Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7427252.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_7427252.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7427252.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.71, per 1000 atoms: 0.51 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: 0.33 Conformation dependent library (CDL) restraints added in 107.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 535 0.91 - 1.17: 1114 1.17 - 1.43: 674 1.43 - 1.69: 807 1.69 - 1.95: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 1.236 1.037 0.200 1.15e-02 7.56e+03 3.01e+02 bond pdb=" CA VAL A 146 " pdb=" C VAL A 146 " ideal model delta sigma weight residual 1.522 1.731 -0.209 1.22e-02 6.72e+03 2.95e+02 bond pdb=" CA SER A 83 " pdb=" C SER A 83 " ideal model delta sigma weight residual 1.523 1.742 -0.219 1.35e-02 5.49e+03 2.62e+02 bond pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 1.335 1.531 -0.196 1.23e-02 6.61e+03 2.55e+02 bond pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 1.330 1.112 0.218 1.37e-02 5.33e+03 2.52e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 2991 4.35 - 8.71: 1859 8.71 - 13.06: 731 13.06 - 17.42: 168 17.42 - 21.77: 28 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 106.78 15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" CA MET A 26 " pdb=" C MET A 26 " pdb=" O MET A 26 " ideal model delta sigma weight residual 120.55 105.53 15.02 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 109.59 12.32 9.80e-01 1.04e+00 1.58e+02 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.53 107.45 13.08 1.07e+00 8.73e-01 1.49e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 129.98 -10.78 9.00e-01 1.23e+00 1.43e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 1303 17.39 - 34.77: 124 34.77 - 52.15: 41 52.15 - 69.54: 10 69.54 - 86.92: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual 123.40 145.69 -22.29 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CA GLU A 143 " pdb=" CB GLU A 143 " ideal model delta harmonic sigma weight residual 122.80 143.00 -20.20 0 2.50e+00 1.60e-01 6.53e+01 dihedral pdb=" C THR A 110 " pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual -122.00 -141.74 19.74 0 2.50e+00 1.60e-01 6.23e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.221: 109 0.221 - 0.441: 73 0.441 - 0.661: 43 0.661 - 0.882: 10 0.882 - 1.102: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.42 1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" CA ALA A 79 " pdb=" N ALA A 79 " pdb=" C ALA A 79 " pdb=" CB ALA A 79 " both_signs ideal model delta sigma weight residual False 2.48 1.52 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA PRO A 184 " pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CB PRO A 184 " both_signs ideal model delta sigma weight residual False 2.72 1.75 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.065 2.00e-02 2.50e+03 5.92e-02 1.05e+02 pdb=" CG PHE A 162 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.141 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.056 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.070 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.023 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.005 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.114 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.055 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " -0.001 9.50e-02 1.11e+02 6.73e-02 1.02e+02 pdb=" NE ARG A 28 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.145 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.129 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.020 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 632 2.25 - 2.84: 7612 2.84 - 3.43: 10742 3.43 - 4.01: 15415 4.01 - 4.60: 22181 Nonbonded interactions: 56582 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.667 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.829 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.837 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.841 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.853 