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_7326401.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_7326401.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7326401.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.27, 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: 0.29 Conformation dependent library (CDL) restraints added in 183.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 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: 467 0.90 - 1.15: 1156 1.15 - 1.40: 583 1.40 - 1.65: 876 1.65 - 1.90: 71 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " ideal model delta sigma weight residual 1.521 1.296 0.226 1.17e-02 7.31e+03 3.72e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.176 0.202 1.10e-02 8.26e+03 3.37e+02 bond pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta sigma weight residual 1.456 1.215 0.241 1.32e-02 5.74e+03 3.33e+02 bond pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 1.523 1.739 -0.216 1.27e-02 6.20e+03 2.90e+02 bond pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 1.238 1.434 -0.197 1.17e-02 7.31e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.73: 3246 4.73 - 9.45: 1828 9.45 - 14.18: 583 14.18 - 18.90: 113 18.90 - 23.63: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 120.39 136.33 -15.94 1.05e+00 9.07e-01 2.31e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 128.63 -14.83 1.00e+00 1.00e+00 2.20e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 136.04 -14.13 9.80e-01 1.04e+00 2.08e+02 angle pdb=" O ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sigma weight residual 121.50 134.80 -13.30 1.00e+00 1.00e+00 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.83: 1346 19.83 - 39.66: 96 39.66 - 59.49: 34 59.49 - 79.32: 4 79.32 - 99.15: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CA PRO A 109 " pdb=" CB PRO A 109 " ideal model delta harmonic sigma weight residual 115.10 137.74 -22.64 0 2.50e+00 1.60e-01 8.20e+01 dihedral pdb=" C PRO A 109 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " pdb=" CB PRO A 109 " ideal model delta harmonic sigma weight residual -120.70 -141.88 21.18 0 2.50e+00 1.60e-01 7.18e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 142.97 -20.17 0 2.50e+00 1.60e-01 6.51e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.223: 95 0.223 - 0.442: 86 0.442 - 0.662: 42 0.662 - 0.881: 16 0.881 - 1.101: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 109 " pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CB PRO A 109 " both_signs ideal model delta sigma weight residual False 2.72 1.62 1.10 2.00e-01 2.50e+01 3.03e+01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 3.52 -1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.61 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.042 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" CG TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.092 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.101 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.053 2.00e-02 2.50e+03 6.77e-02 1.38e+02 pdb=" CG TYR A 139 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.143 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.053 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.044 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.115 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.124 2.00e-02 2.50e+03 6.76e-02 1.37e+02 pdb=" CG PHE A 119 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.139 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.034 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 802 2.28 - 2.86: 7824 2.86 - 3.44: 10634 3.44 - 4.02: 15246 4.02 - 4.60: 22030 Nonbonded interactions: 56536 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.700 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.772 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.800 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.809 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.822 2.450 ... (remaining 56531 