of riding H ========================== r_work=0.1021 r_free=0.1756 r_work=0.1015 r_free=0.1762 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1015 r_free = 0.1762 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 = 0.1015 r_free = 0.1735 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1015 r_free= 0.1735 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014125 | | target function (ls_wunit_k1) not normalized (work): 69.550966 | | target function (ls_wunit_k1) not normalized (free): 10.111862 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1052 0.1015 0.1735 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2086 0.2085 0.2188 n_refl.: 5176 remove outliers: r(all,work,free)=0.2086 0.2085 0.2188 n_refl.: 5176 overall B=-0.97 to atoms: r(all,work,free)=0.2046 0.2044 0.2178 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1054 0.1018 0.1729 n_refl.: 5176 remove outliers: r(all,work,free)=0.1052 0.1016 0.1729 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3328 327.388 306.203 0.659 1.010 0.364 11.894-9.307 99.02 97 4 0.1604 524.499 515.644 0.985 1.011 0.360 9.237-7.194 100.00 213 7 0.1652 428.936 429.292 1.025 1.010 0.326 7.162-5.571 100.00 427 22 0.1635 321.865 318.290 0.986 1.008 0.312 5.546-4.326 100.00 867 58 0.0914 441.874 438.926 0.999 1.004 0.222 4.315-3.360 100.00 1859 96 0.0770 420.227 420.065 1.042 0.999 0.193 3.356-3.002 100.00 1373 60 0.1000 323.677 322.128 1.017 0.993 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.4659 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1016 r_free=0.1729 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1016 r_free=0.1729 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1016 r_free=0.1729 | n_water=258 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1043 r_free=0.1741 | n_water=246 | time (s): 21.360 (total time: 22.050) Filter (q & B) r_work=0.1043 r_free=0.1738 | n_water=243 | time (s): 1.740 (total time: 23.790) Compute maps r_work=0.1043 r_free=0.1738 | n_water=243 | time (s): 0.650 (total time: 24.440) Filter (map) r_work=0.1330 r_free=0.1816 | n_water=150 | time (s): 1.650 (total time: 26.090) Find peaks r_work=0.1330 r_free=0.1816 | n_water=150 | time (s): 0.510 (total time: 26.600) Add new water r_work=0.1668 r_free=0.2121 | n_water=234 | time (s): 1.910 (total time: 28.510) Refine new water occ: r_work=0.1148 r_free=0.1663 adp: r_work=0.1124 r_free=0.1668 occ: r_work=0.1120 r_free=0.1646 adp: r_work=0.1109 r_free=0.1647 occ: r_work=0.1107 r_free=0.1651 adp: r_work=0.1105 r_free=0.1646 ADP+occupancy (water only), MIN, final r_work=0.1105 r_free=0.1646 r_work=0.1105 r_free=0.1646 | n_water=234 | time (s): 2.880 (total time: 31.390) Filter (q & B) r_work=0.1106 r_free=0.1644 | n_water=233 | time (s): 1.600 (total time: 32.990) Filter (dist only) r_work=0.1118 r_free=0.1624 | n_water=229 | time (s): 17.510 (total time: 50.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.128488 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.784724 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 0.1003 0.1766 0.0763 0.009 1.0 4.2 0.5 0.6 0 11.564 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.03 17.66 7.63 4.622 16.764 2.785 0.014 9.31 17.68 8.37 5.474 17.112 2.785 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.03 16.46 6.45 1756 0 Protein: 0.00 107.03 14.87 6.39 1519 0 Water: 0.00 62.76 26.35 N/A 229 0 Other: 21.76 56.96 35.14 N/A 8 0 Chain A: 0.00 107.03 15.65 N/A 1674 0 Chain S: 1.99 56.76 32.99 N/A 82 0 Histogram: Values Number of atoms 0.00 - 10.70 675 10.70 - 21.41 675 21.41 - 32.11 207 32.11 - 42.81 121 42.81 - 53.51 38 53.51 - 64.22 27 64.22 - 74.92 6 74.92 - 85.62 3 85.62 - 96.33 2 96.33 - 107.