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_5296401.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_5296401.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5296401.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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.54, per 1000 atoms: 0.46 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: 0.55 Conformation dependent library (CDL) restraints added in 174.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.74 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: 473 0.90 - 1.15: 1153 1.15 - 1.40: 570 1.40 - 1.65: 892 1.65 - 1.90: 65 Bond restraints: 3153 Sorted by residual: bond pdb=" C PRO A 54 " pdb=" O PRO A 54 " ideal model delta sigma weight residual 1.233 0.986 0.247 1.21e-02 6.83e+03 4.15e+02 bond pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " ideal model delta sigma weight residual 1.326 1.538 -0.212 1.10e-02 8.26e+03 3.72e+02 bond pdb=" C ARG A 48 " pdb=" O ARG A 48 " ideal model delta sigma weight residual 1.233 0.985 0.249 1.30e-02 5.92e+03 3.66e+02 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.461 1.678 -0.217 1.19e-02 7.06e+03 3.32e+02 bond pdb=" CA THR A 154 " pdb=" C THR A 154 " ideal model delta sigma weight residual 1.523 1.305 0.218 1.25e-02 6.40e+03 3.05e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.51: 3629 5.51 - 11.02: 1759 11.02 - 16.53: 351 16.53 - 22.04: 37 22.04 - 27.56: 1 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " pdb=" CG ASN A 144 " ideal model delta sigma weight residual 112.60 126.53 -13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" O ALA A 103 " ideal model delta sigma weight residual 120.36 105.78 14.58 1.08e+00 8.57e-01 1.82e+02 angle pdb=" N ILE A 168 " pdb=" CA ILE A 168 " pdb=" C ILE A 168 " ideal model delta sigma weight residual 110.53 98.22 12.31 9.40e-01 1.13e+00 1.71e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 118.69 127.29 -8.60 6.70e-01 2.23e+00 1.65e+02 angle pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " pdb=" CG ASP A 49 " ideal model delta sigma weight residual 112.60 125.19 -12.59 1.00e+00 1.00e+00 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1315 17.78 - 35.55: 111 35.55 - 53.33: 42 53.33 - 71.10: 12 71.10 - 88.88: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BASN A 97 " pdb=" N BASN A 97 " pdb=" CA BASN A 97 " pdb=" CB BASN A 97 " ideal model delta harmonic sigma weight residual -122.60 -140.64 18.04 0 2.50e+00 1.60e-01 5.21e+01 dihedral pdb=" N LEU A 10 " pdb=" C LEU A 10 " pdb=" CA LEU A 10 " pdb=" CB LEU A 10 " ideal model delta harmonic sigma weight residual 122.80 140.57 -17.77 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" C LEU A 10 " pdb=" N LEU A 10 " pdb=" CA LEU A 10 " pdb=" CB LEU A 10 " ideal model delta harmonic sigma weight residual -122.60 -140.07 17.47 0 2.50e+00 1.60e-01 4.88e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.210: 99 0.210 - 0.419: 84 0.419 - 0.629: 41 0.629 - 0.838: 16 0.838 - 1.047: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BASN A 97 " pdb=" N BASN A 97 " pdb=" C BASN A 97 " pdb=" CB BASN A 97 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA GLN A 180 " pdb=" N GLN A 180 " pdb=" C GLN A 180 " pdb=" CB GLN A 180 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" CA LEU A 10 " pdb=" N LEU A 10 " pdb=" C LEU A 10 " pdb=" CB LEU A 10 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.95e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.001 2.00e-02 2.50e+03 7.55e-02 1.71e+02 pdb=" CG TYR A 139 " -0.131 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.110 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.074 