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_7326401_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= 0.3611 r_free= 0.2047 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.476952 | | target function (ml) not normalized (work): 22071.372008 | | target function (ml) not normalized (free): 1150.190935 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3794 0.2225 4.8549 4.8932| | 2: 3.78 - 3.00 1.00 2430 110 0.3387 0.1745 4.0881 4.1396| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.86 0.83 0.13 6612.31| | 2: 3.78 - 3.00 2430 110 0.94 11.45 1.48 0.26 459.72| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 393.40 max = 12075.91 mean = 3579.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.42| |phase err.(test): min = 0.00 max = 89.93 mean = 33.42| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.261 1557 Z= 5.552 Angle : 5.318 21.366 2118 Z= 3.709 Chirality : 0.386 1.101 243 Planarity : 0.031 0.103 284 Dihedral : 13.847 99.154 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.32 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 27.03 % 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: -2.10 (0.47), residues: 224 helix: -2.20 (0.38), residues: 102 sheet: -1.12 (0.86), residues: 28 loop : -0.19 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.150 0.035 ARG A 28 TYR 0.123 0.059 TYR A 141 PHE 0.085 0.028 PHE A 119 HIS 0.068 0.023 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= 0.3611 r_free= 0.2047 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.476952 | | target function (ml) not normalized (work): 22071.372008 | | target function (ml) not normalized (free): 1150.190935 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3566 0.3644 0.2124 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3566 0.3644 0.2124 n_refl.: 5182 remove outliers: r(all,work,free)=0.2518 0.2543 0.2124 n_refl.: 5178 overall B=-2.87 to atoms: r(all,work,free)=0.2408 0.2430 0.2082 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1574 0.1572 0.1632 n_refl.: 5178 remove outliers: r(all,work,free)=0.1570 0.1567 0.1632 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 0.3855 449.885 410.636 0.670 1.055 0.398 11.894-9.307 99.02 97 4 0.1925 714.679 694.404 0.954 1.053 0.377 9.237-7.194 100.00 213 7 0.2133 584.466 576.354 0.987 1.047 0.374 7.162-5.571 100.00 427 22 0.2427 438.570 424.170 0.946 1.037 0.283 5.546-4.326 100.00 867 58 0.1391 602.095 594.758 0.982 1.020 0.219 4.315-3.360 100.00 1859 96 0.1311 572.599 567.301 1.054 0.991 0.197 3.356-3.002 100.00 1373 60 0.1593 441.040 433.101 1.059 0.962 0.107 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6679 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1567 r_free=0.1632 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1568 r_free=0.1639 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.005738 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.926966 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1795 0.0636 0.010 1.0 3.8 0.5 0.0 0 9.503 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 17.95 6.36 3.013 15.991 1.927 0.018 10.20 17.81 7.61 4.860 16.144 1.927 0.014 Individual atomic B min max mean iso aniso Overall: 1.88 111.57 17.31 5.29 1785 0 Protein: 1.88 111.57 14.61 5.28 1519 0 Water: 4.00 111.43 32.99 N/A 258 0 Other: 17.13 36.55 24.28 N/A 8 0 Chain A: 1.88 111.57 17.31 N/A 1785 0 Histogram: Values Number of atoms 1.88 - 12.85 900 12.85 - 23.81 498 23.81 - 34.78 187 34.78 - 45.75 111 45.75 - 56.72 55 56.72 - 67.69 17 67.69 - 78.66 8 78.66 - 89.63 5 89.63 - 100.60 1 100.60 - 111.57 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1781 r_work=0.1014 r_free=0.1785 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1014 r_free = 0.1785 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 = 0.1005 r_free = 0.1768 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1005 r_free= 0.1768 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013787 | | target function (ls_wunit_k1) not normalized (work): 67.888054 | | target function (ls_wunit_k1) not