2.450 ... (remaining 56577 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_7427252_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= 0.3620 r_free= 0.2021 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475155 | | target function (ml) not normalized (work): 22062.515125 | | target function (ml) not normalized (free): 1146.182006 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3811 0.2211 4.8538 4.9025| | 2: 3.78 - 3.00 1.00 2430 110 0.3386 0.1699 4.0856 4.0911| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.96 0.83 0.13 6618.89| | 2: 3.78 - 3.00 2430 110 0.93 11.43 1.48 0.26 455.71| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 384.91 max = 12072.74 mean = 3581.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.46| |phase err.(test): min = 0.00 max = 89.98 mean = 33.44| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.560 Angle : 5.208 15.963 2118 Z= 3.657 Chirality : 0.383 1.102 243 Planarity : 0.030 0.088 284 Dihedral : 13.827 86.922 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.62 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 30.27 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.44), residues: 224 helix: -2.53 (0.37), residues: 108 sheet: -1.08 (0.81), residues: 28 loop : -0.22 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.024 ARG A 145 TYR 0.084 0.040 TYR A 141 PHE 0.119 0.043 PHE A 162 HIS 0.047 0.024 HIS A 138 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= 0.3620 r_free= 0.2021 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475155 | | target function (ml) not normalized (work): 22062.515125 | | target function (ml) not normalized (free): 1146.182006 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3573 0.3651 0.2122 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3573 0.3651 0.2122 n_refl.: 5182 remove outliers: r(all,work,free)=0.2528 0.2553 0.2122 n_refl.: 5178 overall B=-2.81 to atoms: r(all,work,free)=0.2422 0.2444 0.2079 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1577 0.1575 0.1620 n_refl.: 5178 remove outliers: r(all,work,free)=0.1571 0.1569 0.1620 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3722 453.816 408.205 0.669 1.061 0.401 11.894-9.307 99.02 97 4 0.1823 714.872 695.051 0.943 1.059 0.383 9.237-7.194 100.00 213 7 0.2152 584.623 577.564 0.977 1.052 0.356 7.162-5.571 100.00 427 22 0.2295 438.689 425.047 0.938 1.041 0.298 5.546-4.326 100.00 867 58 0.1440 602.257 595.325 0.984 1.022 0.221 4.315-3.360 100.00 1859 96 0.1314 572.753 566.571 1.056 0.989 0.189 3.356-3.002 100.00 1373 60 0.1608 441.159 432.842 1.061 0.957 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9558 b_overall=-3.5744 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1569 r_free=0.1620 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1570 r_free=0.1625 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.580508 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.730109 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1766 0.0607 0.010 1.0 1.9 0.5 0.0 0 9.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 17.66 6.07 3.013 16.051 1.730 0.018 10.19 17.84 7.65 4.819 16.261 1.730 0.014 Individual atomic B min max mean iso aniso Overall: 2.29 112.18 17.48 5.16 1785 0 Protein: 2.29 112.18 14.78 5.15 1519 0 Water: 4.06 111.49 33.17 N/A 258 0 Other: 16.49 36.12 23.90 N/A 8 0 Chain A: 2.29 112.18 17.48 N/A 1785 0 Histogram: Values Number of atoms 2.29 - 13.28 919 13.28 - 24.27 486 24.27 - 35.26 188 35.26 - 46.25 107 46.25 - 57.24 56 57.24 - 68.23 13 68.23 - 79.21 7 79.21 - 90.20 5 90.20 - 101.19 1 101.19 - 112.18 3 =========================== Idealize ADP of riding H ========================== r_work=0.1019 r_free=0.1784 r_work=0.1013 r_free=0.1789 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1789 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1008 r_free = 0.1774 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1008 r_free= 0.1774 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013781 | | target function (ls_wunit_k1) not normalized (work): 67.842375 | | target