Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.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=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.57, 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: 0.49 Conformation dependent library (CDL) restraints added in 105.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 528 0.91 - 1.16: 1115 1.16 - 1.42: 620 1.42 - 1.67: 851 1.67 - 1.93: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.524 1.772 -0.248 1.26e-02 6.30e+03 3.87e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.163 0.215 1.10e-02 8.26e+03 3.82e+02 bond pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 1.456 1.240 0.215 1.11e-02 8.12e+03 3.76e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.512 -0.191 1.00e-02 1.00e+04 3.63e+02 bond pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 1.466 1.242 0.223 1.19e-02 7.06e+03 3.52e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3338 4.85 - 9.69: 1833 9.69 - 14.54: 495 14.54 - 19.39: 105 19.39 - 24.23: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 71 " pdb=" C VAL A 71 " pdb=" N LEU A 72 " ideal model delta sigma weight residual 123.18 104.97 18.21 1.05e+00 9.07e-01 3.01e+02 angle pdb=" O SER A 47 " pdb=" C SER A 47 " pdb=" N ARG A 48 " ideal model delta sigma weight residual 122.12 138.53 -16.41 1.06e+00 8.90e-01 2.40e+02 angle pdb=" CA AGLU A 94 " pdb=" C AGLU A 94 " pdb=" O AGLU A 94 " ideal model delta sigma weight residual 119.97 104.45 15.52 1.15e+00 7.56e-01 1.82e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 133.76 -12.41 9.20e-01 1.18e+00 1.82e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.83 108.18 13.65 1.03e+00 9.43e-01 1.76e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.43: 1323 18.43 - 36.86: 115 36.86 - 55.29: 30 55.29 - 73.72: 10 73.72 - 92.15: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N LYS A 62 " pdb=" C LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual 122.80 144.01 -21.21 0 2.50e+00 1.60e-01 7.20e+01 dihedral pdb=" C LYS A 62 " pdb=" N LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual -122.60 -143.20 20.60 0 2.50e+00 1.60e-01 6.79e+01 dihedral pdb=" C BLYS A 175 " pdb=" N BLYS A 175 " pdb=" CA BLYS A 175 " pdb=" CB BLYS A 175 " ideal model delta harmonic sigma weight residual -122.60 -142.30 19.70 0 2.50e+00 1.60e-01 6.21e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.218: 109 0.218 - 0.430: 74 0.430 - 0.641: 31 0.641 - 0.853: 24 0.853 - 1.064: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -3.69 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA BLYS A 175 " pdb=" N BLYS A 175 " pdb=" C BLYS A 175 " pdb=" CB BLYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA ILE A 117 " pdb=" N ILE A 117 " pdb=" C ILE A 117 " pdb=" CB ILE A 117 " both_signs ideal model delta sigma weight residual False 2.43 3.39 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.043 2.00e-02 2.50e+03 7.35e-02 1.62e+02 pdb=" CG TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.110 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.145 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.058 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.126 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.058 2.00e-02 2.50e+03 6.04e-02 1.10e+02 pdb=" CG PHE A 119 " -0.114 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.098 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.056 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " -0.002 2.00e-02 2.50e+03 7.06e-02 7.48e+01 pdb=" CG ASN A 173 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " -0.126 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " 0.010 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.101 