Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2fdq.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2fdq.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2fdq.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4164 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Time building chain proxies: 1.55, per 1000 atoms: 0.37 Number of scatterers: 4164 At special positions: 0 Unit cell: (49.11, 49.11, 130.48, 90, 90, 90) Space group: P 41 (No. 76) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 411 8.00 N 342 7.00 C 1326 6.00 H 2076 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 - 3.50 Amino acid : False - 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: 3.00 Conformation dependent library (CDL) restraints added in 466.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 0 sheets defined 68.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.294A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 35 Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.653A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 84 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 49 through 61 removed outlier: 3.562A pdb=" N LYS B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 84 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.705A pdb=" N GLU C 10 " --> pdb=" O ASP C 6 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 13 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN C 14 " --> pdb=" O GLU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 49 through 60 Processing helix chain 'C' and resid 66 through 84 removed outlier: 3.595A pdb=" N SER C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2076 1.15 - 1.33: 551 1.33 - 1.50: 695 1.50 - 1.68: 863 1.68 - 1.85: 18 Bond restraints: 4203 Sorted by residual: bond pdb=" N LYS A 18 " pdb=" H LYS A 18 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR C 35 " pdb=" H THR C 35 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR B 64 " pdb=" H THR B 64 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 63 " pdb=" H GLY A 63 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE B 5 " pdb=" H PHE B 5 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4198 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.00: 110 106.00 - 113.00: 4926 113.00 - 119.99: 1188 119.99 - 126.99: 1387 126.99 - 133.98: 24 Bond angle restraints: 7635 Sorted by residual: angle pdb=" N GLU C 23 " pdb=" CA GLU C 23 " pdb=" C GLU C 23 " ideal model delta sigma weight residual 111.40 103.42 7.98 1.22e+00 6.72e-01 4.28e+01 angle pdb=" N TRP A 58 " pdb=" CA TRP A 58 " pdb=" C TRP A 58 " ideal model delta sigma weight residual 111.36 104.39 6.97 1.09e+00 8.42e-01 4.09e+01 angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 113.15 105.67 7.48 1.19e+00 7.06e-01 3.95e+01 angle pdb=" N LYS B 82 " pdb=" CA LYS B 82 " pdb=" C LYS B 82 " ideal model delta sigma weight residual 111.03 104.08 6.95 1.11e+00 8.12e-01 3.92e+01 angle pdb=" N LEU C 61 " pdb=" CA LEU C 61 " pdb=" C LEU C 61 " ideal model delta sigma weight residual 113.18 120.69 -7.51 1.21e+00 6.83e-01 3.85e+01 ... (remaining 7630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1730 17.57 - 35.13: 129 35.13 - 52.70: 61 52.70 - 70.26: 22 70.26 - 87.83: 5 Dihedral angle restraints: 1947 sinusoidal: 1056 harmonic: 891 Sorted by residual: dihedral pdb=" CB GLU C 42 " pdb=" CG GLU C 42 " pdb=" CD GLU C 42 " pdb=" OE1 GLU C 42 " ideal model delta sinusoidal sigma weight residual 0.00 87.83 -87.83 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB MET C 24 " pdb=" CG MET C 24 " pdb=" SD MET C 24 " pdb=" CE MET C 24 " ideal model delta sinusoidal sigma weight residual -60.00 -118.10 58.10 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET B 24 " pdb=" CG MET B 24 " pdb=" SD MET B 24 " pdb=" CE MET B 24 " ideal model delta sinusoidal sigma weight residual -60.00 -113.30 53.30 3 1.50e+01 4.44e-03 9.19e+00 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.054: 129 0.054 - 0.107: 96 0.107 - 0.160: 47 0.160 - 0.213: 12 0.213 - 0.266: 7 Chirality restraints: 291 Sorted by residual: chirality pdb=" CA VAL B 36 " pdb=" N VAL B 36 " pdb=" C VAL B 36 " pdb=" CB VAL B 36 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA LEU C 61 " pdb=" N LEU C 61 " pdb=" C LEU C 61 " pdb=" CB LEU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 288 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 55 " -0.115 2.00e-02 2.50e+03 3.52e-02 4.95e+01 pdb=" CG TRP B 55 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 55 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 55 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP B 55 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 55 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 55 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 55 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 55 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 55 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP B 55 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 TRP B 55 " -0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP B 55 " 0.044 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 55 " -0.029 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 55 " -0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP B 55 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.097 2.00e-02 2.50e+03 3.78e-02 4.30e+01 pdb=" CG TYR C 28 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR C 28 " -0.029 2.00e-02 2.50e+03 pdb=" HD2 TYR C 28 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR C 28 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR C 28 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 73 " 0.098 2.00e-02 2.50e+03 3.77e-02 4.27e+01 pdb=" CG TYR B 73 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 73 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 73 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 73 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 73 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 73 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 