function (ls_wunit_k1) not normalized (free): 10.490530 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1008 0.1774 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2085 0.2083 0.2241 n_refl.: 5175 remove outliers: r(all,work,free)=0.2085 0.2083 0.2241 n_refl.: 5175 overall B=-0.91 to atoms: r(all,work,free)=0.2048 0.2044 0.2230 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1051 0.1013 0.1782 n_refl.: 5175 remove outliers: r(all,work,free)=0.1051 0.1013 0.1782 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3205 332.615 322.488 0.711 0.998 0.387 11.894-9.307 99.02 97 4 0.1506 523.950 515.839 0.992 1.001 0.361 9.237-7.194 100.00 213 7 0.1685 428.487 428.332 1.025 1.001 0.325 7.162-5.571 100.00 427 22 0.1615 321.527 317.957 0.983 1.001 0.302 5.546-4.326 100.00 867 58 0.0908 441.411 437.973 0.995 1.001 0.206 4.315-3.360 100.00 1859 96 0.0765 419.787 419.911 1.039 1.000 0.193 3.356-3.002 100.00 1373 60 0.1016 323.338 321.777 1.004 0.999 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.2469 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1013 r_free=0.1782 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1013 r_free=0.1782 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1013 r_free=0.1782 | n_water=258 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.1034 r_free=0.1770 | n_water=249 | time (s): 21.950 (total time: 22.490) Filter (q & B) r_work=0.1034 r_free=0.1767 | n_water=246 | time (s): 1.570 (total time: 24.060) Compute maps r_work=0.1034 r_free=0.1767 | n_water=246 | time (s): 0.550 (total time: 24.610) Filter (map) r_work=0.1345 r_free=0.1834 | n_water=145 | time (s): 1.860 (total time: 26.470) Find peaks r_work=0.1345 r_free=0.1834 | n_water=145 | time (s): 0.590 (total time: 27.060) Add new water r_work=0.1690 r_free=0.2056 | n_water=232 | time (s): 1.720 (total time: 28.780) Refine new water occ: r_work=0.1145 r_free=0.1631 adp: r_work=0.1118 r_free=0.1628 occ: r_work=0.1116 r_free=0.1625 adp: r_work=0.1105 r_free=0.1622 occ: r_work=0.1105 r_free=0.1609 adp: r_work=0.1102 r_free=0.1617 ADP+occupancy (water only), MIN, final r_work=0.1102 r_free=0.1617 r_work=0.1102 r_free=0.1617 | n_water=232 | time (s): 8.480 (total time: 37.260) Filter (q & B) r_work=0.1102 r_free=0.1617 | n_water=232 | time (s): 0.680 (total time: 37.940) Filter (dist only) r_work=0.1114 r_free=0.1606 | n_water=228 | time (s): 17.490 (total time: 55.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.182535 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.864682 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1005 0.1788 0.0782 0.009 1.0 4.2 0.5 0.0 0 11.591 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.05 17.88 7.82 4.593 16.905 2.865 0.014 9.41 18.15 8.74 5.373 17.216 2.865 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.91 16.55 6.38 1755 0 Protein: 0.00 108.91 14.94 6.37 1519 0 Water: 0.00 62.87 27.04 N/A 228 0 Other: 11.67 33.35 23.88 N/A 8 0 Chain A: 0.00 108.91 15.70 N/A 1668 0 Chain S: 2.69 61.21 32.82 N/A 87 0 Histogram: Values Number of atoms 0.00 - 10.89 693 10.89 - 21.78 656 21.78 - 32.67 219 32.67 - 43.57 109 43.57 - 54.46 38 54.46 - 65.35 29 65.35 - 76.24 4 76.24 - 87.13 3 87.13 - 98.02 2 98.02 - 108.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.0941 r_free=0.1815 r_work=0.0938 r_free=0.1819 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0938 r_free = 0.1819 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0938 r_free = 0.1794 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0938 r_free= 0.1794 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011892 | | target function (ls_wunit_k1) not normalized (work): 58.545692 | | target function (ls_wunit_k1) not normalized (free): 10.187905 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0981 0.0938 0.1794 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2120 0.2125 0.2183 n_refl.: 5175 remove outliers: r(all,work,free)=0.2120 0.2125 0.2183 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2120 0.2125 0.2183 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0983 0.0940 