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 717 2.27 - 2.85: 7812 2.85 - 3.43: 10581 3.43 - 4.02: 15362 4.02 - 4.60: 22067 Nonbonded interactions: 56539 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.685 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.771 2.450 x-y,-y,-z-4/3 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.773 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.798 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.801 2.450 x-y,-y,-z-4/3 ... (remaining 56534 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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_2963595_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2795 r_free= 0.1834 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.391561 | | target function (ml) not normalized (work): 71332.117899 | | target function (ml) not normalized (free): 3269.530360 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3191 0.2166 7.4661 5.0401| | 2: 3.63 - 2.88 1.00 2711 122 0.2662 0.1832 4.3386 4.3367| | 3: 2.88 - 2.52 1.00 2682 148 0.2584 0.1626 4.1904 4.1967| | 4: 2.52 - 2.29 1.00 2661 139 0.2525 0.1513 3.4912 3.6041| | 5: 2.29 - 2.13 1.00 2678 122 0.2696 0.1465 3.3961 3.3974| | 6: 2.13 - 2.00 1.00 2692 117 0.2733 0.1926 3.306 3.4403| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.89 0.77 0.23 1334.76| | 2: 3.63 - 2.88 2711 122 0.82 24.12 1.32 0.23 1334.76| | 3: 2.88 - 2.52 2682 148 0.73 33.36 1.29 0.23 1334.76| | 4: 2.52 - 2.29 2661 139 0.93 11.33 1.29 0.26 133.46| | 5: 2.29 - 2.13 2678 122 0.92 13.48 1.33 0.26 133.46| | 6: 2.13 - 2.00 2692 117 0.90 16.24 1.33 0.26 133.46| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 133.46 max = 1334.76 mean = 740.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.92 mean = 19.41| |phase err.(test): min = 0.00 max = 89.88 mean = 19.67| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.248 1557 Z= 5.538 Angle : 5.254 18.207 2118 Z= 3.716 Chirality : 0.387 1.064 243 Planarity : 0.031 0.106 284 Dihedral : 14.341 92.155 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % 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: -2.73 (0.47), residues: 224 helix: -2.83 (0.34), residues: 102 sheet: -0.89 (1.00), residues: 28 loop : -0.57 (0.57), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.012 ARG A 145 TYR 0.073 0.033 TYR A 139 PHE 0.119 0.037 PHE A 119 HIS 0.065 0.031 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2795 r_free= 0.1834 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.391561 | | target function (ml) not normalized (work): 71332.117899 | | target function (ml) not normalized (free): 3269.530360 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3224 percent. r_work = 0.2927 r_free = 0.2010 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2875 0.2927 0.2010 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2875 0.2927 0.2010 n_refl.: 17050 remove outliers: r(all,work,free)=0.2163 0.2173 0.2010 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2136 0.2145 0.1993 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1621 0.1618 0.1680 n_refl.: 17045 remove outliers: r(all,work,free)=0.1620 0.1617 0.1680 n_refl.: 17044 ======================== 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 32.574-12.150 100.00 89 5 0.4032 394.837 362.921 0.655 1.011 0.399 11.894-9.307 99.02 97 4 0.1866 633.724 617.091 0.936 1.012 0.390 9.237-7.194 100.00 213 7 0.2182 518.323 510.176 0.958 1.012 0.350 7.162-5.571 100.00 427 22 0.2258 389.002 376.539 0.920 1.011 0.288 5.546-4.326 100.00 867 58 0.1387 534.037 527.952 0.959 1.009 0.220 4.315-3.360 100.00 1859 96 0.1297 507.874 503.394 1.014 1.006 0.201 3.356-2.611 100.00 3867 181 