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_2359181.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_2359181.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2359181.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } 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: 1.30, per 1000 atoms: 0.38 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 124.1 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: 0.65 - 0.90: 484 0.90 - 1.15: 1140 1.15 - 1.41: 607 1.41 - 1.66: 864 1.66 - 1.91: 58 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.236 0.915 0.321 1.15e-02 7.56e+03 7.78e+02 bond pdb=" C ALA A 6 " pdb=" O ALA A 6 " ideal model delta sigma weight residual 1.235 1.487 -0.252 1.28e-02 6.10e+03 3.87e+02 bond pdb=" N MET A 134 " pdb=" CA MET A 134 " ideal model delta sigma weight residual 1.457 1.677 -0.220 1.32e-02 5.74e+03 2.77e+02 bond pdb=" N BGLU A 90 " pdb=" CA BGLU A 90 " ideal model delta sigma weight residual 1.459 1.651 -0.192 1.17e-02 7.31e+03 2.68e+02 bond pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " ideal model delta sigma weight residual 1.326 1.503 -0.177 1.10e-02 8.26e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.32: 3461 5.32 - 10.64: 1796 10.64 - 15.96: 477 15.96 - 21.28: 40 21.28 - 26.60: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.50 123.40 -12.90 6.30e-01 2.52e+00 4.19e+02 angle pdb=" O VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " ideal model delta sigma weight residual 123.00 140.57 -17.57 1.14e+00 7.69e-01 2.37e+02 angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 110.62 123.94 -13.32 1.02e+00 9.61e-01 1.70e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.23 113.29 8.94 6.90e-01 2.10e+00 1.68e+02 angle pdb=" OD1BASN A 97 " pdb=" CG BASN A 97 " pdb=" ND2BASN A 97 " ideal model delta sigma weight residual 122.60 135.43 -12.83 1.00e+00 1.00e+00 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 1310 17.56 - 35.12: 123 35.12 - 52.68: 33 52.68 - 70.23: 13 70.23 - 87.79: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -144.46 21.86 0 2.50e+00 1.60e-01 7.65e+01 dihedral pdb=" C BASN A 76 " pdb=" N BASN A 76 " pdb=" CA BASN A 76 " pdb=" CB BASN A 76 " ideal model delta harmonic sigma weight residual -122.60 -142.31 19.71 0 2.50e+00 1.60e-01 6.22e+01 dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 141.78 -18.98 0 2.50e+00 1.60e-01 5.76e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.210: 102 0.210 - 0.420: 67 0.420 - 0.630: 48 0.630 - 0.840: 18 0.840 - 1.050: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.75e+01 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -3.62 0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CA BASN A 76 " pdb=" N BASN A 76 " pdb=" C BASN A 76 " pdb=" CB BASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 6.43e-02 1.24e+02 pdb=" CG PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.031 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.120 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.033 2.00e-02 2.50e+03 5.07e-02 7.72e+01 pdb=" CG TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.093 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " -0.068 9.50e-02 1.11e+02 6.18e-02 7.51e+01 pdb=" NE ARG A 98 " -0.069 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.112 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.071 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " -0.036 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.038 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.040 