normalized (free): 10.423587 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1045 0.1005 0.1768 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2081 0.2079 0.2228 n_refl.: 5176 remove outliers: r(all,work,free)=0.2081 0.2079 0.2228 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2041 0.2038 0.2215 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1047 0.1008 0.1769 n_refl.: 5176 remove outliers: r(all,work,free)=0.1047 0.1008 0.1769 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 0.3290 331.082 313.110 0.684 1.006 0.382 11.894-9.307 99.02 97 4 0.1507 525.951 519.128 0.991 1.008 0.352 9.237-7.194 100.00 213 7 0.1699 430.123 430.653 1.024 1.007 0.316 7.162-5.571 100.00 427 22 0.1612 322.755 319.738 0.982 1.006 0.294 5.546-4.326 100.00 867 58 0.0899 443.097 440.339 0.996 1.003 0.202 4.315-3.360 100.00 1859 96 0.0761 421.390 421.262 1.042 0.998 0.193 3.356-3.002 100.00 1373 60 0.1001 324.572 322.990 1.015 0.994 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4208 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1008 r_free=0.1769 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1008 r_free=0.1769 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1008 r_free=0.1769 | n_water=258 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1041 r_free=0.1766 | n_water=247 | time (s): 20.300 (total time: 20.940) Filter (q & B) r_work=0.1041 r_free=0.1767 | n_water=244 | time (s): 1.450 (total time: 22.390) Compute maps r_work=0.1041 r_free=0.1767 | n_water=244 | time (s): 0.540 (total time: 22.930) Filter (map) r_work=0.1348 r_free=0.1835 | n_water=147 | time (s): 1.880 (total time: 24.810) Find peaks r_work=0.1348 r_free=0.1835 | n_water=147 | time (s): 0.420 (total time: 25.230) Add new water r_work=0.1702 r_free=0.2065 | n_water=236 | time (s): 1.490 (total time: 26.720) Refine new water occ: r_work=0.1153 r_free=0.1681 adp: r_work=0.1130 r_free=0.1683 occ: r_work=0.1126 r_free=0.1666 adp: r_work=0.1115 r_free=0.1671 occ: r_work=0.1113 r_free=0.1663 adp: r_work=0.1110 r_free=0.1668 ADP+occupancy (water only), MIN, final r_work=0.1110 r_free=0.1668 r_work=0.1110 r_free=0.1668 | n_water=236 | time (s): 4.770 (total time: 31.490) Filter (q & B) r_work=0.1110 r_free=0.1668 | n_water=236 | time (s): 0.680 (total time: 32.170) Filter (dist only) r_work=0.1114 r_free=0.1662 | n_water=234 | time (s): 18.480 (total time: 50.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.379676 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.645287 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 0.1005 0.1773 0.0768 0.009 1.0 3.5 0.5 0.6 0 11.190 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.05 17.73 7.68 4.655 16.721 2.645 0.014 9.42 17.97 8.55 5.314 17.101 2.645 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 108.83 16.55 6.31 1761 0 Protein: 0.00 108.83 14.87 6.28 1519 0 Water: 0.00 63.45 27.13 N/A 234 0 Other: 11.17 39.41 26.26 N/A 8 0 Chain A: 0.00 108.83 15.67 N/A 1672 0 Chain S: 1.89 59.19 33.20 N/A 89 0 Histogram: Values Number of atoms 0.00 - 10.88 715 10.88 - 21.77 641 21.77 - 32.65 209 32.65 - 43.53 118 43.53 - 54.42 42 54.42 - 65.30 24 65.30 - 76.18 6 76.18 - 87.07 1 87.07 - 97.95 3 97.95 - 108.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.0942 r_free=0.1797 r_work=0.0940 r_free=0.1801 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0940 r_free = 0.1801 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0937 r_free = 0.1786 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 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= 0.0937 r_free= 0.1786 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.012144 | | target function (ls_wunit_k1) not normalized (work): 59.797373 | | target function (ls_wunit_k1) not normalized (free): 10.071229 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0981 0.0937 0.1786 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2096 0.2095 0.2216 n_refl.: 5176 remove outliers: r(all,work,free)=0.2096 0.2095 0.2216 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2096 