0.1791 n_refl.: 5175 remove outliers: r(all,work,free)=0.0981 0.0938 0.1791 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 0.3261 329.837 311.133 0.677 1.004 0.358 11.894-9.307 99.02 97 4 0.1461 523.950 519.668 0.989 1.007 0.350 9.237-7.194 100.00 213 7 0.1446 428.487 427.631 1.019 1.007 0.310 7.162-5.571 100.00 427 22 0.1404 321.527 319.044 0.991 1.006 0.310 5.546-4.326 100.00 867 58 0.0820 441.411 438.539 1.005 1.004 0.240 4.315-3.360 100.00 1859 96 0.0717 419.787 419.783 1.053 1.000 0.200 3.356-3.002 100.00 1373 60 0.0969 323.338 322.222 1.025 0.996 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.0080 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0938 r_free=0.1791 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0938 r_free=0.1791 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0938 r_free=0.1791 | n_water=228 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.0942 r_free=0.1796 | n_water=227 | time (s): 17.790 (total time: 18.440) Filter (q & B) r_work=0.1020 r_free=0.1783 | n_water=224 | time (s): 1.870 (total time: 20.310) Compute maps r_work=0.1020 r_free=0.1783 | n_water=224 | time (s): 0.630 (total time: 20.940) Filter (map) r_work=0.1260 r_free=0.1848 | n_water=153 | time (s): 1.750 (total time: 22.690) Find peaks r_work=0.1260 r_free=0.1848 | n_water=153 | time (s): 0.490 (total time: 23.180) Add new water r_work=0.1622 r_free=0.2123 | n_water=234 | time (s): 1.280 (total time: 24.460) Refine new water occ: r_work=0.1045 r_free=0.1729 adp: r_work=0.1038 r_free=0.1748 occ: r_work=0.1028 r_free=0.1733 adp: r_work=0.1028 r_free=0.1740 occ: r_work=0.1018 r_free=0.1723 adp: r_work=0.1017 r_free=0.1729 ADP+occupancy (water only), MIN, final r_work=0.1017 r_free=0.1729 r_work=0.1017 r_free=0.1729 | n_water=234 | time (s): 9.540 (total time: 34.000) Filter (q & B) r_work=0.1018 r_free=0.1728 | n_water=233 | time (s): 1.390 (total time: 35.390) Filter (dist only) r_work=0.1024 r_free=0.1697 | n_water=229 | time (s): 18.650 (total time: 54.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.099096 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.257768 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 0.0932 0.1799 0.0867 0.011 1.1 4.2 0.5 0.6 0 0.550 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.32 17.99 8.67 5.346 17.725 0.258 5.151 8.90 18.05 9.15 7.268 17.729 0.258 5.061 Individual atomic B min max mean iso aniso Overall: 0.00 108.17 16.33 8.94 1756 0 Protein: 0.00 108.17 15.07 8.92 1519 0 Water: 0.00 57.87 24.40 N/A 229 0 Other: 7.68 36.55 24.33 N/A 8 0 Chain A: 0.00 108.17 15.79 N/A 1659 0 Chain S: 0.00 56.05 25.46 N/A 97 0 Histogram: Values Number of atoms 0.00 - 10.82 694 10.82 - 21.63 641 21.63 - 32.45 240 32.45 - 43.27 109 43.27 - 54.09 36 54.09 - 64.90 18 64.90 - 75.72 11 75.72 - 86.54 2 86.54 - 97.35 3 97.35 - 108.17 2 =========================== Idealize ADP of riding H ========================== r_work=0.0890 r_free=0.1805 r_work=0.0897 r_free=0.1814 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1814 target_work(ml) = 5.066 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0886 r_free = 0.1798 target_work(ml) = 5.059 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0886 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.059114 | | target function (ml) not normalized (work): 24900.961150 | | target function (ml) not normalized (free): 1796.710252 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0932 0.0886 0.1798 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2115 0.2125 0.2121 n_refl.: 5174 remove outliers: r(all,work,free)=0.2115 0.2125 0.2121 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2115 0.2125 0.2121 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0923 0.0877 0.1804 n_refl.: 5174 remove outliers: r(all,work,free)=0.0923 0.0877 0.1804 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 0.3536 329.837 304.220 0.642 0.993 0.367 11.894-9.307 99.02 97 4 0.1762 523.950 510.832 0.950 0.997 0.350 9.237-7.194 100.00 213 7 0.1869 428.487 421.335 0.990 0.999 0.305 7.162-5.571 100.00 427 22 0.1778 