0.1681 333.645 328.935 1.016 1.001 0.101 2.608-2.000 99.99 8818 434 0.1647 217.479 213.230 1.028 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4700 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1617 r_free=0.1680 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1617 r_free=0.1680 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.748354 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.939470 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1351 0.1636 0.0285 0.009 1.0 1.3 0.5 0.0 0 11.874 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.36 2.85 3.013 18.447 0.939 0.023 12.78 16.56 3.78 3.634 18.710 0.939 0.020 Individual atomic B min max mean iso aniso Overall: 6.01 113.89 19.97 4.12 1785 0 Protein: 6.01 113.50 17.20 4.12 1519 0 Water: 8.93 113.89 36.10 N/A 258 0 Other: 21.62 37.45 26.34 N/A 8 0 Chain A: 6.01 113.89 19.97 N/A 1785 0 Histogram: Values Number of atoms 6.01 - 16.80 1075 16.80 - 27.59 347 27.59 - 38.37 188 38.37 - 49.16 97 49.16 - 59.95 50 59.95 - 70.74 13 70.74 - 81.52 7 81.52 - 92.31 4 92.31 - 103.10 1 103.10 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1656 r_work=0.1281 r_free=0.1662 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1662 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1277 r_free = 0.1656 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1277 r_free= 0.1656 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020052 | | target function (ls_wunit_k1) not normalized (work): 325.591406 | | target function (ls_wunit_k1) not normalized (free): 26.973008 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1277 0.1656 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1911 0.1910 0.1985 n_refl.: 17044 remove outliers: r(all,work,free)=0.1911 0.1910 0.1985 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1882 0.1881 0.1970 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1278 0.1650 n_refl.: 17044 remove outliers: r(all,work,free)=0.1294 0.1276 0.1650 n_refl.: 17042 ======================== 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 0.3509 303.500 279.569 0.626 1.010 0.368 11.894-9.307 99.02 97 4 0.1714 488.132 477.478 0.917 1.010 0.367 9.237-7.194 100.00 213 7 0.1810 399.242 396.968 0.959 1.010 0.341 7.162-5.571 100.00 427 22 0.1842 299.632 294.700 0.930 1.009 0.301 5.546-4.326 100.00 867 58 0.1038 411.346 409.065 0.957 1.008 0.205 4.315-3.360 100.00 1859 96 0.0928 391.194 390.886 1.016 1.005 0.191 3.356-2.611 100.00 3867 181 0.1297 256.992 255.717 1.017 1.000 0.101 2.608-2.000 99.99 8818 434 0.1357 167.515 166.055 1.023 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3974 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1650 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1650 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1650 | n_water=258 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1285 r_free=0.1644 | n_water=252 | time (s): 21.000 (total time: 21.640) Filter (q & B) r_work=0.1285 r_free=0.1643 | n_water=250 | time (s): 1.370 (total time: 23.010) Compute maps r_work=0.1285 r_free=0.1643 | n_water=250 | time (s): 0.550 (total time: 23.560) Filter (map) r_work=0.1317 r_free=0.1631 | n_water=214 | time (s): 1.490 (total time: 25.050) Find peaks r_work=0.1317 r_free=0.1631 | n_water=214 | time (s): 0.500 (total time: 25.550) Add new water r_work=0.1525 r_free=0.1869 | n_water=371 | time (s): 1.380 (total time: 26.930) Refine new water occ: r_work=0.1326 r_free=0.1588 adp: r_work=0.1270 r_free=0.1589 occ: r_work=0.1276 r_free=0.1552 adp: r_work=0.1244 r_free=0.1559 occ: r_work=0.1246 r_free=0.1544 adp: r_work=0.1235 r_free=0.1547 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1547 r_work=0.1235 r_free=0.1547 | n_water=371 | time (s): 17.250 (total time: 44.180) Filter (q & B) r_work=0.1238 r_free=0.1555 | n_water=360 | time (s): 2.120 (total time: 46.300) Filter (dist only) r_work=0.1238 r_free=0.1557 | n_water=359 | time (s): 29.930 (total time: 76.