0.2095 0.2216 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0979 0.0936 0.1784 n_refl.: 5176 remove outliers: r(all,work,free)=0.0979 0.0936 0.1784 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 0.3258 331.082 312.323 0.676 1.008 0.369 11.894-9.307 99.02 97 4 0.1455 525.951 522.218 0.977 1.010 0.325 9.237-7.194 100.00 213 7 0.1535 430.123 431.046 1.024 1.009 0.305 7.162-5.571 100.00 427 22 0.1410 322.755 320.424 0.990 1.007 0.300 5.546-4.326 100.00 867 58 0.0792 443.097 440.365 1.006 1.004 0.220 4.315-3.360 100.00 1859 96 0.0718 421.390 421.248 1.054 0.997 0.210 3.356-3.002 100.00 1373 60 0.0960 324.572 323.516 1.032 0.991 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.0288 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0936 r_free=0.1784 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0936 r_free=0.1784 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0936 r_free=0.1784 | n_water=234 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0952 r_free=0.1785 | n_water=230 | time (s): 18.260 (total time: 18.780) Filter (q & B) r_work=0.1008 r_free=0.1798 | n_water=228 | time (s): 1.330 (total time: 20.110) Compute maps r_work=0.1008 r_free=0.1798 | n_water=228 | time (s): 0.430 (total time: 20.540) Filter (map) r_work=0.1270 r_free=0.1851 | n_water=155 | time (s): 1.570 (total time: 22.110) Find peaks r_work=0.1270 r_free=0.1851 | n_water=155 | time (s): 0.420 (total time: 22.530) Add new water r_work=0.1654 r_free=0.2150 | n_water=240 | time (s): 1.340 (total time: 23.870) Refine new water occ: r_work=0.1051 r_free=0.1710 adp: r_work=0.1048 r_free=0.1725 occ: r_work=0.1037 r_free=0.1705 adp: r_work=0.1037 r_free=0.1714 occ: r_work=0.1027 r_free=0.1695 adp: r_work=0.1026 r_free=0.1704 ADP+occupancy (water only), MIN, final r_work=0.1026 r_free=0.1704 r_work=0.1026 r_free=0.1704 | n_water=240 | time (s): 8.400 (total time: 32.270) Filter (q & B) r_work=0.1027 r_free=0.1705 | n_water=238 | time (s): 1.510 (total time: 33.780) Filter (dist only) r_work=0.1041 r_free=0.1705 | n_water=236 | time (s): 18.850 (total time: 52.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.101650 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.226415 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 0.0942 0.1780 0.0838 0.011 1.1 3.5 0.5 0.0 0 0.551 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.42 17.80 8.38 5.300 17.687 0.226 5.164 8.98 18.02 9.04 6.977 17.675 0.226 5.070 Individual atomic B min max mean iso aniso Overall: 0.00 108.29 16.33 8.55 1763 0 Protein: 0.00 108.29 14.95 8.53 1519 0 Water: 0.00 58.45 24.86 N/A 236 0 Other: 9.78 43.56 26.98 N/A 8 0 Chain A: 0.00 108.29 15.74 N/A 1662 0 Chain S: 0.00 56.39 25.98 N/A 101 0 Histogram: Values Number of atoms 0.00 - 10.83 680 10.83 - 21.66 671 21.66 - 32.49 225 32.49 - 43.32 111 43.32 - 54.14 42 54.14 - 64.97 17 64.97 - 75.80 11 75.80 - 86.63 1 86.63 - 97.46 4 97.46 - 108.29 1 =========================== Idealize ADP of riding H ========================== r_work=0.0898 r_free=0.1802 r_work=0.0903 r_free=0.1812 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0903 r_free = 0.1812 target_work(ml) = 5.075 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0892 r_free = 0.1801 target_work(ml) = 5.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0892 r_free= 0.1801 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.066005 | | target function (ml) not normalized (work): 24945.008352 | | target function (ml) not normalized (free): 1804.014783 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0938 0.0892 0.1801 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2121 0.2131 0.2098 n_refl.: 5176 remove outliers: r(all,work,free)=0.2121 0.2131 0.2098 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2121 0.2131 0.2098 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0887 0.1797 n_refl.: 5176 remove outliers: r(all,work,free)=0.0931 0.0885 0.1797 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 0.3812 328.294 298.330 0.617 0.999 0.355 11.894-9.307 