321.527 313.607 0.969 1.000 0.300 5.546-4.326 100.00 867 58 0.0905 441.411 436.855 0.984 1.001 0.250 4.315-3.360 100.00 1859 96 0.0584 419.787 419.178 1.038 1.003 0.210 3.356-3.002 100.00 1373 60 0.0614 323.338 322.551 1.012 1.004 0.084 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.5343 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0877 r_free=0.1804 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0877 r_free=0.1802 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0877 r_free=0.1802 | n_water=229 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0884 r_free=0.1814 | n_water=226 | time (s): 18.280 (total time: 18.820) Filter (q & B) r_work=0.0963 r_free=0.1858 | n_water=223 | time (s): 1.910 (total time: 20.730) Compute maps r_work=0.0963 r_free=0.1858 | n_water=223 | time (s): 0.590 (total time: 21.320) Filter (map) r_work=0.1223 r_free=0.1868 | n_water=154 | time (s): 1.740 (total time: 23.060) Find peaks r_work=0.1223 r_free=0.1868 | n_water=154 | time (s): 0.600 (total time: 23.660) Add new water r_work=0.1579 r_free=0.2123 | n_water=239 | time (s): 1.480 (total time: 25.140) Refine new water occ: r_work=0.1015 r_free=0.1789 adp: r_work=0.1011 r_free=0.1789 occ: r_work=0.1002 r_free=0.1771 adp: r_work=0.1001 r_free=0.1780 occ: r_work=0.0992 r_free=0.1761 adp: r_work=0.0991 r_free=0.1768 ADP+occupancy (water only), MIN, final r_work=0.0991 r_free=0.1768 r_work=0.0991 r_free=0.1768 | n_water=239 | time (s): 10.070 (total time: 35.210) Filter (q & B) r_work=0.0992 r_free=0.1771 | n_water=233 | time (s): 1.290 (total time: 36.500) Filter (dist only) r_work=0.1015 r_free=0.1770 | n_water=230 | time (s): 17.900 (total time: 54.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.009420 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.247495 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 0.0917 0.1873 0.0956 0.011 1.0 3.8 0.5 0.6 0 0.505 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.17 18.73 9.56 6.959 17.849 0.247 5.045 8.93 19.14 10.20 8.095 17.943 0.247 4.979 Individual atomic B min max mean iso aniso Overall: 0.00 107.05 16.57 10.48 1757 0 Protein: 0.00 107.05 15.43 10.46 1519 0 Water: 0.00 59.04 23.75 N/A 230 0 Other: 10.46 36.76 25.25 N/A 8 0 Chain A: 0.00 107.05 16.02 N/A 1642 0 Chain S: 0.55 50.02 24.41 N/A 115 0 Histogram: Values Number of atoms 0.00 - 10.71 676 10.71 - 21.41 630 21.41 - 32.12 269 32.12 - 42.82 101 42.82 - 53.53 49 53.53 - 64.23 12 64.23 - 74.94 11 74.94 - 85.64 4 85.64 - 96.35 4 96.35 - 107.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.0893 r_free=0.1914 r_work=0.0897 r_free=0.1922 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1922 target_work(ml) = 4.984 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0883 r_free = 0.1910 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.25 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= 0.0883 r_free= 0.1910 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.975117 | | target function (ml) not normalized (work): 24487.525477 | | target function (ml) not normalized (free): 2078.792912 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0883 0.1910 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2167 0.2174 0.2222 n_refl.: 5174 remove outliers: r(all,work,free)=0.2167 0.2174 0.2222 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2167 0.2174 0.2222 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0881 0.1912 n_refl.: 5174 remove outliers: r(all,work,free)=0.0930 0.0878 0.1912 n_refl.: 5173 ======================== 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 0.3696 332.067 290.411 0.595 0.987 0.336 11.894-9.307 99.02 97 4 0.1912 523.950 510.634 0.957 0.993 0.333 9.237-7.194 100.00 213 7 0.2106 428.487 417.506 1.005 0.996 0.292 7.162-5.571 100.00 427 22 0.2035 321.527 310.499 0.989 0.998 0.284 5.546-4.326 100.00 867 58 0.0967 441.411 435.983 1.008 1.000 0.240 4.315-3.360 100.00 1859 96 0.0549 419.787 419.767 1.075 1.003 0.210 3.356-3.002 100.00 1373 60 0.0473 323.338 323.056 1.052 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.2655 