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " -0.030 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 476 2.21 - 2.81: 7244 2.81 - 3.41: 10799 3.41 - 4.00: 15502 4.00 - 4.60: 22527 Nonbonded interactions: 56548 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.618 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.721 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.761 2.270 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.803 2.450 nonbonded pdb=" O GLY A 75 " pdb=" H ALA A 79 " model vdw 1.831 2.450 ... (remaining 56543 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_2359181_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= 0.3618 r_free= 0.1985 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468539 | | target function (ml) not normalized (work): 22029.897162 | | target function (ml) not normalized (free): 1144.230360 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3800 0.2187 4.8572 4.8831| | 2: 3.78 - 3.00 1.00 2430 110 0.3396 0.1643 4.0687 4.0985| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.49 49.07 0.83 0.13 6625.74| | 2: 3.78 - 3.00 2430 110 0.94 11.24 1.48 0.26 443.36| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 371.56 max = 12088.52 mean = 3578.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.43| |phase err.(test): min = 0.00 max = 89.91 mean = 33.40| |-----------------------------------------------------------------------------| ----------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 0.321 1557 Z= 5.432 Angle : 5.425 18.199 2118 Z= 3.832 Chirality : 0.393 1.050 243 Planarity : 0.033 0.107 284 Dihedral : 13.757 87.793 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.70 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.35 % Favored : 94.41 % Cbeta Deviations : 44.86 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.45), residues: 224 helix: -3.02 (0.38), residues: 109 sheet: -1.50 (0.82), residues: 28 loop : -0.87 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.023 ARG A 98 TYR 0.077 0.038 TYR A 141 PHE 0.090 0.034 PHE A 119 HIS 0.071 0.024 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3618 r_free= 0.1985 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468539 | | target function (ml) not normalized (work): 22029.897162 | | target function (ml) not normalized (free): 1144.230360 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3575 0.3650 0.2077 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3575 0.3650 0.2077 n_refl.: 5182 remove outliers: r(all,work,free)=0.2529 0.2554 0.2077 n_refl.: 5178 overall B=-2.67 to atoms: r(all,work,free)=0.2427 0.2449 0.2030 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1559 0.1561 0.1526 n_refl.: 5178 remove outliers: r(all,work,free)=0.1555 0.1556 0.1526 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 0.3885 449.787 402.082 0.638 1.063 0.399 11.894-9.307 99.02 97 4 0.1806 714.523 686.202 0.915 1.061 0.385 9.237-7.194 100.00 213 7 0.2169 584.338 573.249 0.943 1.054 0.348 7.162-5.571 100.00 427 22 0.2336 438.475 421.465 0.913 1.042 0.326 5.546-4.326 100.00 867 58 0.1381 601.963 591.515 0.951 1.023 0.220 4.315-3.360 100.00 1859 96 0.1306 572.474 566.710 1.028 0.989 0.199 3.356-3.002 100.00 1373 60 0.1600 440.943 436.365 1.052 0.956 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.6416 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1556 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1556 r_free=0.1526 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.765847 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.814937 