99.02 97 4 0.1877 525.951 509.076 0.938 1.002 0.321 9.237-7.194 100.00 213 7 0.1924 430.123 424.668 1.002 1.003 0.297 7.162-5.571 100.00 427 22 0.1797 322.755 314.172 0.971 1.003 0.283 5.546-4.326 100.00 867 58 0.0892 443.097 438.085 0.995 1.002 0.224 4.315-3.360 100.00 1859 96 0.0584 421.390 420.598 1.050 1.000 0.210 3.356-3.002 100.00 1373 60 0.0610 324.572 323.892 1.033 0.999 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.1045 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0885 r_free=0.1797 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=0.0886 r_free=0.1793 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0886 r_free=0.1793 | n_water=236 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0897 r_free=0.1803 | n_water=232 | time (s): 19.680 (total time: 20.250) Filter (q & B) r_work=0.0983 r_free=0.1828 | n_water=228 | time (s): 1.450 (total time: 21.700) Compute maps r_work=0.0983 r_free=0.1828 | n_water=228 | time (s): 0.480 (total time: 22.180) Filter (map) r_work=0.1252 r_free=0.1895 | n_water=160 | time (s): 1.390 (total time: 23.570) Find peaks r_work=0.1252 r_free=0.1895 | n_water=160 | time (s): 0.420 (total time: 23.990) Add new water r_work=0.1552 r_free=0.2103 | n_water=236 | time (s): 1.540 (total time: 25.530) Refine new water r_work=0.1552 r_free=0.2103 | n_water=236 | time (s): 0.100 (total time: 25.630) Filter (q & B) r_work=0.1252 r_free=0.1895 | n_water=160 | time (s): 1.800 (total time: 27.430) Filter (dist only) r_work=0.1258 r_free=0.1897 | n_water=156 | time (s): 12.450 (total time: 39.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.409747 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.347261 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 0.1110 0.2005 0.0895 0.012 1.1 4.2 0.5 0.6 0 0.705 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.10 20.05 8.95 6.705 17.518 0.347 5.342 10.52 20.46 9.94 8.188 17.535 0.347 5.259 Individual atomic B min max mean iso aniso Overall: 0.00 107.87 15.84 10.24 1683 0 Protein: 0.00 107.87 15.03 10.21 1519 0 Water: 1.02 53.45 23.15 N/A 156 0 Other: 13.77 44.44 27.28 N/A 8 0 Chain A: 0.00 107.87 15.62 N/A 1642 0 Chain S: 1.02 51.48 24.87 N/A 41 0 Histogram: Values Number of atoms 0.00 - 10.79 698 10.79 - 21.57 601 21.57 - 32.36 221 32.36 - 43.15 91 43.15 - 53.94 39 53.94 - 64.72 14 64.72 - 75.51 12 75.51 - 86.30 2 86.30 - 97.09 4 97.09 - 107.87 1 =========================== Idealize ADP of riding H ========================== r_work=0.1052 r_free=0.2046 r_work=0.1057 r_free=0.2051 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1057 r_free = 0.2051 target_work(ml) = 5.263 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1053 r_free = 0.2049 target_work(ml) = 5.261 | | occupancies: max = 1.00 min = 0.21 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= 0.1053 r_free= 0.2049 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 5.260644 | | target function (ml) not normalized (work): 25898.148260 | | target function (ml) not normalized (free): 1753.061225 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1105 0.1053 0.2049 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2324 0.2326 0.2428 n_refl.: 5175 remove outliers: r(all,work,free)=0.2324 0.2326 0.2428 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2324 0.2326 0.2428 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1089 0.1036 0.2062 n_refl.: 5175 remove outliers: r(all,work,free)=0.1089 0.1036 0.2062 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 0.3943 328.294 295.526 0.667 0.993 0.370 11.894-9.307 99.02 97 4 0.1661 525.951 509.872 0.981 0.997 0.358 9.237-7.194 100.00 213 7 0.1988 430.123 423.974 1.008 0.999 0.350 7.162-5.571 100.00 427 22 0.1919 322.755 315.725 0.982 1.000 0.320 5.546-4.326 100.00 867 58 0.1093 443.097 437.090 0.991 1.001 0.258 4.315-3.360 100.00 1859 96 0.0737 421.390 419.857 1.064 1.001 0.240 3.356-3.002 100.00 1373 60 0.0788 324.572 323.540 1.058 1.002 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0197 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1036 