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.110 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.000 2.00e-02 2.50e+03 6.93e-02 1.44e+02 pdb=" CG BTYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.115 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.063 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.124 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.082 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.076 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.072 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" CG HIS A 138 " 0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.108 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.096 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 800 2.29 - 2.87: 8017 2.87 - 3.45: 10551 3.45 - 4.02: 15288 4.02 - 4.60: 21979 Nonbonded interactions: 56635 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.715 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.735 2.270 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.776 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.824 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.840 2.450 ... (remaining 56630 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_5296401_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= 0.3619 r_free= 0.2019 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466722 | | target function (ml) not normalized (work): 22020.937526 | | target function (ml) not normalized (free): 1152.652658 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3790 0.2181 4.8474 4.8871| | 2: 3.78 - 3.00 1.00 2430 110 0.3411 0.1745 4.0751 4.1698| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.76 0.83 0.13 6603.62| | 2: 3.78 - 3.00 2430 110 0.94 11.35 1.48 0.26 449.47| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 384.88 max = 12072.41 mean = 3570.24| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.32| |phase err.(test): min = 0.00 max = 90.00 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 : 0.084 0.257 1557 Z= 5.612 Angle : 5.206 18.205 2118 Z= 3.695 Chirality : 0.361 1.047 243 Planarity : 0.031 0.078 284 Dihedral : 13.883 88.878 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.62 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.81 % 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: -3.24 (0.44), residues: 224 helix: -2.80 (0.35), residues: 109 sheet: -0.82 (0.72), residues: 38 loop : -1.43 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.026 ARG A 156 TYR 0.123 0.052 TYR A 141 PHE 0.067 0.030 PHE A 164 HIS 0.051 0.026 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= 0.3619 r_free= 0.2019 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466722 | | target function (ml) not normalized (work): 22020.937526 | | target function (ml) not normalized (free): 1152.652658 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3574 0.3651 0.2140 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3574 0.3651 0.2140 n_refl.: 5182 remove outliers: r(all,work,free)=0.2532 0.2556 0.2140 n_refl.: 5178 overall B=-2.80 to atoms: r(all,work,free)=0.2424 0.2445 0.2099 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1568 0.1564 0.1636 n_refl.: 5178 remove outliers: r(all,work,free)=0.1563 0.1559 0.1636 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 0.3790 449.901 402.246 0.670 1.006 0.392 11.894-9.307 99.02 97 4 0.1819 714.703 688.939 0.965 1.009 0.372 9.237-7.194 100.00 213 7 0.2157 584.485 571.249 0.988 1.008 0.374 7.162-5.571 100.00 427 22 0.2326 438.585 419.311 0.937 1.007 0.299 5.546-4.326 100.00 867 58 0.1382 602.115 591.946 0.979 1.004 0.268 4.315-3.360 