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 0.1809 0.0654 0.010 1.0 2.2 0.5 0.0 0 9.383 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.55 18.09 6.54 3.012 16.185 1.815 0.018 10.17 17.98 7.81 4.873 16.445 1.815 0.014 Individual atomic B min max mean iso aniso Overall: 2.43 111.63 17.70 5.24 1785 0 Protein: 2.43 111.42 15.00 5.23 1519 0 Water: 4.19 111.63 33.39 N/A 258 0 Other: 17.30 36.89 24.83 N/A 8 0 Chain A: 2.43 111.63 17.70 N/A 1785 0 Histogram: Values Number of atoms 2.43 - 13.35 910 13.35 - 24.27 485 24.27 - 35.19 192 35.19 - 46.11 110 46.11 - 57.03 57 57.03 - 67.95 14 67.95 - 78.87 8 78.87 - 89.79 5 89.79 - 100.71 1 100.71 - 111.63 3 =========================== Idealize ADP of riding H ========================== r_work=0.1017 r_free=0.1798 r_work=0.1010 r_free=0.1804 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1010 r_free = 0.1804 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 = 0.1006 r_free = 0.1808 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1006 r_free= 0.1808 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013807 | | target function (ls_wunit_k1) not normalized (work): 67.985682 | | target function (ls_wunit_k1) not normalized (free): 10.727133 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1006 0.1808 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2107 0.2105 0.2252 n_refl.: 5176 remove outliers: r(all,work,free)=0.2107 0.2105 0.2252 n_refl.: 5176 overall B=-0.93 to atoms: r(all,work,free)=0.2067 0.2064 0.2240 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1051 0.1010 0.1801 n_refl.: 5176 remove outliers: r(all,work,free)=0.1051 0.1010 0.1801 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 0.3280 320.097 302.606 0.659 1.008 0.384 11.894-9.307 99.02 97 4 0.1526 508.500 502.292 0.956 1.010 0.365 9.237-7.194 100.00 213 7 0.1614 415.852 417.307 0.989 1.009 0.316 7.162-5.571 100.00 427 22 0.1618 312.047 309.131 0.948 1.007 0.312 5.546-4.326 100.00 867 58 0.0907 428.396 425.576 0.963 1.004 0.202 4.315-3.360 100.00 1859 96 0.0770 407.409 407.293 1.012 0.998 0.193 3.356-3.002 100.00 1373 60 0.1000 313.804 312.169 0.997 0.992 0.079 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.1825 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1010 r_free=0.1801 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1010 r_free=0.1801 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1801 | n_water=258 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1037 r_free=0.1791 | n_water=248 | time (s): 20.960 (total time: 21.560) Filter (q & B) r_work=0.1037 r_free=0.1795 | n_water=245 | time (s): 1.360 (total time: 22.920) Compute maps r_work=0.1037 r_free=0.1795 | n_water=245 | time (s): 0.470 (total time: 23.390) Filter (map) r_work=0.1377 r_free=0.1844 | n_water=140 | time (s): 1.320 (total time: 24.710) Find peaks r_work=0.1377 r_free=0.1844 | n_water=140 | time (s): 0.410 (total time: 25.120) Add new water r_work=0.1715 r_free=0.2119 | n_water=222 | time (s): 1.390 (total time: 26.510) Refine new water occ: r_work=0.1176 r_free=0.1670 adp: r_work=0.1155 r_free=0.1672 occ: r_work=0.1153 r_free=0.1652 adp: r_work=0.1143 r_free=0.1656 occ: r_work=0.1143 r_free=0.1647 adp: r_work=0.1140 r_free=0.1651 ADP+occupancy (water only), MIN, final r_work=0.1140 r_free=0.1651 r_work=0.1140 r_free=0.1651 | n_water=222 | time (s): 3.200 (total time: 29.710) Filter (q & B) r_work=0.1140 r_free=0.1651 | n_water=222 | time (s): 1.020 (total time: 30.730) Filter (dist only) r_work=0.1150 r_free=0.1642 | n_water=219 | time (s): 16.620 (total time: 47.