r_free=0.2062 After: r_work=0.1039 r_free=0.2062 ================================== NQH flips ================================== r_work=0.1039 r_free=0.2062 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1039 r_free=0.2062 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1039 r_free=0.2062 | n_water=156 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.1073 r_free=0.2060 | n_water=150 | time (s): 12.530 (total time: 13.100) Filter (q & B) r_work=0.1073 r_free=0.2060 | n_water=150 | time (s): 0.660 (total time: 13.760) Compute maps r_work=0.1073 r_free=0.2060 | n_water=150 | time (s): 0.440 (total time: 14.200) Filter (map) r_work=0.1130 r_free=0.2075 | n_water=138 | time (s): 1.450 (total time: 15.650) Find peaks r_work=0.1130 r_free=0.2075 | n_water=138 | time (s): 0.400 (total time: 16.050) Add new water r_work=0.1377 r_free=0.2292 | n_water=187 | time (s): 1.490 (total time: 17.540) Refine new water occ: r_work=0.1109 r_free=0.2067 adp: r_work=0.1111 r_free=0.2079 occ: r_work=0.1098 r_free=0.2058 adp: r_work=0.1100 r_free=0.2070 occ: r_work=0.1087 r_free=0.2050 adp: r_work=0.1088 r_free=0.2061 ADP+occupancy (water only), MIN, final r_work=0.1088 r_free=0.2061 r_work=0.1088 r_free=0.2061 | n_water=187 | time (s): 11.610 (total time: 29.150) Filter (q & B) r_work=0.1088 r_free=0.2061 | n_water=187 | time (s): 0.850 (total time: 30.000) Filter (dist only) r_work=0.1088 r_free=0.2069 | n_water=186 | time (s): 15.160 (total time: 45.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.214691 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.259136 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 0.1054 0.2080 0.1026 0.012 1.2 6.1 0.5 0.6 0 0.607 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.54 20.80 10.26 7.799 17.673 0.259 5.224 10.30 20.47 10.17 8.853 17.770 0.259 5.177 Individual atomic B min max mean iso aniso Overall: 0.00 106.78 16.44 11.49 1713 0 Protein: 0.00 106.78 15.33 11.44 1519 0 Water: 0.00 56.67 25.02 N/A 186 0 Other: 11.51 53.60 27.49 N/A 8 0 Chain A: 0.00 106.78 15.82 N/A 1631 0 Chain S: 0.00 56.67 28.75 N/A 82 0 Histogram: Values Number of atoms 0.00 - 10.68 662 10.68 - 21.36 618 21.36 - 32.03 246 32.03 - 42.71 105 42.71 - 53.39 45 53.39 - 64.07 15 64.07 - 74.74 13 74.74 - 85.42 5 85.42 - 96.10 2 96.10 - 106.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1030 r_free=0.2047 r_work=0.1035 r_free=0.2049 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1035 r_free = 0.2049 target_work(ml) = 5.182 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1007 r_free = 0.2017 target_work(ml) = 5.165 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1007 r_free= 0.2017 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 5.165376 | | target function (ml) not normalized (work): 25429.146404 | | target function (ml) not normalized (free): 1789.512619 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1330 0.2040 5.6057 6.2244| | 2: 3.78 - 3.00 1.00 2430 110 0.0614 0.1980 4.7136 8.2332| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2493 142 0.91 12.73 1.00 0.98 13769.71| | 2: 3.78 - 3.00 2430 110 0.98 3.67 1.01 1.01 1794.99| |alpha: min = 0.96 max = 1.01 mean = 1.00| |beta: min = 1283.66 max = 22017.36 mean = 7858.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.57 mean = 8.26| |phase err.(test): min = 0.00 max = 89.12 mean = 7.86| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1059 0.1007 0.2017 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2332 0.2338 0.2371 n_refl.: 5175 remove outliers: r(all,work,free)=0.2332 0.2338 0.2371 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2332 0.2338 0.2371 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1053 0.1002 0.1999 n_refl.: 5175 remove outliers: r(all,work,free)=0.1051 0.1000 0.1999 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 0.3876 330.477 291.817 0.632 0.990 0.346 11.894-9.307 99.02 97 4 0.1832 525.951 508.746 0.987 0.995 0.336 9.237-7.194 100.00 213 7 0.2112 430.123 421.515 1.018 0.997 0.330 7.162-5.571 