100.00 1859 96 0.1305 572.618 566.990 1.026 0.999 0.200 3.356-3.002 100.00 1373 60 0.1625 441.055 436.437 1.011 0.994 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9174 b_overall=-4.8608 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1559 r_free=0.1636 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1559 r_free=0.1636 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.153769 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.834945 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 0.1175 0.1790 0.0615 0.010 1.0 2.9 0.5 0.0 0 9.577 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.75 17.90 6.15 3.013 16.059 1.835 0.018 10.30 18.03 7.73 4.991 16.360 1.835 0.015 Individual atomic B min max mean iso aniso Overall: 1.97 112.22 17.66 5.34 1785 0 Protein: 1.97 112.22 14.96 5.33 1519 0 Water: 4.27 111.50 33.30 N/A 258 0 Other: 16.81 36.67 24.22 N/A 8 0 Chain A: 1.97 112.22 17.66 N/A 1785 0 Histogram: Values Number of atoms 1.97 - 13.00 879 13.00 - 24.02 517 24.02 - 35.05 194 35.05 - 46.07 108 46.07 - 57.09 57 57.09 - 68.12 14 68.12 - 79.14 7 79.14 - 90.17 5 90.17 - 101.19 1 101.19 - 112.22 3 =========================== Idealize ADP of riding H ========================== r_work=0.1030 r_free=0.1803 r_work=0.1023 r_free=0.1805 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1023 r_free = 0.1805 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1022 r_free = 0.1797 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= 0.1022 r_free= 0.1797 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014268 | | target function (ls_wunit_k1) not normalized (work): 70.254929 | | target function (ls_wunit_k1) not normalized (free): 10.540737 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1062 0.1022 0.1797 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2126 0.2126 0.2221 n_refl.: 5176 remove outliers: r(all,work,free)=0.2126 0.2126 0.2221 n_refl.: 5176 overall B=-0.96 to atoms: r(all,work,free)=0.2085 0.2084 0.2208 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1059 0.1019 0.1789 n_refl.: 5176 remove outliers: r(all,work,free)=0.1059 0.1019 0.1789 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 0.3306 321.540 303.822 0.652 1.001 0.377 11.894-9.307 99.02 97 4 0.1506 510.792 501.861 0.954 1.003 0.354 9.237-7.194 100.00 213 7 0.1717 417.727 416.657 0.988 1.003 0.317 7.162-5.571 100.00 427 22 0.1632 313.453 309.997 0.950 1.003 0.292 5.546-4.326 100.00 867 58 0.0927 430.327 427.159 0.972 1.002 0.253 4.315-3.360 100.00 1859 96 0.0768 409.245 409.114 1.017 0.999 0.203 3.356-3.002 100.00 1373 60 0.1001 315.218 314.023 0.992 0.997 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.3400 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1019 r_free=0.1789 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1019 r_free=0.1789 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1789 | n_water=258 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.1049 r_free=0.1781 | n_water=247 | time (s): 19.950 (total time: 20.450) Filter (q & B) r_work=0.1048 r_free=0.1780 | n_water=244 | time (s): 1.260 (total time: 21.710) Compute maps r_work=0.1048 r_free=0.1780 | n_water=244 | time (s): 0.450 (total time: 22.160) Filter (map) r_work=0.1386 r_free=0.1829 | n_water=138 | time (s): 1.570 (total time: 23.730) Find peaks r_work=0.1386 r_free=0.1829 | n_water=138 | time (s): 0.590 (total time: 24.320) Add new water r_work=0.1729 r_free=0.2063 | n_water=228 | time (s): 1.770 (total time: 26.090) Refine new water occ: r_work=0.1154 r_free=0.1669 adp: r_work=0.1129 r_free=0.1659 occ: r_work=0.1127 r_free=0.1651 adp: r_work=0.1117 r_free=0.1645 occ: r_work=0.1115 r_free=0.1637 adp: r_work=0.1114 r_free=0.1633 ADP+occupancy (water only), MIN, final r_work=0.1114 r_free=0.1633 r_work=0.1114 r_free=0.1633 | n_water=228 | time (s): 4.490 (total time: 30.580) Filter (q & B) r_work=0.1114 r_free=0.1633 | n_water=228 | time (s): 0.930 (total time: 31.510) Filter (dist only) r_work=0.1123 r_free=0.1638 | n_water=224 | time (s): 16.850 (total time: 48.