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.800069 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.701814 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 0.1028 0.1786 0.0758 0.009 1.0 4.5 0.5 0.6 0 11.400 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.28 17.86 7.58 4.650 17.046 2.702 0.014 9.56 18.00 8.44 5.544 17.450 2.702 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.89 16.79 6.59 1746 0 Protein: 0.00 107.89 15.31 6.56 1519 0 Water: 0.00 63.57 26.57 N/A 219 0 Other: 16.44 48.20 29.54 N/A 8 0 Chain A: 0.00 107.89 16.08 N/A 1665 0 Chain S: 0.00 55.13 31.25 N/A 81 0 Histogram: Values Number of atoms 0.00 - 10.79 668 10.79 - 21.58 678 21.58 - 32.37 201 32.37 - 43.16 119 43.16 - 53.95 44 53.95 - 64.74 22 64.74 - 75.53 7 75.53 - 86.32 3 86.32 - 97.10 2 97.10 - 107.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.0956 r_free=0.1800 r_work=0.0953 r_free=0.1798 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0953 r_free = 0.1798 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0949 r_free = 0.1795 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0949 r_free= 0.1795 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012232 | | target function (ls_wunit_k1) not normalized (work): 60.229986 | | target function (ls_wunit_k1) not normalized (free): 10.099211 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0992 0.0949 0.1795 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2188 0.2197 0.2175 n_refl.: 5176 remove outliers: r(all,work,free)=0.2188 0.2197 0.2175 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2188 0.2197 0.2175 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0991 0.0947 0.1803 n_refl.: 5176 remove outliers: r(all,work,free)=0.0989 0.0946 0.1803 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 0.3067 317.401 306.403 0.693 1.012 0.371 11.894-9.307 99.02 97 4 0.1496 508.500 503.557 0.985 1.013 0.350 9.237-7.194 100.00 213 7 0.1458 415.852 418.223 1.021 1.012 0.310 7.162-5.571 100.00 427 22 0.1425 312.047 309.968 0.992 1.010 0.310 5.546-4.326 100.00 867 58 0.0809 428.396 426.116 1.008 1.006 0.240 4.315-3.360 100.00 1859 96 0.0742 407.409 407.117 1.064 0.998 0.210 3.356-3.002 100.00 1373 60 0.0966 313.804 312.410 1.052 0.990 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.6594 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0946 r_free=0.1803 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=0.0946 r_free=0.1804 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0946 r_free=0.1804 | n_water=219 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0964 r_free=0.1814 | n_water=215 | time (s): 17.900 (total time: 18.540) Filter (q & B) r_work=0.1003 r_free=0.1844 | n_water=213 | time (s): 1.670 (total time: 20.210) Compute maps r_work=0.1003 r_free=0.1844 | n_water=213 | time (s): 0.540 (total time: 20.750) Filter (map) r_work=0.1266 r_free=0.1870 | n_water=144 | time (s): 1.330 (total time: 22.080) Find peaks r_work=0.1266 r_free=0.1870 | n_water=144 | time (s): 0.480 (total time: 22.560) Add new water r_work=0.1648 r_free=0.2227 | n_water=225 | time (s): 1.400 (total time: 23.960) Refine new water occ: r_work=0.1057 r_free=0.1766 adp: r_work=0.1055 r_free=0.1776 occ: r_work=0.1045 r_free=0.1746 adp: r_work=0.1045 r_free=0.1759 occ: r_work=0.1037 r_free=0.1732 adp: r_work=0.1036 r_free=0.1745 ADP+occupancy (water only), MIN, final r_work=0.1036 r_free=0.1745 r_work=0.1036 r_free=0.1745 | n_water=225 | time (s): 8.980 (total time: 32.940) Filter (q & B) r_work=0.1037 r_free=0.1750 | n_water=224 | time (s): 2.030 (total time: 34.970) Filter (dist only) r_work=0.1055 r_free=0.1768 | n_water=221 | time (s): 18.230 (total time: 53.