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.0931 r_free=0.1768 r_work=0.0930 r_free=0.1774 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0930 r_free = 0.1774 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0928 r_free = 0.1776 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0928 r_free= 0.1776 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011821 | | target function (ls_wunit_k1) not normalized (work): 58.195135 | | target function (ls_wunit_k1) not normalized (free): 9.872622 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0971 0.0928 0.1776 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2100 0.2100 0.2208 n_refl.: 5175 remove outliers: r(all,work,free)=0.2100 0.2100 0.2208 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2100 0.2100 0.2208 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0971 0.0928 0.1780 n_refl.: 5175 remove outliers: r(all,work,free)=0.0969 0.0926 0.1780 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 0.3115 329.565 308.583 0.651 1.013 0.354 11.894-9.307 99.02 97 4 0.1529 524.499 519.765 0.972 1.014 0.350 9.237-7.194 100.00 213 7 0.1442 428.936 428.444 1.019 1.013 0.320 7.162-5.571 100.00 427 22 0.1432 321.865 319.397 0.993 1.011 0.310 5.546-4.326 100.00 867 58 0.0794 441.874 439.153 1.006 1.006 0.250 4.315-3.360 100.00 1859 96 0.0716 420.227 419.689 1.053 0.998 0.200 3.356-3.002 100.00 1373 60 0.0936 323.677 322.736 1.034 0.990 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-4.0438 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0926 r_free=0.1780 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=0.0930 r_free=0.1770 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0930 r_free=0.1770 | n_water=229 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.0958 r_free=0.1789 | n_water=224 | time (s): 18.390 (total time: 19.110) Filter (q & B) r_work=0.1021 r_free=0.1790 | n_water=222 | time (s): 2.060 (total time: 21.170) Compute maps r_work=0.1021 r_free=0.1790 | n_water=222 | time (s): 0.690 (total time: 21.860) Filter (map) r_work=0.1266 r_free=0.1847 | n_water=151 | time (s): 1.510 (total time: 23.370) Find peaks r_work=0.1266 r_free=0.1847 | n_water=151 | time (s): 0.430 (total time: 23.800) Add new water r_work=0.1656 r_free=0.2206 | n_water=233 | time (s): 1.440 (total time: 25.240) Refine new water occ: r_work=0.1068 r_free=0.1740 adp: r_work=0.1062 r_free=0.1749 occ: r_work=0.1050 r_free=0.1728 adp: r_work=0.1050 r_free=0.1734 occ: r_work=0.1040 r_free=0.1711 adp: r_work=0.1040 r_free=0.1718 ADP+occupancy (water only), MIN, final r_work=0.1040 r_free=0.1718 r_work=0.1040 r_free=0.1718 | n_water=233 | time (s): 13.580 (total time: 38.820) Filter (q & B) r_work=0.1040 r_free=0.1722 | n_water=232 | time (s): 1.760 (total time: 40.580) Filter (dist only) r_work=0.1047 r_free=0.1726 | n_water=229 | time (s): 17.420 (total time: 58.