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.280734 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.983057 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1215 0.1588 0.0374 0.008 0.9 2.6 0.5 0.0 0 12.140 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.15 15.88 3.74 4.192 21.069 0.983 0.018 12.01 16.24 4.24 4.224 21.415 0.983 0.018 Individual atomic B min max mean iso aniso Overall: 6.84 108.11 21.52 4.31 1886 0 Protein: 6.84 108.11 17.85 4.30 1519 0 Water: 8.91 68.10 36.75 N/A 359 0 Other: 24.39 45.35 35.34 N/A 8 0 Chain A: 6.84 108.11 19.65 N/A 1741 0 Chain S: 18.40 68.10 43.95 N/A 145 0 Histogram: Values Number of atoms 6.84 - 16.96 1029 16.96 - 27.09 378 27.09 - 37.22 221 37.22 - 47.35 148 47.35 - 57.47 68 57.47 - 67.60 31 67.60 - 77.73 3 77.73 - 87.86 6 87.86 - 97.98 0 97.98 - 108.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1624 r_work=0.1203 r_free=0.1624 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1624 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1626 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1201 r_free= 0.1626 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017128 | | target function (ls_wunit_k1) not normalized (work): 278.072213 | | target function (ls_wunit_k1) not normalized (free): 25.225223 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1201 0.1626 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1777 0.1770 0.1953 n_refl.: 17042 remove outliers: r(all,work,free)=0.1777 0.1770 0.1953 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1751 0.1744 0.1935 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1194 0.1618 n_refl.: 17042 remove outliers: r(all,work,free)=0.1213 0.1193 0.1618 n_refl.: 17041 ======================== 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 0.3156 300.337 285.386 0.609 1.002 0.350 11.894-9.307 99.02 97 4 0.1435 488.132 484.806 0.917 1.003 0.350 9.237-7.194 100.00 213 7 0.1683 399.242 400.442 0.976 1.003 0.290 7.162-5.571 100.00 427 22 0.1576 299.632 295.874 0.937 1.003 0.271 5.546-4.326 100.00 867 58 0.0865 411.346 409.004 0.961 1.003 0.216 4.315-3.360 100.00 1859 96 0.0843 391.194 390.364 1.017 1.002 0.211 3.356-2.611 100.00 3867 181 0.1208 256.992 255.866 1.012 1.002 0.121 2.608-2.000 99.99 8818 434 0.1331 167.515 166.450 1.016 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3937 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1618 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1618 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1618 | n_water=359 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1193 r_free=0.1617 | n_water=358 | time (s): 28.850 (total time: 29.650) Filter (q & B) r_work=0.1193 r_free=0.1617 | n_water=358 | time (s): 0.720 (total time: 30.370) Compute maps r_work=0.1193 r_free=0.1617 | n_water=358 | time (s): 0.530 (total time: 30.900) Filter (map) r_work=0.1262 r_free=0.1616 | n_water=256 | time (s): 1.450 (total time: 32.350) Find peaks r_work=0.1262 r_free=0.1616 | n_water=256 | time (s): 0.420 (total time: 32.770) Add new water r_work=0.1453 r_free=0.1800 | n_water=401 | time (s): 1.870 (total time: 34.640) Refine new water occ: r_work=0.1253 r_free=0.1569 adp: r_work=0.1245 r_free=0.1573 occ: r_work=0.1226 r_free=0.1540 adp: r_work=0.1215 r_free=0.1541 occ: r_work=0.1207 r_free=0.1533 adp: r_work=0.1197 r_free=0.1529 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1529 r_work=0.1197 r_free=0.1529 | n_water=401 | time (s): 37.270 (total time: 71.910) Filter (q & B) r_work=0.1200 r_free=0.1528 | n_water=390 | time (s): 2.140 (total time: 74.050) Filter (dist only) r_work=0.1200 r_free=0.1528 | n_water=390 | time (s): 28.000 (total time: 102.