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.464933 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.828487 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 0.1014 0.1820 0.0806 0.009 1.0 5.8 0.5 0.6 0 11.232 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.14 18.20 8.06 4.704 17.004 2.828 0.014 9.48 18.86 9.38 5.506 17.449 2.828 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 109.30 16.85 6.53 1751 0 Protein: 0.00 109.30 15.38 6.52 1519 0 Water: 0.00 63.30 26.61 N/A 224 0 Other: 11.53 32.46 21.78 N/A 8 0 Chain A: 0.00 109.30 16.07 N/A 1661 0 Chain S: 3.58 63.30 31.15 N/A 90 0 Histogram: Values Number of atoms 0.00 - 10.93 668 10.93 - 21.86 671 21.86 - 32.79 219 32.79 - 43.72 118 43.72 - 54.65 38 54.65 - 65.58 26 65.58 - 76.51 5 76.51 - 87.44 2 87.44 - 98.37 3 98.37 - 109.30 1 =========================== Idealize ADP of riding H ========================== r_work=0.0948 r_free=0.1886 r_work=0.0946 r_free=0.1889 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0946 r_free = 0.1889 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0944 r_free = 0.1875 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0944 r_free= 0.1875 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011985 | | target function (ls_wunit_k1) not normalized (work): 59.015354 | | target function (ls_wunit_k1) not normalized (free): 10.534573 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0991 0.0944 0.1875 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2184 0.2186 0.2294 n_refl.: 5176 remove outliers: r(all,work,free)=0.2184 0.2186 0.2294 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2184 0.2186 0.2294 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0992 0.0945 0.1884 n_refl.: 5176 remove outliers: r(all,work,free)=0.0992 0.0945 0.1884 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 0.3231 321.540 306.097 0.701 1.009 0.381 11.894-9.307 99.02 97 4 0.1390 510.792 505.345 0.989 1.010 0.360 9.237-7.194 100.00 213 7 0.1490 417.727 417.619 1.014 1.010 0.310 7.162-5.571 100.00 427 22 0.1374 313.453 311.867 0.990 1.008 0.300 5.546-4.326 100.00 867 58 0.0812 430.327 427.659 1.009 1.005 0.260 4.315-3.360 100.00 1859 96 0.0732 409.245 409.025 1.065 0.998 0.211 3.356-3.002 100.00 1373 60 0.0983 315.218 314.121 1.047 0.992 0.083 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.6154 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0945 r_free=0.1884 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=0.0945 r_free=0.1886 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0945 r_free=0.1886 | n_water=224 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0957 r_free=0.1887 | n_water=220 | time (s): 19.090 (total time: 19.640) Filter (q & B) r_work=0.0989 r_free=0.1907 | n_water=219 | time (s): 1.610 (total time: 21.250) Compute maps r_work=0.0989 r_free=0.1907 | n_water=219 | time (s): 0.670 (total time: 21.920) Filter (map) r_work=0.1272 r_free=0.1948 | n_water=141 | time (s): 1.920 (total time: 23.840) Find peaks r_work=0.1272 r_free=0.1948 | n_water=141 | time (s): 0.520 (total time: 24.360) Add new water r_work=0.1675 r_free=0.2332 | n_water=228 | time (s): 1.530 (total time: 25.890) Refine new water occ: r_work=0.1100 r_free=0.1801 adp: r_work=0.1098 r_free=0.1806 occ: r_work=0.1086 r_free=0.1786 adp: r_work=0.1086 r_free=0.1792 occ: r_work=0.1077 r_free=0.1775 adp: r_work=0.1076 r_free=0.1781 ADP+occupancy (water only), MIN, final r_work=0.1076 r_free=0.1781 r_work=0.1076 r_free=0.1781 | n_water=228 | time (s): 12.140 (total time: 38.030) Filter (q & B) r_work=0.1076 r_free=0.1778 | n_water=227 | time (s): 1.930 (total time: 39.960) Filter (dist only) r_work=0.1091 r_free=0.1791 | n_water=224 | time (s): 18.020 (total time: 57.