100.00 427 22 0.2023 322.755 314.048 0.994 0.998 0.310 5.546-4.326 100.00 867 58 0.1109 443.097 437.668 1.011 1.000 0.245 4.315-3.360 100.00 1859 96 0.0688 421.390 420.216 1.098 1.003 0.240 3.356-3.002 100.00 1373 60 0.0633 324.572 324.317 1.093 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-8.5841 ================= 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 : 0.3611 0.2047 0.084 5.318 8.8 119.3 19.9 258 0.000 1_bss: 0.1567 0.1632 0.084 5.318 6.0 116.4 17.0 258 0.000 1_settarget: 0.1567 0.1632 0.084 5.318 6.0 116.4 17.0 258 0.000 1_nqh: 0.1568 0.1639 0.084 5.318 6.0 116.4 17.0 258 0.003 1_weight: 0.1568 0.1639 0.084 5.318 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1159 0.1795 0.010 0.975 6.0 116.4 17.0 258 0.211 1_adp: 0.1020 0.1781 0.010 0.975 1.9 111.6 17.3 258 0.211 1_regHadp: 0.1014 0.1785 0.010 0.975 1.9 111.6 17.3 258 0.211 1_occ: 0.1005 0.1768 0.010 0.975 1.9 111.6 17.3 258 0.211 2_bss: 0.1008 0.1769 0.010 0.975 0.9 110.6 16.4 258 0.211 2_settarget: 0.1008 0.1769 0.010 0.975 0.9 110.6 16.4 258 0.211 2_updatecdl: 0.1008 0.1769 0.010 0.995 0.9 110.6 16.4 258 0.211 2_nqh: 0.1008 0.1769 0.010 0.995 0.9 110.6 16.4 258 0.211 2_sol: 0.1114 0.1662 0.010 0.995 0.9 110.6 15.8 234 n/a 2_weight: 0.1114 0.1662 0.010 0.995 0.9 110.6 15.8 234 n/a 2_xyzrec: 0.1005 0.1773 0.009 0.959 0.9 110.6 15.8 234 n/a 2_adp: 0.0942 0.1797 0.009 0.959 0.0 108.8 16.6 234 n/a 2_regHadp: 0.0940 0.1801 0.009 0.959 0.0 108.8 16.6 234 n/a 2_occ: 0.0937 0.1786 0.009 0.959 0.0 108.8 16.6 234 n/a 3_bss: 0.0936 0.1784 0.009 0.959 0.0 108.8 16.6 234 n/a 3_settarget: 0.0936 0.1784 0.009 0.959 0.0 108.8 16.6 234 n/a 3_updatecdl: 0.0936 0.1784 0.009 0.968 0.0 108.8 16.6 234 n/a 3_nqh: 0.0936 0.1784 0.009 0.968 0.0 108.8 16.6 234 n/a 3_sol: 0.1041 0.1705 0.009 0.968 0.0 108.8 16.4 236 n/a 3_weight: 0.1041 0.1705 0.009 0.968 0.0 108.8 16.4 236 n/a 3_xyzrec: 0.0942 0.1780 0.011 1.052 0.0 108.8 16.4 236 n/a 3_adp: 0.0898 0.1802 0.011 1.052 0.0 108.3 16.3 236 n/a 3_regHadp: 0.0903 0.1812 0.011 1.052 0.0 108.3 16.3 236 n/a 3_occ: 0.0892 0.1801 0.011 1.052 0.0 108.3 16.3 236 n/a 4_bss: 0.0885 0.1797 0.011 1.052 0.0 108.3 16.3 236 n/a 4_settarget: 0.0885 0.1797 0.011 1.052 0.0 108.3 16.3 236 n/a 4_updatecdl: 0.0885 0.1797 0.011 1.060 0.0 108.3 16.3 236 n/a 4_nqh: 0.0886 0.1793 0.011 1.060 0.0 108.3 16.3 236 n/a 4_sol: 0.1258 0.1897 0.011 1.060 0.0 108.3 15.8 156 n/a 4_weight: 0.1258 0.1897 0.011 1.060 0.0 108.3 15.8 156 n/a 4_xyzrec: 0.1110 0.2005 0.012 1.103 0.0 108.3 15.8 156 n/a 4_adp: 0.1052 0.2046 0.012 1.103 0.0 107.9 15.8 156 n/a 4_regHadp: 0.1057 0.2051 0.012 1.103 0.0 107.9 15.8 156 n/a 4_occ: 0.1053 0.2049 0.012 1.103 0.0 107.9 15.8 156 n/a 5_bss: 0.1036 0.2062 0.012 1.103 0.0 107.9 15.8 156 n/a 5_settarget: 0.1036 0.2062 0.012 1.103 0.0 107.9 15.8 156 n/a 5_updatecdl: 0.1036 0.2062 0.012 1.122 0.0 107.9 15.8 156 n/a 5_setrh: 0.1039 0.2062 0.012 1.122 0.0 107.9 15.8 156 n/a 5_nqh: 0.1039 0.2062 0.012 1.122 0.0 107.9 15.8 156 n/a 5_sol: 0.1088 0.2069 0.012 1.122 0.0 107.9 16.3 186 n/a 5_weight: 0.1088 0.2069 0.012 1.122 0.0 107.9 16.3 186 n/a 5_xyzrec: 0.1054 0.2080 0.012 1.240 0.0 107.9 16.3 186 n/a 5_adp: 0.1030 0.2047 0.012 1.240 0.0 106.8 16.4 186 n/a 5_regHadp: 0.1035 0.2049 0.012 1.240 0.0 106.8 16.4 186 n/a 5_occ: 0.1007 0.2017 0.012 1.240 0.0 106.8 16.4 186 n/a end: 0.1000 0.1999 0.012 1.240 0.0 106.8 16.4 186 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7326401_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7326401_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2500 Refinement macro-cycles (run) : 455.4600 Write final files (write_after_run_outputs) : 12.9500 Total : 471.6600 Total CPU time: 8.19 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:33 PST -0800 (1735492713.02 s) Start R-work = 0.1567, R-free = 0.1632 Final R-work = 0.1000, R-free = 0.1999 =============================================================================== Job complete usr+sys time: 499.82 seconds wall clock time: 8 minutes 41.92 seconds (521.92 seconds total)