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.924569 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.151269 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1173 0.1529 0.0356 0.009 1.0 4.2 0.5 0.0 0 0.962 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.73 15.29 3.56 4.370 21.597 0.151 4.991 11.53 15.42 3.89 4.839 21.475 0.151 4.969 Individual atomic B min max mean iso aniso Overall: 6.41 105.67 20.81 4.58 1917 0 Protein: 6.41 105.67 17.09 4.57 1519 0 Water: 8.92 63.64 35.04 N/A 390 0 Other: 26.83 46.34 34.43 N/A 8 0 Chain A: 6.41 105.67 18.82 N/A 1734 0 Chain S: 13.28 63.64 39.72 N/A 183 0 Histogram: Values Number of atoms 6.41 - 16.34 1069 16.34 - 26.26 341 26.26 - 36.19 229 36.19 - 46.11 170 46.11 - 56.04 66 56.04 - 65.96 30 65.96 - 75.89 5 75.89 - 85.82 3 85.82 - 95.74 2 95.74 - 105.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1542 r_work=0.1153 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1544 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1545 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1145 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.963105 | | target function (ml) not normalized (work): 80571.041291 | | target function (ml) not normalized (free): 4182.008294 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1164 0.1145 0.1545 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1694 0.1687 0.1880 n_refl.: 17041 remove outliers: r(all,work,free)=0.1694 0.1687 0.1880 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1668 0.1660 0.1868 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1142 0.1547 n_refl.: 17041 remove outliers: r(all,work,free)=0.1161 0.1142 0.1547 n_refl.: 17041 ======================== 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 0.3439 300.337 280.169 0.578 1.008 0.340 11.894-9.307 99.02 97 4 0.1655 488.132 482.815 0.914 1.009 0.340 9.237-7.194 100.00 213 7 0.1794 399.242 398.598 0.983 1.009 0.277 7.162-5.571 100.00 427 22 0.1587 299.632 294.431 0.935 1.008 0.246 5.546-4.326 100.00 867 58 0.0936 411.346 407.832 0.960 1.007 0.221 4.315-3.360 100.00 1859 96 0.0880 391.194 388.803 1.010 1.004 0.221 3.356-2.611 100.00 3867 181 0.1270 256.992 254.975 1.012 1.000 0.162 2.608-2.000 99.99 8818 434 0.1101 167.515 166.164 1.021 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3502 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1142 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1547 | n_water=390 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1144 r_free=0.1548 | n_water=389 | time (s): 30.460 (total time: 31.170) Filter (q & B) r_work=0.1144 r_free=0.1550 | n_water=388 | time (s): 1.990 (total time: 33.160) Compute maps r_work=0.1144 r_free=0.1550 | n_water=388 | time (s): 0.810 (total time: 33.970) Filter (map) r_work=0.1197 r_free=0.1572 | n_water=309 | time (s): 2.000 (total time: 35.970) Find peaks r_work=0.1197 r_free=0.1572 | n_water=309 | time (s): 0.640 (total time: 36.610) Add new water r_work=0.1341 r_free=0.1690 | n_water=448 | time (s): 2.120 (total time: 38.730) Refine new water occ: r_work=0.1183 r_free=0.1533 adp: r_work=0.1173 r_free=0.1531 occ: r_work=0.1161 r_free=0.1515 adp: r_work=0.1150 r_free=0.1514 occ: r_work=0.1145 r_free=0.1503 adp: r_work=0.1137 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1503 r_work=0.1137 r_free=0.1503 | n_water=448 | time (s): 35.010 (total time: 73.740) Filter (q & B) r_work=0.1141 r_free=0.1506 | n_water=433 | time (s): 1.790 (total time: 75.530) Filter (dist only) r_work=0.1145 r_free=0.1506 | n_water=432 | time (s): 34.580 (total time: 110.