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.138137 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.227494 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 0.0977 0.1851 0.0874 0.011 1.0 4.8 0.5 0.6 0 0.569 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.77 18.51 8.74 5.460 18.141 0.227 5.176 9.33 18.65 9.32 6.967 18.084 0.227 5.089 Individual atomic B min max mean iso aniso Overall: 0.00 108.25 16.55 8.45 1751 0 Protein: 0.00 108.25 15.36 8.44 1519 0 Water: 0.00 57.82 24.33 N/A 224 0 Other: 12.85 37.84 24.29 N/A 8 0 Chain A: 0.00 108.25 16.00 N/A 1647 0 Chain S: 0.00 55.88 25.19 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.82 653 10.82 - 21.65 682 21.65 - 32.47 237 32.47 - 43.30 115 43.30 - 54.12 32 54.12 - 64.95 17 64.95 - 75.77 8 75.77 - 86.60 2 86.60 - 97.42 4 97.42 - 108.25 1 =========================== Idealize ADP of riding H ========================== r_work=0.0933 r_free=0.1865 r_work=0.0938 r_free=0.1869 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0938 r_free = 0.1869 target_work(ml) = 5.092 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0923 r_free = 0.1851 target_work(ml) = 5.084 | | occupancies: max = 1.00 min = 0.28 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= 0.0923 r_free= 0.1851 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.083944 | | target function (ml) not normalized (work): 25033.340600 | | target function (ml) not normalized (free): 1815.656118 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0970 0.0923 0.1851 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2200 0.2207 0.2202 n_refl.: 5176 remove outliers: r(all,work,free)=0.2200 0.2207 0.2202 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2200 0.2207 0.2202 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0964 0.0917 0.1844 n_refl.: 5176 remove outliers: r(all,work,free)=0.0960 0.0913 0.1844 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 0.3686 320.953 289.635 0.622 0.992 0.348 11.894-9.307 99.02 97 4 0.1743 510.792 499.885 0.962 0.997 0.320 9.237-7.194 100.00 213 7 0.1912 417.727 411.314 1.004 0.998 0.300 7.162-5.571 100.00 427 22 0.1829 313.453 306.640 0.985 0.999 0.300 5.546-4.326 100.00 867 58 0.0931 430.327 424.192 1.000 1.000 0.250 4.315-3.360 100.00 1859 96 0.0615 409.245 408.516 1.067 1.002 0.220 3.356-3.002 100.00 1373 60 0.0660 315.218 314.544 1.048 1.003 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-6.9110 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0913 r_free=0.1844 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=0.0913 r_free=0.1842 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0913 r_free=0.1842 | n_water=224 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.0923 r_free=0.1836 | n_water=221 | time (s): 16.870 (total time: 17.570) Filter (q & B) r_work=0.0956 r_free=0.1844 | n_water=220 | time (s): 1.490 (total time: 19.060) Compute maps r_work=0.0956 r_free=0.1844 | n_water=220 | time (s): 0.490 (total time: 19.550) Filter (map) r_work=0.1183 r_free=0.1910 | n_water=160 | time (s): 1.250 (total time: 20.800) Find peaks r_work=0.1183 r_free=0.1910 | n_water=160 | time (s): 0.490 (total time: 21.290) Add new water