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.113480 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.240147 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 0.0943 0.1793 0.0851 0.011 1.0 3.8 0.5 0.0 0 0.557 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.43 17.93 8.51 5.388 17.715 0.240 5.156 9.01 17.87 8.86 7.220 17.699 0.240 5.057 Individual atomic B min max mean iso aniso Overall: 0.00 107.26 16.23 8.89 1756 0 Protein: 0.00 107.26 14.96 8.84 1519 0 Water: 0.00 57.76 24.01 N/A 229 0 Other: 20.78 61.07 35.93 N/A 8 0 Chain A: 0.00 107.26 15.70 N/A 1661 0 Chain S: 0.00 57.54 25.53 N/A 95 0 Histogram: Values Number of atoms 0.00 - 10.73 682 10.73 - 21.45 663 21.45 - 32.18 225 32.18 - 42.90 116 42.90 - 53.63 36 53.63 - 64.35 16 64.35 - 75.08 11 75.08 - 85.81 3 85.81 - 96.53 3 96.53 - 107.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1787 r_work=0.0908 r_free=0.1801 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0908 r_free = 0.1801 target_work(ml) = 5.062 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0896 r_free = 0.1783 target_work(ml) = 5.054 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0896 r_free= 0.1783 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.053661 | | target function (ml) not normalized (work): 24874.119367 | | target function (ml) not normalized (free): 1802.628928 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0941 0.0896 0.1783 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2055 0.2054 0.2163 n_refl.: 5174 remove outliers: r(all,work,free)=0.2055 0.2054 0.2163 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2055 0.2054 0.2163 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0887 0.1777 n_refl.: 5174 remove outliers: r(all,work,free)=0.0932 0.0887 0.1777 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 0.3466 329.565 304.551 0.603 0.989 0.330 11.894-9.307 99.02 97 4 0.1835 524.499 510.072 0.947 0.993 0.330 9.237-7.194 100.00 213 7 0.1948 428.936 421.694 1.000 0.995 0.310 7.162-5.571 100.00 427 22 0.1897 321.865 311.701 0.984 0.997 0.300 5.546-4.326 100.00 867 58 0.0925 441.874 436.340 1.000 0.999 0.260 4.315-3.360 100.00 1859 96 0.0583 420.227 419.635 1.051 1.002 0.210 3.356-3.002 100.00 1373 60 0.0585 323.677 323.582 1.028 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.1897 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0887 r_free=0.1777 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 Total number of N/Q/H flips: 2 r_work=0.0888 r_free=0.1786 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0888 r_free=0.1786 | n_water=229 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0905 r_free=0.1800 | n_water=224 | time (s): 18.540 (total time: 19.010) Filter (q & B) r_work=0.0950 r_free=0.1825 | n_water=222 | time (s): 2.010 (total time: 21.020) Compute maps r_work=0.0950 r_free=0.1825 | n_water=222 | time (s): 0.600 (total time: 21.620) Filter (map) r_work=0.1201 r_free=0.1873 | n_water=163 | time (s): 1.820 (total time: 23.440) Find peaks r_work=0.1201 r_free=0.1873 | n_water=163 | time (s): 0.580 (total time: 24.020) Add new water r_work=0.1505 r_free=0.2171 | n_water=232 | time (s): 1.800 (total time: 25.820) Refine new water occ: r_work=0.1005 r_free=0.1812 adp: r_work=0.1000 r_free=0.1830 occ: r_work=0.0988 r_free=0.1801 adp: r_work=0.0988 r_free=0.1816 occ: r_work=0.0976 r_free=0.1791 adp: r_work=0.0976 r_free=0.1804 ADP+occupancy (water only), MIN, final r_work=0.0976 r_free=0.1804 r_work=0.0976 r_free=0.1804 | n_water=232 | time (s): 10.860 (total time: 36.680) Filter (q & B) r_work=0.0976 r_free=0.1804 | n_water=232 | time (s): 0.750 (total time: 37.430) Filter (dist only) r_work=0.0980 r_free=0.1786 | n_water=231 | time (s): 17.390 (total time: 54.