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.850151 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.177771 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1134 0.1544 0.0410 0.009 1.0 3.5 0.5 0.0 0 0.925 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 15.44 4.10 4.445 21.134 0.178 4.963 11.20 15.41 4.21 4.653 21.145 0.178 4.954 Individual atomic B min max mean iso aniso Overall: 5.97 101.89 20.96 4.85 1959 0 Protein: 5.97 101.89 16.60 4.85 1519 0 Water: 8.46 68.22 36.03 N/A 432 0 Other: 26.50 48.10 34.89 N/A 8 0 Chain A: 5.97 101.89 18.28 N/A 1732 0 Chain S: 13.76 68.22 41.40 N/A 227 0 Histogram: Values Number of atoms 5.97 - 15.56 1047 15.56 - 25.15 363 25.15 - 34.75 196 34.75 - 44.34 188 44.34 - 53.93 119 53.93 - 63.52 29 63.52 - 73.11 9 73.11 - 82.70 2 82.70 - 92.29 4 92.29 - 101.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1120 r_free=0.1541 r_work=0.1120 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1120 r_free = 0.1541 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1112 r_free = 0.1544 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1112 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.950672 | | target function (ml) not normalized (work): 80369.216630 | | target function (ml) not normalized (free): 4178.739917 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1112 0.1544 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1619 0.1608 0.1869 n_refl.: 17041 remove outliers: r(all,work,free)=0.1619 0.1608 0.1869 n_refl.: 17041 overall B=-0.29 to atoms: r(all,work,free)=0.1600 0.1589 0.1861 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1111 0.1541 n_refl.: 17041 remove outliers: r(all,work,free)=0.1131 0.1110 0.1541 n_refl.: 17040 ======================== 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 93.75 85 5 0.3517 296.771 279.986 0.572 1.003 0.336 11.894-9.307 99.02 97 4 0.1705 488.132 480.613 0.920 1.004 0.333 9.237-7.194 100.00 213 7 0.1719 399.242 398.822 0.992 1.004 0.250 7.162-5.571 100.00 427 22 0.1535 299.632 294.663 0.940 1.004 0.240 5.546-4.326 100.00 867 58 0.0921 411.346 407.520 0.963 1.003 0.211 4.315-3.360 100.00 1859 96 0.0861 391.194 388.660 1.006 1.002 0.211 3.356-2.611 100.00 3867 181 0.1237 256.992 255.058 1.005 1.001 0.171 2.608-2.000 99.99 8818 434 0.1061 167.515 166.295 1.002 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0097 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1110 r_free=0.1541 After: r_work=0.1112 r_free=0.1539 ================================== NQH flips ================================== r_work=0.1112 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1112 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1112 r_free=0.1539 | n_water=432 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1112 r_free=0.1537 | n_water=431 | time (s): 35.620 (total time: 36.310) Filter (q & B) r_work=0.1112 r_free=0.1537 | n_water=431 | time (s): 1.160 (total time: 37.470) Compute maps r_work=0.1112 r_free=0.1537 | n_water=431 | time (s): 0.840 (total time: 38.310) Filter (map) r_work=0.1188 r_free=0.1561 | n_water=329 | time (s): 2.050 (total time: 40.360) Find peaks r_work=0.1188 r_free=0.1561 | n_water=329 | time (s): 0.530 (total time: 40.890) Add new water r_work=0.1319 r_free=0.1671 | n_water=471 | time (s): 1.490 (total time: 42.380) Refine new water occ: r_work=0.1152 r_free=0.1499 adp: r_work=0.1146 r_free=0.1506 occ: r_work=0.1131 r_free=0.1480 adp: r_work=0.1124 r_free=0.1485 occ: r_work=0.1116 r_free=0.1469 adp: r_work=0.1110 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1110 r_free=0.1472 r_work=0.1110 r_free=0.1472 | n_water=471 | time (s): 42.890 (total time: 85.270) Filter (q & B) r_work=0.1116 r_free=0.1488 | n_water=454 | time (s): 1.870 (total time: 87.140) Filter (dist only) r_work=0.1116 r_free=0.1488 | n_water=454 | time (s): 34.550 (total time: 121.