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0878 r_free=0.1912 After: r_work=0.0881 r_free=0.1911 ================================== NQH flips ================================== r_work=0.0881 r_free=0.1911 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN Total number of N/Q/H flips: 1 r_work=0.0885 r_free=0.1910 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0885 r_free=0.1910 | n_water=230 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0909 r_free=0.1908 | n_water=223 | time (s): 17.300 (total time: 17.880) Filter (q & B) r_work=0.1007 r_free=0.1932 | n_water=220 | time (s): 1.780 (total time: 19.660) Compute maps r_work=0.1007 r_free=0.1932 | n_water=220 | time (s): 0.490 (total time: 20.150) Filter (map) r_work=0.1299 r_free=0.2016 | n_water=144 | time (s): 1.690 (total time: 21.840) Find peaks r_work=0.1299 r_free=0.2016 | n_water=144 | time (s): 0.590 (total time: 22.430) Add new water r_work=0.1588 r_free=0.2276 | n_water=216 | time (s): 1.830 (total time: 24.260) Refine new water occ: r_work=0.1046 r_free=0.1893 adp: r_work=0.1039 r_free=0.1898 occ: r_work=0.1033 r_free=0.1887 adp: r_work=0.1032 r_free=0.1890 occ: r_work=0.1027 r_free=0.1879 adp: r_work=0.1027 r_free=0.1879 ADP+occupancy (water only), MIN, final r_work=0.1027 r_free=0.1879 r_work=0.1027 r_free=0.1879 | n_water=216 | time (s): 9.790 (total time: 34.050) Filter (q & B) r_work=0.1027 r_free=0.1883 | n_water=214 | time (s): 1.540 (total time: 35.590) Filter (dist only) r_work=0.1027 r_free=0.1887 | n_water=211 | time (s): 16.040 (total time: 51.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.064597 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.206659 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 0.0946 0.1834 0.0888 0.011 1.1 6.4 0.5 0.6 0 0.532 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.46 18.34 8.88 7.980 18.073 0.207 5.078 9.16 18.45 9.28 8.639 18.163 0.207 5.009 Individual atomic B min max mean iso aniso Overall: 0.00 105.34 16.62 11.17 1738 0 Protein: 0.00 105.34 15.76 11.14 1519 0 Water: 1.08 64.93 22.50 N/A 211 0 Other: 9.26 44.65 25.22 N/A 8 0 Chain A: 0.00 105.34 16.20 N/A 1627 0 Chain S: 1.08 46.62 22.85 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.53 639 10.53 - 21.07 624 21.07 - 31.60 306 31.60 - 42.14 84 42.14 - 52.67 50 52.67 - 63.21 13 63.21 - 73.74 10 73.74 - 84.27 5 84.27 - 94.81 5 94.81 - 105.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.0916 r_free=0.1845 r_work=0.0919 r_free=0.1847 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0919 r_free = 0.1847 target_work(ml) = 5.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0914 r_free = 0.1840 target_work(ml) = 5.010 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0914 r_free= 0.1840 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.009680 | | target function (ml) not normalized (work): 24652.633876 | | target function (ml) not normalized (free): 2029.918448 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2491 142 0.1276 0.1856 5.5478 6.264| | 2: 3.78 - 3.00 1.00 2430 110 0.0473 0.1814 4.4581 10.368| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2491 142 0.91 12.31 1.00 0.98 13200.78| | 2: 3.78 - 3.00 2430 110 0.99 2.23 1.00 1.00 1086.31| |alpha: min = 0.98 max = 1.00 mean = 0.99| |beta: min = 708.62 max = 21771.77 mean = 7218.63| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.51 mean = 7.33| |phase err.(test): min = 0.00 max = 87.88 mean = 7.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0961 0.0914 0.1840 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2163 0.2163 0.2265 n_refl.: 5173 remove outliers: r(all,work,free)=0.2163 0.2163 0.2265 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2163 0.2163 0.2265 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0959 0.0911 0.1853 n_refl.: 5173 remove outliers: r(all,work,free)=0.0959 0.0911 0.1853 n_refl.: 5173 ======================== 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 0.3593 332.067 302.342 0.609 0.983 0.323 11.894-9.307 99.02 97 4 0.1904 523.950 509.463 0.967 0.991 0.318 9.237-7.194 