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.168506 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.267619 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 0.0950 0.1828 0.0879 0.011 1.1 3.8 0.5 0.0 0 0.584 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.50 18.28 8.79 5.496 18.101 0.268 5.139 9.06 18.55 9.49 7.429 18.147 0.268 5.043 Individual atomic B min max mean iso aniso Overall: 0.00 107.97 16.69 9.22 1748 0 Protein: 0.00 107.97 15.50 9.19 1519 0 Water: 0.00 58.57 24.39 N/A 221 0 Other: 16.18 51.69 30.93 N/A 8 0 Chain A: 0.00 107.97 16.19 N/A 1653 0 Chain S: 0.00 51.64 25.43 N/A 95 0 Histogram: Values Number of atoms 0.00 - 10.80 644 10.80 - 21.59 667 21.59 - 32.39 247 32.39 - 43.19 114 43.19 - 53.98 42 53.98 - 64.78 17 64.78 - 75.58 8 75.58 - 86.37 4 86.37 - 97.17 4 97.17 - 107.97 1 =========================== Idealize ADP of riding H ========================== r_work=0.0906 r_free=0.1855 r_work=0.0912 r_free=0.1865 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1865 target_work(ml) = 5.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0901 r_free = 0.1843 target_work(ml) = 5.041 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0901 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.040764 | | target function (ml) not normalized (work): 24815.681375 | | target function (ml) not normalized (free): 1798.218073 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0950 0.0901 0.1843 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2167 0.2179 0.2086 n_refl.: 5175 remove outliers: r(all,work,free)=0.2167 0.2179 0.2086 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2167 0.2179 0.2086 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0941 0.0895 0.1828 n_refl.: 5175 remove outliers: r(all,work,free)=0.0941 0.0895 0.1828 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 0.3746 317.401 296.442 0.638 0.990 0.347 11.894-9.307 99.02 97 4 0.1845 508.500 491.751 0.953 0.994 0.330 9.237-7.194 100.00 213 7 0.1869 415.852 414.089 1.005 0.997 0.305 7.162-5.571 100.00 427 22 0.1860 312.047 303.462 0.982 0.998 0.300 5.546-4.326 100.00 867 58 0.0930 428.396 422.896 1.000 1.000 0.234 4.315-3.360 100.00 1859 96 0.0592 407.409 407.017 1.063 1.002 0.220 3.356-3.002 100.00 1373 60 0.0606 313.804 313.186 1.048 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.8695 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0895 r_free=0.1828 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0896 r_free=0.1825 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0896 r_free=0.1825 | n_water=221 | time (s): 0.480 (total time: 0.480) Filter (dist) r_work=0.0915 r_free=0.1826 | n_water=215 | time (s): 16.500 (total time: 16.980) Filter (q & B) r_work=0.1023 r_free=0.1791 | n_water=211 | time (s): 1.640 (total time: 18.620) Compute maps r_work=0.1023 r_free=0.1791 | n_water=211 | time (s): 0.650 (total time: 19.270) Filter (map) r_work=0.1279 r_free=0.1849 | n_water=154 | time (s): 1.630 (total time: 20.900) Find peaks r_work=0.1279 r_free=0.1849 | n_water=154 | time (s): 0.470 (total time: 21.370) Add new water r_work=0.1616 r_free=0.2145 | n_water=227 | time (s): 1.230 (total time: 22.600) Refine new water occ: r_work=0.1033 r_free=0.1791 adp: r_work=0.1020 r_free=0.1817 occ: r_work=0.1011 r_free=0.1795 adp: r_work=0.1010 r_free=0.1805 occ: r_work=0.1002 r_free=0.1783 adp: r_work=0.1001 r_free=0.1794 ADP+occupancy (water only), MIN, final r_work=0.1001 r_free=0.1794 r_work=0.1001 r_free=0.1794 | n_water=227 | time (s): 8.830 (total time: 31.430) Filter (q & B) r_work=0.1001 r_free=0.1794 | n_water=227 | time (s): 0.990 (total time: 32.420) Filter (dist only) r_work=0.1004 r_free=0.1798 | n_water=224 | time (s): 15.640 (total time: 48.