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.989036 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.182668 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1126 0.1518 0.0393 0.011 1.1 3.8 0.5 0.0 0 0.995 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.18 3.93 4.557 20.856 0.183 4.947 11.15 15.06 3.91 4.622 20.927 0.183 4.937 Individual atomic B min max mean iso aniso Overall: 5.48 101.04 20.94 4.99 1981 0 Protein: 5.48 101.04 16.34 4.98 1519 0 Water: 8.35 64.54 36.09 N/A 454 0 Other: 26.04 45.64 33.93 N/A 8 0 Chain A: 5.48 101.04 18.00 N/A 1732 0 Chain S: 17.07 64.54 41.34 N/A 249 0 Histogram: Values Number of atoms 5.48 - 15.04 1016 15.04 - 24.59 385 24.59 - 34.15 210 34.15 - 43.70 192 43.70 - 53.26 127 53.26 - 62.82 32 62.82 - 72.37 9 72.37 - 81.93 3 81.93 - 91.49 4 91.49 - 101.04 3 =========================== Idealize ADP of riding H ========================== r_work=0.1115 r_free=0.1506 r_work=0.1115 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1115 r_free = 0.1505 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1509 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1108 r_free= 0.1509 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.932904 | | target function (ml) not normalized (work): 80075.835048 | | target function (ml) not normalized (free): 4160.462693 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1114 0.1367 5.446 5.6322| | 2: 3.63 - 2.88 1.00 2711 122 0.1095 0.1574 5.2222 5.4046| | 3: 2.88 - 2.52 1.00 2681 148 0.1350 0.1625 5.1278 5.1881| | 4: 2.52 - 2.29 1.00 2661 139 0.0939 0.1510 4.6239 4.9235| | 5: 2.29 - 2.13 1.00 2678 122 0.0969 0.1458 4.577 4.864| | 6: 2.13 - 2.00 1.00 2692 117 0.1128 0.1781 4.5714 4.7862| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2810 159 0.95 9.04 1.00 0.96 6350.59| | 2: 3.63 - 2.88 2711 122 0.92 12.77 1.01 0.96 6350.59| | 3: 2.88 - 2.52 2681 148 0.88 18.89 0.99 0.96 6350.59| | 4: 2.52 - 2.29 2661 139 0.93 12.00 1.01 0.97 2096.44| | 5: 2.29 - 2.13 2678 122 0.91 14.05 1.00 0.97 2096.44| | 6: 2.13 - 2.00 2692 117 0.89 16.73 0.99 0.97 2096.44| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2096.44 max = 6350.59 mean = 4245.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.98 mean = 13.88| |phase err.(test): min = 0.00 max = 86.55 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1127 0.1108 0.1509 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1596 0.1588 0.1794 n_refl.: 17040 remove outliers: r(all,work,free)=0.1596 0.1588 0.1794 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1581 0.1572 0.1787 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1128 0.1109 0.1505 n_refl.: 17040 remove outliers: r(all,work,free)=0.1128 0.1109 0.1505 n_refl.: 17040 ======================== 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 93.75 85 5 0.3595 296.771 278.807 0.554 1.002 0.330 11.894-9.307 99.02 97 4 0.1728 488.132 479.756 0.920 1.003 0.330 9.237-7.194 100.00 213 7 0.1755 399.242 400.197 0.992 1.003 0.238 7.162-5.571 100.00 427 22 0.1519 299.632 293.948 0.940 1.003 0.217 5.546-4.326 100.00 867 58 0.0930 411.346 407.469 0.963 1.003 0.202 4.315-3.360 100.00 1859 96 0.0878 391.194 389.028 1.005 1.002 0.191 3.356-2.611 100.00 3867 181 0.1236 256.992 254.780 1.001 1.001 0.161 2.608-2.000 99.99 8818 434 0.1044 167.515 166.221 0.992 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8417 ================= 