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.025994 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.242700 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 0.0899 0.1893 0.0994 0.011 1.0 5.4 0.5 0.0 0 0.513 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.99 18.93 9.94 6.926 17.840 0.243 5.015 8.76 18.97 10.22 8.087 17.938 0.243 4.956 Individual atomic B min max mean iso aniso Overall: 0.00 110.35 16.59 10.52 1758 0 Protein: 0.00 110.35 15.32 10.47 1519 0 Water: 0.00 61.26 24.22 N/A 231 0 Other: 18.88 60.82 36.43 N/A 8 0 Chain A: 0.00 110.35 15.95 N/A 1653 0 Chain S: 0.00 61.26 26.61 N/A 105 0 Histogram: Values Number of atoms 0.00 - 11.04 694 11.04 - 22.07 636 22.07 - 33.11 243 33.11 - 44.14 113 44.14 - 55.18 42 55.18 - 66.21 12 66.21 - 77.25 12 77.25 - 88.28 3 88.28 - 99.32 2 99.32 - 110.35 1 =========================== Idealize ADP of riding H ========================== r_work=0.0876 r_free=0.1897 r_work=0.0880 r_free=0.1899 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0880 r_free = 0.1899 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0866 r_free = 0.1877 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.19 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= 0.1877 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.951408 | | target function (ml) not normalized (work): 24370.830019 | | target function (ml) not normalized (free): 2100.798104 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0917 0.0866 0.1877 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2090 0.2090 0.2202 n_refl.: 5174 remove outliers: r(all,work,free)=0.2090 0.2090 0.2202 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2090 0.2090 0.2202 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0917 0.0867 0.1875 n_refl.: 5174 remove outliers: r(all,work,free)=0.0917 0.0867 0.1875 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 0.3717 329.565 299.791 0.600 0.986 0.327 11.894-9.307 99.02 97 4 0.1970 524.499 511.037 0.950 0.992 0.324 9.237-7.194 100.00 213 7 0.2101 428.936 420.830 1.005 0.995 0.310 7.162-5.571 100.00 427 22 0.1951 321.865 312.234 0.991 0.997 0.300 5.546-4.326 100.00 867 58 0.0977 441.874 436.155 1.007 0.999 0.234 4.315-3.360 100.00 1859 96 0.0551 420.227 419.683 1.067 1.002 0.219 3.356-3.002 100.00 1373 60 0.0431 323.677 323.627 1.047 1.005 0.069 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.9841 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0867 r_free=0.1875 After: r_work=0.0870 r_free=0.1875 ================================== NQH flips ================================== r_work=0.0870 r_free=0.1875 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0870 r_free=0.1875 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0870 r_free=0.1875 | n_water=231 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.0886 r_free=0.1887 | n_water=226 | time (s): 20.030 (total time: 20.680) Filter (q & B) r_work=0.0954 r_free=0.1909 | n_water=224 | time (s): 1.470 (total time: 22.150) Compute maps r_work=0.0954 r_free=0.1909 | n_water=224 | time (s): 0.480 (total time: 22.630) Filter (map) r_work=0.1205 r_free=0.1924 | n_water=162 | time (s): 1.350 (total time: 23.980) Find peaks r_work=0.1205 r_free=0.1924 | n_water=162 | time (s): 0.420 (total time: 24.400) Add new water r_work=0.1477 r_free=0.2125 | n_water=225 | time (s): 1.410 (total time: 25.810) Refine new water occ: r_work=0.0989 r_free=0.1870 adp: r_work=0.0982 r_free=0.1876 occ: r_work=0.0977 r_free=0.1862 adp: r_work=0.0976 r_free=0.1868 occ: r_work=0.0972 r_free=0.1855 adp: r_work=0.0970 r_free=0.1862 ADP+occupancy (water only), MIN, final r_work=0.0970 r_free=0.1862 r_work=0.0970 r_free=0.1862 | n_water=225 | time (s): 8.470 (total time: 34.280) Filter (q & B) r_work=0.0970 r_free=0.1862 | n_water=224 | time (s): 2.040 (total time: 36.320) Filter (dist only) r_work=0.0970 r_free=0.1862 | n_water=224 | time (s): 16.020 (total time: 52.