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.001374 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.266668 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 0.0919 0.1846 0.0927 0.011 1.0 5.1 0.5 0.6 0 0.501 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.19 18.46 9.27 7.168 18.353 0.267 5.024 9.01 18.44 9.43 8.447 18.494 0.267 4.964 Individual atomic B min max mean iso aniso Overall: 0.00 108.00 17.10 11.05 1751 0 Protein: 0.00 108.00 15.95 11.02 1519 0 Water: 0.00 61.08 24.38 N/A 224 0 Other: 20.39 53.76 33.30 N/A 8 0 Chain A: 0.00 108.00 16.55 N/A 1642 0 Chain S: 0.00 61.08 25.50 N/A 109 0 Histogram: Values Number of atoms 0.00 - 10.80 634 10.80 - 21.60 666 21.60 - 32.40 254 32.40 - 43.20 107 43.20 - 54.00 54 54.00 - 64.80 15 64.80 - 75.60 12 75.60 - 86.40 5 86.40 - 97.20 2 97.20 - 108.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1844 r_work=0.0906 r_free=0.1850 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0906 r_free = 0.1850 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0896 r_free = 0.1843 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0896 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.960531 | | target function (ml) not normalized (work): 24420.695491 | | target function (ml) not normalized (free): 1985.728476 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0944 0.0896 0.1843 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2216 0.2226 0.2208 n_refl.: 5175 remove outliers: r(all,work,free)=0.2216 0.2226 0.2208 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2216 0.2226 0.2208 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0943 0.0895 0.1837 n_refl.: 5175 remove outliers: r(all,work,free)=0.0940 0.0893 0.1837 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 0.3687 319.512 284.834 0.587 0.993 0.330 11.894-9.307 99.02 97 4 0.1984 508.500 491.697 0.954 0.998 0.310 9.237-7.194 100.00 213 7 0.2089 415.852 410.245 1.006 1.000 0.290 7.162-5.571 100.00 427 22 0.2051 312.047 302.992 0.991 1.001 0.290 5.546-4.326 100.00 867 58 0.0998 428.396 423.551 1.019 1.001 0.234 4.315-3.360 100.00 1859 96 0.0572 407.409 407.415 1.094 1.002 0.228 3.356-3.002 100.00 1373 60 0.0458 313.804 313.364 1.078 1.002 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-8.1546 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0893 r_free=0.1837 After: r_work=0.0896 r_free=0.1835 ================================== NQH flips ================================== r_work=0.0896 r_free=0.1835 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0896 r_free=0.1837 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0896 r_free=0.1837 | n_water=224 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0903 r_free=0.1831 | n_water=222 | time (s): 16.760 (total time: 17.280) Filter (q & B) r_work=0.1009 r_free=0.1821 | n_water=219 | time (s): 1.360 (total time: 18.640) Compute maps r_work=0.1009 r_free=0.1821 | n_water=219 | time (s): 0.440 (total time: 19.080) Filter (map) r_work=0.1264 r_free=0.1927 | n_water=157 | time (s): 1.350 (total time: 20.430) Find peaks r_work=0.1264 r_free=0.1927 | n_water=157 | time (s): 0.470 (total time: 20.900) Add new water r_work=0.1536 r_free=0.2168 | n_water=216 | time (s): 1.380 (total time: 22.280) Refine new water occ: r_work=0.1013 r_free=0.1816 adp: r_work=0.1001 r_free=0.1829 occ: r_work=0.0995 r_free=0.1818 adp: r_work=0.0995 r_free=0.1818 occ: r_work=0.0995 r_free=0.1818 adp: r_work=0.0995 r_free=0.1818 ADP+occupancy (water only), MIN, final r_work=0.0995 r_free=0.1818 r_work=0.0995 r_free=0.1818 | n_water=216 | time (s): 6.460 (total time: 28.740) Filter (q & B) r_work=0.0995 r_free=0.1818 | n_water=216 | time (s): 0.790 (total time: 29.530) Filter (dist only) r_work=0.0993 r_free=0.1817 | n_water=215 | time (s): 16.550 (total time: 46.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.961604 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.244036 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 0.0935 0.1815 0.0881 0.011 1.1 6.1 0.5 0.0 0 0.481 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.35 18.15 8.81 8.391 18.743 0.244 5.012 9.14 18.55 9.41 9.189 18.836 0.244 4.953 Individual atomic B min max mean iso aniso Overall: 0.00 109.26 17.16 12.14 1742 0 Protein: 0.00 109.26 16.29 12.12 1519 0 Water: 0.00 54.80 22.77 N/A 215 0 Other: 18.84 54.98 32.93 N/A 8 0 Chain A: 0.00 109.26 16.84 N/A 1636 0 Chain S: 0.00 52.80 22.10 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.93 628 10.93 - 21.85 666 21.85 - 32.78 267 32.78 - 43.70 99 43.70 - 54.63 41 54.63 - 65.56 20 65.56 - 76.48 10 76.48 - 87.41 5 87.41 - 98.33 3 98.33 - 109.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.0914 r_free=0.1855 r_work=0.0918 r_free=0.1857 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0918 r_free = 0.1857 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0912 r_free = 0.1847 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0912 r_free= 0.1847 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.954457 | | target function (ml) not normalized (work): 24385.834998 | | target function (ml) not normalized (free): 2033.939784 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1288 0.1893 5.5174 6.2617| | 2: 3.78 - 3.00 1.00 2430 110 0.0453 0.1771 4.3771 10.407| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.42 1.00 0.94 12903.35| | 2: 3.78 - 3.00 2430 110 0.99 2.06 1.00 0.96 931.75| |alpha: min = 0.93 max = 0.96 mean = 0.95| |beta: min = 604.11 max = 21652.38 mean = 6992.95| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.29 mean = 7.31| |phase err.(test): min = 0.00 max = 86.70 mean = 7.77| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0959 0.0912 0.1847 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2189 0.2194 0.2213 n_refl.: 5174 remove outliers: r(all,work,free)=0.2189 0.2194 0.2213 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2189 0.2194 0.2213 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0957 0.0910 0.1853 n_refl.: 5174 remove outliers: r(all,work,free)=0.0957 0.0910 0.1853 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 0.3916 319.512 293.255 0.624 0.988 0.319 11.894-9.307 99.02 97 4 0.2009 508.500 492.972 1.005 0.994 0.317 9.237-7.194 100.00 213 7 0.2165 415.852 405.833 1.051 0.997 0.316 7.162-5.571 100.00 427 22 0.2093 312.047 302.639 1.032 0.999 0.300 5.546-4.326 100.00 867 58 0.1045 428.396 422.707 1.069 1.000 0.239 4.315-3.360 100.00 1859 96 0.0579 407.409 407.274 1.154 1.002 0.229 3.356-3.002 100.00 1373 60 0.0436 313.804 313.173 1.140 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.8353 ================= 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 : 0.3618 0.1985 0.082 5.425 8.8 119.3 19.9 258 0.000 1_bss: 0.1556 0.1526 0.082 5.425 6.2 