r_work=0.1503 r_free=0.2135 | n_water=234 | time (s): 1.630 (total time: 22.920) Refine new water occ: r_work=0.1028 r_free=0.1811 adp: r_work=0.1024 r_free=0.1821 occ: r_work=0.1015 r_free=0.1804 adp: r_work=0.1015 r_free=0.1812 occ: r_work=0.1005 r_free=0.1797 adp: r_work=0.1005 r_free=0.1802 ADP+occupancy (water only), MIN, final r_work=0.1005 r_free=0.1802 r_work=0.1005 r_free=0.1802 | n_water=234 | time (s): 11.740 (total time: 34.660) Filter (q & B) r_work=0.1004 r_free=0.1806 | n_water=232 | time (s): 1.870 (total time: 36.530) Filter (dist only) r_work=0.1004 r_free=0.1806 | n_water=232 | time (s): 17.160 (total time: 53.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.030887 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.217850 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 0.0916 0.1865 0.0949 0.011 1.0 4.8 0.5 0.0 0 0.515 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.16 18.65 9.49 6.649 18.155 0.218 5.026 8.92 18.79 9.87 8.030 18.296 0.218 4.958 Individual atomic B min max mean iso aniso Overall: 0.00 109.19 17.00 10.38 1759 0 Protein: 0.00 109.19 15.85 10.37 1519 0 Water: 0.00 56.13 24.17 N/A 232 0 Other: 12.03 40.84 27.66 N/A 8 0 Chain A: 0.00 109.19 16.34 N/A 1639 0 Chain S: 0.00 56.13 26.00 N/A 120 0 Histogram: Values Number of atoms 0.00 - 10.92 653 10.92 - 21.84 655 21.84 - 32.76 255 32.76 - 43.68 123 43.68 - 54.59 39 54.59 - 65.51 19 65.51 - 76.43 7 76.43 - 87.35 4 87.35 - 98.27 3 98.27 - 109.19 1 =========================== Idealize ADP of riding H ========================== r_work=0.0892 r_free=0.1879 r_work=0.0897 r_free=0.1883 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1883 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1868 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1868 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.952555 | | target function (ml) not normalized (work): 24376.473741 | | target function (ml) not normalized (free): 2127.744228 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0931 0.0881 0.1868 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2114 0.2116 0.2195 n_refl.: 5174 remove outliers: r(all,work,free)=0.2114 0.2116 0.2195 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2114 0.2116 0.2195 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0929 0.0880 0.1862 n_refl.: 5174 remove outliers: r(all,work,free)=0.0929 0.0880 0.1862 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 0.3882 320.953 290.501 0.591 0.988 0.329 11.894-9.307 99.02 97 4 0.1885 510.792 497.172 0.966 0.992 0.328 9.237-7.194 100.00 213 7 0.2082 417.727 408.060 1.006 0.995 0.298 7.162-5.571 100.00 427 22 0.1993 313.453 305.074 0.994 0.997 0.280 5.546-4.326 100.00 867 58 0.0995 430.327 424.196 1.018 0.999 0.250 4.315-3.360 100.00 1859 96 0.0550 409.245 408.770 1.089 1.002 0.220 3.356-3.002 100.00 1373 60 0.0463 315.218 315.279 1.070 1.006 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9892 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0880 r_free=0.1863 After: r_work=0.0883 r_free=0.1861 ================================== NQH flips ================================== r_work=0.0883 r_free=0.1861 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0883 r_free=0.1861 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1861 | n_water=232 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.0898 r_free=0.1855 | n_water=227 | time (s): 19.650 (total time: 20.350) Filter (q & B) r_work=0.0975 r_free=0.1886 | n_water=225 | time (s): 1.710 (total time: 22.060) Compute maps r_work=0.0975 r_free=0.1886 | n_water=225 | time (s): 0.600 (total time: 22.660) Filter (map) r_work=0.1221 r_free=0.1890 | n_water=153 | time (s): 1.410 (total time: 24.070) Find peaks r_work=0.1221 r_free=0.1890 | n_water=153 | time (s): 0.390 (total time: 24.460) Add new water r_work=0.1554 r_free=0.2166 | n_water=229 | time (s): 1.230 (total time: 25.690) Refine new water occ: r_work=0.1001 r_free=0.1830 adp: r_work=0.0994 r_free=0.1831 occ: r_work=0.0988 r_free=0.1825 adp: r_work=0.0986 r_free=0.1826 occ: r_work=0.0980 r_free=0.1820 adp: r_work=0.0978 r_free=0.1822 ADP+occupancy (water only), MIN, final r_work=0.0978 r_free=0.1822 r_work=0.0978 r_free=0.1822 | n_water=229 | time (s): 9.010 (total time: 34.700) Filter (q & B) r_work=0.0979 r_free=0.1826 | n_water=227 | time (s): 1.840 (total time: 36.540) Filter (dist only) r_work=0.0984 r_free=0.1828 | n_water=225 | time (s): 18.350 (total time: 54.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.968051 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.220366 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0924 0.1846 0.0922 0.011 1.1 7.0 0.5 0.6 0 0.484 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.24 18.46 9.22 7.931 18.561 0.220 4.999 9.05 18.54 9.49 8.904 18.666 0.220 4.943 Individual atomic B min max mean iso aniso Overall: 0.00 111.53 17.20 11.77 1752 0 Protein: 0.00 111.53 16.20 11.76 1519 0 Water: 0.00 61.81 23.52 N/A 225 0 Other: 11.87 43.75 28.72 N/A 8 0 Chain A: 0.00 111.53 16.62 N/A 1633 0 Chain S: 0.00 61.81 25.16 N/A 119 0 Histogram: Values Number of atoms 0.00 - 11.15 658 11.15 - 22.31 638 22.31 - 33.46 270 33.46 - 44.61 119 44.61 - 55.77 35 55.77 - 66.92 15 66.92 - 78.07 8 78.07 - 89.23 5 89.23 - 100.38 2 100.38 - 111.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.0905 r_free=0.1854 r_work=0.0908 r_free=0.1861 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0908 r_free = 0.1861 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0901 r_free = 0.1856 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0901 r_free= 0.1856 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.942076 | | target function (ml) not normalized (work): 24324.895886 | | target function (ml) not normalized (free): 2225.256363 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1284 0.1796 5.5203 6.1547| | 2: 3.78 - 3.00 1.00 2430 110 0.0434 0.1957 4.3491 12.284| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.44 1.00 0.95 12911.20| | 2: 3.78 - 3.00 2430 110 0.99 1.84 1.00 0.97 878.64| |alpha: min = 0.94 max = 0.97 mean = 0.96| |beta: min = 561.51 max = 21697.37 mean = 6970.70| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.77 mean = 7.21| |phase err.(test): min = 0.00 max = 83.77 mean = 7.35| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0949 0.0901 0.1856 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2175 0.2176 0.2270 n_refl.: 5174 remove outliers: r(all,work,free)=0.2175 0.2176 0.2270 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2175 0.2176 0.2270 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0948 0.0900 0.1858 n_refl.: 5174 remove outliers: r(all,work,free)=0.0948 0.0900 0.1858 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 0.4059 320.953 286.688 0.626 0.985 0.330 11.894-9.307 99.02 97 4 0.1934 510.792 495.459 1.006 0.992 0.318 9.237-7.194 100.00 213 7 0.2153 417.727 407.379 1.051 0.995 0.289 7.162-5.571 100.00 427 22 0.2075 313.453 303.748 1.036 0.997 0.273 5.546-4.326 100.00 867 58 0.1052 430.327 423.816 1.068 1.000 0.230 4.315-3.360 100.00 1859 96 0.0567 409.245 409.080 1.158 1.003 0.229 3.356-3.002 100.00 1373 60 0.0416 315.218 315.481 1.141 1.006 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.9634 ================= 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 : 0.3619 0.2019 0.084 5.206 8.8 119.3 19.9 258 0.000 1_bss: 0.1559 0.1636 0.084 5.206 6.0 116.5 17.1 258 0.000 1_settarget: 0.1559 0.1636 0.084 5.206 6.0 116.5 17.1 258 0.000 1_nqh: 0.1559 0.1636 0.084 5.206 6.0 116.5 17.1 258 0.000 1_weight: 0.1559 0.1636 0.084 5.206 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1175 0.1790 0.010 0.972 6.0 116.5 17.1 258 0.198 1_adp: 0.1030 0.1803 0.010 0.972 2.0 112.2 17.7 258 0.198 1_regHadp: 0.1023 0.1805 0.010 0.972 2.0 112.2 17.7 258 0.198 1_occ: 0.1022 0.1797 0.010 0.972 2.0 112.2 17.7 258 0.198 2_bss: 0.1019 0.1789 0.010 0.972 1.0 111.3 16.7 258 0.198 2_settarget: 0.1019 0.1789 0.010 0.972 1.0 111.3 16.7 258 0.198 2_updatecdl: 0.1019 0.1789 0.010 1.003 1.0 111.3 16.7 258 0.198 2_nqh: 0.1019 0.1789 0.010 1.003 1.0 111.3 16.7 258 0.198 2_sol: 0.1123 0.1638 0.010 1.003 1.0 111.3 16.0 224 n/a 2_weight: 0.1123 0.1638 0.010 1.003 1.0 111.3 16.0 224 n/a 2_xyzrec: 0.1014 0.1820 0.009 0.973 1.0 111.3 16.0 224 n/a 2_adp: 0.0948 0.1886 0.009 0.973 0.0 109.3 16.8 224 n/a 2_regHadp: 0.0946 0.1889 0.009 0.973 0.0 109.3 16.8 224 n/a 2_occ: 0.0944 0.1875 0.009 0.973 0.0 109.3 16.8 224 n/a 3_bss: 0.0945 0.1884 0.009 0.973 0.0 109.3 16.8 224 n/a 3_settarget: 0.0945 0.1884 0.009 0.973 0.0 109.3 16.8 224 n/a 3_updatecdl: 0.0945 0.1884 0.009 0.976 0.0 109.3 16.8 224 n/a 3_nqh: 0.0945 0.1886 0.009 0.976 0.0 109.3 16.8 224 n/a 3_sol: 0.1091 0.1791 0.009 0.976 0.0 109.3 16.7 224 n/a 3_weight: 0.1091 0.1791 0.009 0.976 0.0 109.3 16.7 224 n/a 3_xyzrec: 0.0977 0.1851 0.011 1.046 0.0 109.3 16.7 224 n/a 3_adp: 0.0933 0.1865 0.011 1.046 0.0 108.2 16.5 224 n/a 3_regHadp: 0.0938 0.1869 0.011 1.046 0.0 108.2 16.5 224 n/a 3_occ: 0.0923 0.1851 0.011 1.046 0.0 108.2 16.5 224 n/a 4_bss: 0.0913 0.1844 0.011 1.046 0.0 108.2 16.5 224 n/a 4_settarget: 0.0913 0.1844 0.011 1.046 0.0 108.2 16.5 224 n/a 4_updatecdl: 0.0913 0.1844 0.011 1.051 0.0 108.2 16.5 224 n/a 4_nqh: 0.0913 0.1842 0.011 1.051 0.0 108.2 16.5 224 n/a 4_sol: 0.1004 0.1806 0.011 1.051 0.0 108.2 16.7 232 n/a 4_weight: 0.1004 0.1806 0.011 1.051 0.0 108.2 16.7 232 n/a 4_xyzrec: 0.0916 0.1865 0.011 1.013 0.0 108.2 16.7 232 n/a 4_adp: 0.0892 0.1879 0.011 1.013 0.0 109.2 17.0 232 n/a 4_regHadp: 0.0897 0.1883 0.011 1.013 0.0 109.2 17.0 232 n/a 4_occ: 0.0881 0.1868 0.011 1.013 0.0 109.2 17.0 232 n/a 5_bss: 0.0880 0.1863 0.011 1.013 0.0 109.2 17.0 232 n/a 5_settarget: 0.0880 0.1863 0.011 1.013 0.0 109.2 17.0 232 n/a 5_updatecdl: 0.0880 0.1863 0.011 1.024 0.0 109.2 17.0 232 n/a 5_setrh: 0.0883 0.1861 0.011 1.024 0.0 109.2 17.0 232 n/a 5_nqh: 0.0883 0.1861 0.011 1.024 0.0 109.2 17.0 232 n/a 5_sol: 0.0984 0.1828 0.011 1.024 0.0 109.2 17.0 225 n/a 5_weight: 0.0984 0.1828 0.011 1.024 0.0 109.2 17.0 225 n/a 5_xyzrec: 0.0924 0.1846 0.011 1.093 0.0 109.2 17.0 225 n/a 5_adp: 0.0905 0.1854 0.011 1.093 0.0 111.5 17.2 225 n/a 5_regHadp: 0.0908 0.1861 0.011 1.093 0.0 111.5 17.2 225 n/a 5_occ: 0.0901 0.1856 0.011 1.093 0.0 111.5 17.2 225 n/a end: 0.0900 0.1858 0.011 1.093 0.0 111.5 17.2 225 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5296401_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5296401_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3300 Refinement macro-cycles (run) : 480.7800 Write final files (write_after_run_outputs) : 10.9500 Total : 495.0600 Total CPU time: 8.62 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:58 PST -0800 (1735492738.96 s) Start R-work = 0.1559, R-free = 0.1636 Final R-work = 0.0900, R-free = 0.1858 =============================================================================== Job complete usr+sys time: 525.53 seconds wall clock time: 9 minutes 7.70 seconds (547.70 seconds total)