100.00 213 7 0.2170 428.487 417.916 1.007 0.995 0.290 7.162-5.571 100.00 427 22 0.2027 321.527 310.592 0.987 0.997 0.274 5.546-4.326 100.00 867 58 0.1049 441.411 434.808 1.014 0.999 0.260 4.315-3.360 100.00 1859 96 0.0598 419.787 419.568 1.087 1.002 0.220 3.356-3.002 100.00 1373 60 0.0458 323.338 322.625 1.067 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8275 ================= 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 : 0.3620 0.2021 0.084 5.208 8.8 119.3 19.9 258 0.000 1_bss: 0.1569 0.1620 0.084 5.208 6.0 116.5 17.1 258 0.000 1_settarget: 0.1569 0.1620 0.084 5.208 6.0 116.5 17.1 258 0.000 1_nqh: 0.1570 0.1625 0.084 5.208 6.0 116.5 17.1 258 0.003 1_weight: 0.1570 0.1625 0.084 5.208 6.0 116.5 17.1 258 0.003 1_xyzrec: 0.1159 0.1766 0.010 0.988 6.0 116.5 17.1 258 0.196 1_adp: 0.1019 0.1784 0.010 0.988 2.3 112.2 17.5 258 0.196 1_regHadp: 0.1013 0.1789 0.010 0.988 2.3 112.2 17.5 258 0.196 1_occ: 0.1008 0.1774 0.010 0.988 2.3 112.2 17.5 258 0.196 2_bss: 0.1013 0.1782 0.010 0.988 1.4 111.3 16.6 258 0.196 2_settarget: 0.1013 0.1782 0.010 0.988 1.4 111.3 16.6 258 0.196 2_updatecdl: 0.1013 0.1782 0.010 1.023 1.4 111.3 16.6 258 0.196 2_nqh: 0.1013 0.1782 0.010 1.023 1.4 111.3 16.6 258 0.196 2_sol: 0.1114 0.1606 0.010 1.023 1.0 111.3 16.0 228 n/a 2_weight: 0.1114 0.1606 0.010 1.023 1.0 111.3 16.0 228 n/a 2_xyzrec: 0.1005 0.1788 0.009 0.978 1.0 111.3 16.0 228 n/a 2_adp: 0.0941 0.1815 0.009 0.978 0.0 108.9 16.5 228 n/a 2_regHadp: 0.0938 0.1819 0.009 0.978 0.0 108.9 16.5 228 n/a 2_occ: 0.0938 0.1794 0.009 0.978 0.0 108.9 16.5 228 n/a 3_bss: 0.0938 0.1791 0.009 0.978 0.0 108.9 16.5 228 n/a 3_settarget: 0.0938 0.1791 0.009 0.978 0.0 108.9 16.5 228 n/a 3_updatecdl: 0.0938 0.1791 0.009 0.985 0.0 108.9 16.5 228 n/a 3_nqh: 0.0938 0.1791 0.009 0.985 0.0 108.9 16.5 228 n/a 3_sol: 0.1024 0.1697 0.009 0.985 0.0 108.9 16.3 229 n/a 3_weight: 0.1024 0.1697 0.009 0.985 0.0 108.9 16.3 229 n/a 3_xyzrec: 0.0932 0.1799 0.011 1.080 0.0 108.9 16.3 229 n/a 3_adp: 0.0890 0.1805 0.011 1.080 0.0 108.2 16.3 229 n/a 3_regHadp: 0.0897 0.1814 0.011 1.080 0.0 108.2 16.3 229 n/a 3_occ: 0.0886 0.1798 0.011 1.080 0.0 108.2 16.3 229 n/a 4_bss: 0.0877 0.1804 0.011 1.080 0.0 108.2 16.3 229 n/a 4_settarget: 0.0877 0.1804 0.011 1.080 0.0 108.2 16.3 229 n/a 4_updatecdl: 0.0877 0.1804 0.011 1.085 0.0 108.2 16.3 229 n/a 4_nqh: 0.0877 0.1802 0.011 1.085 0.0 108.2 16.3 229 n/a 4_sol: 0.1015 0.1770 0.011 1.085 0.0 108.2 16.4 230 n/a 4_weight: 0.1015 0.1770 0.011 1.085 0.0 108.2 16.4 230 n/a 4_xyzrec: 0.0917 0.1873 0.011 1.032 0.0 108.2 16.4 230 n/a 4_adp: 0.0893 0.1914 0.011 1.032 0.0 107.1 16.6 230 n/a 4_regHadp: 0.0897 0.1922 0.011 1.032 0.0 107.1 16.6 230 n/a 4_occ: 0.0883 0.1910 0.011 1.032 0.0 107.1 16.6 230 n/a 5_bss: 0.0878 0.1912 0.011 1.032 0.0 107.1 16.6 230 n/a 5_settarget: 0.0878 0.1912 0.011 1.032 0.0 107.1 16.6 230 n/a 5_updatecdl: 0.0878 0.1912 0.011 1.035 0.0 107.1 16.6 230 n/a 5_setrh: 0.0881 0.1911 0.011 1.035 0.0 107.1 16.6 230 n/a 5_nqh: 0.0885 0.1910 0.011 1.035 0.0 107.1 16.6 230 n/a 5_sol: 0.1027 0.1887 0.011 1.035 0.0 107.1 16.4 211 n/a 5_weight: 0.1027 0.1887 0.011 1.035 0.0 107.1 16.4 211 n/a 5_xyzrec: 0.0946 0.1834 0.011 1.146 0.0 107.1 16.4 211 n/a 5_adp: 0.0916 0.1845 0.011 1.146 0.0 105.3 16.6 211 n/a 5_regHadp: 0.0919 0.1847 0.011 1.146 0.0 105.3 16.6 211 n/a 5_occ: 0.0914 0.1840 0.011 1.146 0.0 105.3 16.6 211 n/a end: 0.0911 0.1853 0.011 1.146 0.0 105.3 16.6 211 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7427252_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7427252_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4900 Refinement macro-cycles (run) : 485.1500 Write final files (write_after_run_outputs) : 11.2200 Total : 499.8600 Total CPU time: 8.66 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:02 PST -0800 (1735492742.90 s) Start R-work = 0.1569, R-free = 0.1620 Final R-work = 0.0911, R-free = 0.1853 =============================================================================== Job complete usr+sys time: 527.32 seconds wall clock time: 9 minutes 10.84 seconds (550.84 seconds total)