116.6 17.2 258 0.000 1_settarget: 0.1556 0.1526 0.082 5.425 6.2 116.6 17.2 258 0.000 1_nqh: 0.1556 0.1526 0.082 5.425 6.2 116.6 17.2 258 0.000 1_weight: 0.1556 0.1526 0.082 5.425 6.2 116.6 17.2 258 0.000 1_xyzrec: 0.1155 0.1809 0.010 0.970 6.2 116.6 17.2 258 0.204 1_adp: 0.1017 0.1798 0.010 0.970 2.4 111.6 17.7 258 0.204 1_regHadp: 0.1010 0.1804 0.010 0.970 2.4 111.6 17.7 258 0.204 1_occ: 0.1006 0.1808 0.010 0.970 2.4 111.6 17.7 258 0.204 2_bss: 0.1010 0.1801 0.010 0.970 1.5 110.7 16.8 258 0.204 2_settarget: 0.1010 0.1801 0.010 0.970 1.5 110.7 16.8 258 0.204 2_updatecdl: 0.1010 0.1801 0.010 0.992 1.5 110.7 16.8 258 0.204 2_nqh: 0.1010 0.1801 0.010 0.992 1.5 110.7 16.8 258 0.204 2_sol: 0.1150 0.1642 0.010 0.992 1.0 110.5 16.0 219 n/a 2_weight: 0.1150 0.1642 0.010 0.992 1.0 110.5 16.0 219 n/a 2_xyzrec: 0.1028 0.1786 0.009 0.965 1.0 110.5 16.0 219 n/a 2_adp: 0.0956 0.1800 0.009 0.965 0.0 107.9 16.8 219 n/a 2_regHadp: 0.0953 0.1798 0.009 0.965 0.0 107.9 16.8 219 n/a 2_occ: 0.0949 0.1795 0.009 0.965 0.0 107.9 16.8 219 n/a 3_bss: 0.0946 0.1803 0.009 0.965 0.0 107.9 16.8 219 n/a 3_settarget: 0.0946 0.1803 0.009 0.965 0.0 107.9 16.8 219 n/a 3_updatecdl: 0.0946 0.1803 0.009 0.972 0.0 107.9 16.8 219 n/a 3_nqh: 0.0946 0.1804 0.009 0.972 0.0 107.9 16.8 219 n/a 3_sol: 0.1055 0.1768 0.009 0.972 0.0 107.9 16.6 221 n/a 3_weight: 0.1055 0.1768 0.009 0.972 0.0 107.9 16.6 221 n/a 3_xyzrec: 0.0950 0.1828 0.011 1.081 0.0 107.9 16.6 221 n/a 3_adp: 0.0906 0.1855 0.011 1.081 0.0 108.0 16.7 221 n/a 3_regHadp: 0.0912 0.1865 0.011 1.081 0.0 108.0 16.7 221 n/a 3_occ: 0.0901 0.1843 0.011 1.081 0.0 108.0 16.7 221 n/a 4_bss: 0.0895 0.1828 0.011 1.081 0.0 108.0 16.7 221 n/a 4_settarget: 0.0895 0.1828 0.011 1.081 0.0 108.0 16.7 221 n/a 4_updatecdl: 0.0895 0.1828 0.011 1.082 0.0 108.0 16.7 221 n/a 4_nqh: 0.0896 0.1825 0.011 1.082 0.0 108.0 16.7 221 n/a 4_sol: 0.1004 0.1798 0.011 1.082 0.0 108.0 16.8 224 n/a 4_weight: 0.1004 0.1798 0.011 1.082 0.0 108.0 16.8 224 n/a 4_xyzrec: 0.0919 0.1846 0.011 1.038 0.0 108.0 16.8 224 n/a 4_adp: 0.0901 0.1844 0.011 1.038 0.0 108.0 17.1 224 n/a 4_regHadp: 0.0906 0.1850 0.011 1.038 0.0 108.0 17.1 224 n/a 4_occ: 0.0896 0.1843 0.011 1.038 0.0 108.0 17.1 224 n/a 5_bss: 0.0893 0.1837 0.011 1.038 0.0 108.0 17.1 224 n/a 5_settarget: 0.0893 0.1837 0.011 1.038 0.0 108.0 17.1 224 n/a 5_updatecdl: 0.0893 0.1837 0.011 1.049 0.0 108.0 17.1 224 n/a 5_setrh: 0.0896 0.1835 0.011 1.049 0.0 108.0 17.1 224 n/a 5_nqh: 0.0896 0.1837 0.011 1.049 0.0 108.0 17.1 224 n/a 5_sol: 0.0993 0.1817 0.011 1.049 0.0 108.0 17.0 215 n/a 5_weight: 0.0993 0.1817 0.011 1.049 0.0 108.0 17.0 215 n/a 5_xyzrec: 0.0935 0.1815 0.011 1.108 0.0 108.0 17.0 215 n/a 5_adp: 0.0914 0.1855 0.011 1.108 0.0 109.3 17.2 215 n/a 5_regHadp: 0.0918 0.1857 0.011 1.108 0.0 109.3 17.2 215 n/a 5_occ: 0.0912 0.1847 0.011 1.108 0.0 109.3 17.2 215 n/a end: 0.0910 0.1853 0.011 1.108 0.0 109.3 17.2 215 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2359181_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2359181_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3700 Refinement macro-cycles (run) : 464.0100 Write final files (write_after_run_outputs) : 11.3000 Total : 478.6800 Total CPU time: 8.34 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:42 PST -0800 (1735492722.14 s) Start R-work = 0.1556, R-free = 0.1526 Final R-work = 0.0910, R-free = 0.1853 =============================================================================== Job complete usr+sys time: 509.35 seconds wall clock time: 8 minutes 51.56 seconds (531.56 seconds total)