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.933275 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.236692 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 0.0906 0.1836 0.0929 0.010 1.0 6.1 0.5 0.0 0 0.467 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.06 18.36 9.29 8.008 18.126 0.237 5.009 8.92 18.44 9.52 8.933 18.231 0.237 4.960 Individual atomic B min max mean iso aniso Overall: 0.00 114.43 16.76 11.83 1751 0 Protein: 0.00 114.43 15.68 11.77 1519 0 Water: 0.00 60.82 23.42 N/A 224 0 Other: 14.27 61.75 35.10 N/A 8 0 Chain A: 0.00 114.43 16.20 N/A 1645 0 Chain S: 0.00 60.82 25.40 N/A 106 0 Histogram: Values Number of atoms 0.00 - 11.44 700 11.44 - 22.89 635 22.89 - 34.33 247 34.33 - 45.77 103 45.77 - 57.21 37 57.21 - 68.66 12 68.66 - 80.10 11 80.10 - 91.54 3 91.54 - 102.99 2 102.99 - 114.43 1 =========================== Idealize ADP of riding H ========================== r_work=0.0892 r_free=0.1844 r_work=0.0895 r_free=0.1845 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0895 r_free = 0.1845 target_work(ml) = 4.966 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0889 r_free = 0.1838 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0889 r_free= 0.1838 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.961859 | | target function (ml) not normalized (work): 24422.268178 | | target function (ml) not normalized (free): 2091.945500 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1258 0.1836 5.5303 6.2312| | 2: 3.78 - 3.00 1.00 2430 110 0.0439 0.1842 4.3789 10.974| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 12.06 1.00 0.98 13080.06| | 2: 3.78 - 3.00 2430 110 0.99 1.94 1.01 1.00 948.35| |alpha: min = 0.97 max = 1.01 mean = 0.99| |beta: min = 611.50 max = 21870.01 mean = 7090.62| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.32 mean = 7.06| |phase err.(test): min = 0.00 max = 71.15 mean = 7.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0936 0.0889 0.1838 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2140 0.2141 0.2221 n_refl.: 5174 remove outliers: r(all,work,free)=0.2140 0.2141 0.2221 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2140 0.2141 0.2221 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0936 0.0889 0.1838 n_refl.: 5174 remove outliers: r(all,work,free)=0.0936 0.0889 0.1838 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 0.3705 329.565 299.674 0.604 0.988 0.327 11.894-9.307 99.02 97 4 0.1940 524.499 512.452 0.960 0.993 0.325 9.237-7.194 100.00 213 7 0.2126 428.936 420.284 1.004 0.996 0.310 7.162-5.571 100.00 427 22 0.2049 321.865 313.017 0.988 0.998 0.290 5.546-4.326 100.00 867 58 0.1013 441.874 436.285 1.016 1.000 0.237 4.315-3.360 100.00 1859 96 0.0582 420.227 419.615 1.086 1.002 0.225 3.356-3.002 100.00 1373 60 0.0411 323.677 323.115 1.070 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8315 ================= 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 : 0.3616 0.1982 0.083 5.182 8.8 119.3 19.9 258 0.000 1_bss: 0.1559 0.1552 0.083 5.182 6.0 116.4 17.0 258 0.000 1_settarget: 0.1559 0.1552 0.083 5.182 6.0 116.4 17.0 258 0.000 1_nqh: 0.1561 