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 : 0.2795 0.1834 0.082 5.254 8.8 119.3 19.9 258 0.000 1_bss: 0.1617 0.1680 0.082 5.254 8.4 118.9 19.5 258 0.000 1_settarget: 0.1617 0.1680 0.082 5.254 8.4 118.9 19.5 258 0.000 1_nqh: 0.1617 0.1680 0.082 5.254 8.4 118.9 19.5 258 0.000 1_weight: 0.1617 0.1680 0.082 5.254 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1351 0.1636 0.009 0.989 8.4 118.9 19.5 258 0.146 1_adp: 0.1278 0.1656 0.009 0.989 6.0 113.9 20.0 258 0.146 1_regHadp: 0.1281 0.1662 0.009 0.989 6.0 113.9 20.0 258 0.146 1_occ: 0.1277 0.1656 0.009 0.989 6.0 113.9 20.0 258 0.146 2_bss: 0.1276 0.1650 0.009 0.989 5.6 113.5 19.6 258 0.146 2_settarget: 0.1276 0.1650 0.009 0.989 5.6 113.5 19.6 258 0.146 2_updatecdl: 0.1276 0.1650 0.009 1.004 5.6 113.5 19.6 258 0.146 2_nqh: 0.1276 0.1650 0.009 1.004 5.6 113.5 19.6 258 0.146 2_sol: 0.1238 0.1557 0.009 1.004 5.6 113.1 20.9 359 n/a 2_weight: 0.1238 0.1557 0.009 1.004 5.6 113.1 20.9 359 n/a 2_xyzrec: 0.1215 0.1588 0.008 0.933 5.6 113.1 20.9 359 n/a 2_adp: 0.1201 0.1624 0.008 0.933 6.8 108.1 21.5 359 n/a 2_regHadp: 0.1203 0.1624 0.008 0.933 6.8 108.1 21.5 359 n/a 2_occ: 0.1201 0.1626 0.008 0.933 6.8 108.1 21.5 359 n/a 3_bss: 0.1193 0.1618 0.008 0.933 6.4 107.7 21.1 359 n/a 3_settarget: 0.1193 0.1618 0.008 0.933 6.4 107.7 21.1 359 n/a 3_updatecdl: 0.1193 0.1618 0.008 0.929 6.4 107.7 21.1 359 n/a 3_nqh: 0.1193 0.1618 0.008 0.929 6.4 107.7 21.1 359 n/a 3_sol: 0.1200 0.1528 0.008 0.929 6.4 107.7 21.0 390 n/a 3_weight: 0.1200 0.1528 0.008 0.929 6.4 107.7 21.0 390 n/a 3_xyzrec: 0.1173 0.1529 0.009 0.969 6.4 107.7 21.0 390 n/a 3_adp: 0.1153 0.1542 0.009 0.969 6.4 105.7 20.8 390 n/a 3_regHadp: 0.1153 0.1544 0.009 0.969 6.4 105.7 20.8 390 n/a 3_occ: 0.1145 0.1545 0.009 0.969 6.4 105.7 20.8 390 n/a 4_bss: 0.1142 0.1547 0.009 0.969 6.0 105.3 20.4 390 n/a 4_settarget: 0.1142 0.1547 0.009 0.969 6.0 105.3 20.4 390 n/a 4_updatecdl: 0.1142 0.1547 0.009 0.968 6.0 105.3 20.4 390 n/a 4_nqh: 0.1142 0.1547 0.009 0.968 6.0 105.3 20.4 390 n/a 4_sol: 0.1145 0.1506 0.009 0.968 6.0 105.3 20.9 432 n/a 4_weight: 0.1145 0.1506 0.009 0.968 6.0 105.3 20.9 432 n/a 4_xyzrec: 0.1134 0.1544 0.009 0.964 6.0 105.3 20.9 432 n/a 4_adp: 0.1120 0.1541 0.009 0.964 6.0 101.9 21.0 432 n/a 4_regHadp: 0.1120 0.1541 0.009 0.964 6.0 101.9 21.0 432 n/a 4_occ: 0.1112 0.1544 0.009 0.964 6.0 101.9 21.0 432 n/a 5_bss: 0.1110 0.1541 0.009 0.964 5.7 101.6 20.7 432 n/a 5_settarget: 0.1110 0.1541 0.009 0.964 5.7 101.6 20.7 432 n/a 5_updatecdl: 0.1110 0.1541 0.009 0.967 5.7 101.6 20.7 432 n/a 5_setrh: 0.1112 0.1539 0.009 0.967 5.7 101.6 20.7 432 n/a 5_nqh: 0.1112 0.1539 0.009 0.967 5.7 101.6 20.7 432 n/a 5_sol: 0.1116 0.1488 0.009 0.967 5.7 101.6 20.8 454 n/a 5_weight: 0.1116 0.1488 0.009 0.967 5.7 101.6 20.8 454 n/a 5_xyzrec: 0.1126 0.1518 0.011 1.097 5.7 101.6 20.8 454 n/a 5_adp: 0.1115 0.1506 0.011 1.097 5.5 101.0 20.9 454 n/a 5_regHadp: 0.1115 0.1505 0.011 1.097 5.5 101.0 20.9 454 n/a 5_occ: 0.1108 0.1509 0.011 1.097 5.5 101.0 20.9 454 n/a end: 0.1109 0.1505 0.011 1.097 5.2 100.8 20.7 454 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2963595_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2963595_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0600 Refinement macro-cycles (run) : 937.5000 Write final files (write_after_run_outputs) : 19.6800 Total : 960.2400 Total CPU time: 16.36 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:23 PST -0800 (1735494083.22 s) Start R-work = 0.1617, R-free = 0.1680 Final R-work = 0.1109, R-free = 0.1505 =============================================================================== Job complete usr+sys time: 1002.13 seconds wall clock time: 17 minutes 5.33 seconds (1025.33 seconds total)