0.1553 0.083 5.182 6.0 116.4 17.0 258 0.003 1_weight: 0.1561 0.1553 0.083 5.182 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1163 0.1769 0.010 0.973 6.0 116.4 17.0 258 0.206 1_adp: 0.1021 0.1756 0.010 0.973 2.2 111.4 17.4 258 0.206 1_regHadp: 0.1015 0.1762 0.010 0.973 2.2 111.4 17.4 258 0.206 1_occ: 0.1015 0.1735 0.010 0.973 2.2 111.4 17.4 258 0.206 2_bss: 0.1016 0.1729 0.010 0.973 1.3 110.5 16.4 258 0.206 2_settarget: 0.1016 0.1729 0.010 0.973 1.3 110.5 16.4 258 0.206 2_updatecdl: 0.1016 0.1729 0.010 0.998 1.3 110.5 16.4 258 0.206 2_nqh: 0.1016 0.1729 0.010 0.998 1.3 110.5 16.4 258 0.206 2_sol: 0.1118 0.1624 0.010 0.998 1.0 110.0 15.8 229 n/a 2_weight: 0.1118 0.1624 0.010 0.998 1.0 110.0 15.8 229 n/a 2_xyzrec: 0.1003 0.1766 0.009 0.977 1.0 110.0 15.8 229 n/a 2_adp: 0.0931 0.1768 0.009 0.977 0.0 107.0 16.5 229 n/a 2_regHadp: 0.0930 0.1774 0.009 0.977 0.0 107.0 16.5 229 n/a 2_occ: 0.0928 0.1776 0.009 0.977 0.0 107.0 16.5 229 n/a 3_bss: 0.0926 0.1780 0.009 0.977 0.0 107.0 16.5 229 n/a 3_settarget: 0.0926 0.1780 0.009 0.977 0.0 107.0 16.5 229 n/a 3_updatecdl: 0.0926 0.1780 0.009 0.984 0.0 107.0 16.5 229 n/a 3_nqh: 0.0930 0.1770 0.009 0.984 0.0 107.0 16.5 229 n/a 3_sol: 0.1047 0.1726 0.009 0.984 0.0 107.0 16.3 229 n/a 3_weight: 0.1047 0.1726 0.009 0.984 0.0 107.0 16.3 229 n/a 3_xyzrec: 0.0943 0.1793 0.011 1.047 0.0 107.0 16.3 229 n/a 3_adp: 0.0901 0.1787 0.011 1.047 0.0 107.3 16.2 229 n/a 3_regHadp: 0.0908 0.1801 0.011 1.047 0.0 107.3 16.2 229 n/a 3_occ: 0.0896 0.1783 0.011 1.047 0.0 107.3 16.2 229 n/a 4_bss: 0.0887 0.1777 0.011 1.047 0.0 107.3 16.2 229 n/a 4_settarget: 0.0887 0.1777 0.011 1.047 0.0 107.3 16.2 229 n/a 4_updatecdl: 0.0887 0.1777 0.011 1.060 0.0 107.3 16.2 229 n/a 4_nqh: 0.0888 0.1786 0.011 1.060 0.0 107.3 16.2 229 n/a 4_sol: 0.0980 0.1786 0.011 1.060 0.0 107.3 16.4 231 n/a 4_weight: 0.0980 0.1786 0.011 1.060 0.0 107.3 16.4 231 n/a 4_xyzrec: 0.0899 0.1893 0.011 1.036 0.0 107.3 16.4 231 n/a 4_adp: 0.0876 0.1897 0.011 1.036 0.0 110.4 16.6 231 n/a 4_regHadp: 0.0880 0.1899 0.011 1.036 0.0 110.4 16.6 231 n/a 4_occ: 0.0866 0.1877 0.011 1.036 0.0 110.4 16.6 231 n/a 5_bss: 0.0867 0.1875 0.011 1.036 0.0 110.4 16.6 231 n/a 5_settarget: 0.0867 0.1875 0.011 1.036 0.0 110.4 16.6 231 n/a 5_updatecdl: 0.0867 0.1875 0.011 1.037 0.0 110.4 16.6 231 n/a 5_setrh: 0.0870 0.1875 0.011 1.037 0.0 110.4 16.6 231 n/a 5_nqh: 0.0870 0.1875 0.011 1.037 0.0 110.4 16.6 231 n/a 5_sol: 0.0970 0.1862 0.011 1.037 0.0 110.4 16.6 224 n/a 5_weight: 0.0970 0.1862 0.011 1.037 0.0 110.4 16.6 224 n/a 5_xyzrec: 0.0906 0.1836 0.010 1.046 0.0 110.4 16.6 224 n/a 5_adp: 0.0892 0.1844 0.010 1.046 0.0 114.4 16.8 224 n/a 5_regHadp: 0.0895 0.1845 0.010 1.046 0.0 114.4 16.8 224 n/a 5_occ: 0.0889 0.1838 0.010 1.046 0.0 114.4 16.8 224 n/a end: 0.0889 0.1838 0.010 1.046 0.0 114.4 16.8 224 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8569971_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8569971_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.4700 Refinement macro-cycles (run) : 491.3000 Write final files (write_after_run_outputs) : 9.5900 Total : 505.3600 Total CPU time: 8.79 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:09 PST -0800 (1735492749.41 s) Start R-work = 0.1559, R-free = 0.1552 Final R-work = 0.0889, R-free = 0.1838 =============================================================================== Job complete usr+sys time: 535.49 seconds wall clock time: 9 minutes 17.79 seconds (557.79 seconds total)