73 " 0.059 2.00e-02 2.50e+03 pdb=" HD1 TYR B 73 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR B 73 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TYR B 73 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR B 73 " -0.004 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 214 1.98 - 2.63: 5187 2.63 - 3.29: 13314 3.29 - 3.94: 16960 3.94 - 4.60: 25486 Nonbonded interactions: 61161 Sorted by model distance: nonbonded pdb=" HE ARG B 43 " pdb=" OD1 ASP B 56 " model vdw 1.324 1.850 nonbonded pdb=" HB2 ALA A 8 " pdb="HG23 ILE A 74 " model vdw 1.348 2.440 nonbonded pdb=" OE2 GLU B 23 " pdb=" HZ3 LYS B 83 " model vdw 1.372 1.850 nonbonded pdb=" HG2 LYS B 81 " pdb="HD11 ILE B 86 " model vdw 1.385 2.440 nonbonded pdb=" O TYR C 31 " pdb=" HG1 THR C 35 " model vdw 1.428 1.850 ... (remaining 61156 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: 5 Type Number sf(0) Gaussians S 9 15.91 1 O 411 7.97 1 N 342 6.97 1 C 1326 5.97 1 H 2076 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 ===================== Setting occupancies to: 1.000: selected atoms: 2076 of 4164 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4164 n_use_u_iso = 4164 n_use_u_aniso = 0 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 = 4164 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4164 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4164 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 2 through 14 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 21 through 35 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 49 through 61 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 66 through 84 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'B' and resid 2 through 11 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 21 through 35 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 49 through 61 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 66 through 84 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'C' and resid 2 through 14 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'C' and resid 21 through 35 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'C' and resid 49 through 60 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'C' and resid 66 through 84 } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "2fdq_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2076 occupancy sum: 2076.00 (% of total atoms 49.86) Rotatable: count: 531 occupancy sum: 531.00 (% of total atoms 12.75) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 24.56 A, n_refl.=3901 (all), 4.54 % free)-------------| | | | r_work= 0.3367 r_free= 0.3847 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 5.414009 | | target function (ml) not normalized (work): 20161.769398 | | target function (ml) not normalized (free): 955.736830 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 24.56 - 3.50 1.00 3724 177 0.3367 0.3847 5.414 5.3996| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 24.56 - 3.50 3724 177 0.80 27.40 1.00 0.42 10659.71| |alpha: min = 0.23 max = 0.54 mean = 0.42| |beta: min = 3856.36 max = 48303.69 mean = 10659.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.81 mean = 27.40| |phase err.(test): min = 0.00 max = 88.12 mean = 26.74| |-----------------------------------------------------------------------------| ----------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 : 0.009 0.063 2127 Z= 0.584 Angle : 1.450 14.176 2844 Z= 0.982 Chirality : 0.089 0.266 291 Planarity : 0.007 0.042 363 Dihedral : 15.771 87.829 822 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 36.98 Ramachandran Plot: Outliers : 5.56 % Allowed : 25.79 % Favored : 68.65 % Rotamer: Outliers : 0.91 % Allowed : 6.39 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.58 (0.37), residues: 252 helix: -4.70 (0.19), residues: 156 sheet: None (None), residues: 0 loop : -3.42 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG C 43 TYR 0.079 0.021 TYR C 28 PHE 0.033 0.008 PHE C 49 TRP 0.078 0.015 TRP B 55 HIS 0.003 0.002 HIS A 30 Individual atomic B min max mean iso aniso Overall: 20.45 55.43 29.36 1.83 2088 0 Protein: 20.45 55.43 29.36 1.83 2088 0 Chain A: 20.45 53.24 31.53 N/A 696 0 Chain B: 20.45 55.43 28.80 N/A 696 0 Chain C: 20.45 53.74 27.73 N/A 696 0 Histogram: Values Number of atoms 20.45 - 23.95 483 23.95 - 27.45 430 27.45 - 30.94 501 30.94 - 34.44 253 34.44 - 37.94 186 37.94 - 41.44 93 41.44 - 44.94 81 44.94 - 48.43 32 48.43 - 51.93 25 51.93 - 55.43 4 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3901 (all), 4.54 % free)-------------| | | | r_work= 0.3367 r_free= 0.3847 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 5.414009 | | target function (ml) not normalized (work): 20161.769398 | | target function (ml) not normalized (free): 955.736830 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3389 0.3367 0.3847 n_refl.: 3901 re-set all scales: r(all,work,free)=0.3389 0.3367 0.3847 n_refl.: 3901 remove outliers: r(all,work,free)=0.3390 0.3368 0.3847 n_refl.: 3900 overall B=1.29 to atoms: r(all,work,free)=0.3430 0.3408 0.3898 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.2158 0.2170 0.1921 n_refl.: 3900 remove outliers: r(all,work,free)=0.2158 0.2170 0.1921 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1718 879.253 859.871 1.015 1.135 0.339 11.543-9.422 100.00 94 5 0.1500 860.103 832.148 1.071 1.117 0.339 9.405-7.656 100.00 172 7 0.1517 693.173 674.933 1.053 1.097 0.354 7.645-6.234 100.00 300 18 0.2153 507.673 488.103 1.003 1.068 0.357 6.230-5.074 100.00 574 24 0.2379 440.704 420.298 0.982 1.023 0.356 5.067-4.130 100.00 1040 46 0.2173 488.029 470.997 1.068 0.957 0.285 4.129-3.498 99.54 1446 73 0.2378 390.867 374.550 1.143 0.872 0.156 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.8065 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.103823 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.451772 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 0.1675 0.2051 0.0376 0.014 1.2 13.2 2.0 1.8 0 7.052 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.75 20.51 3.76 1.305 30.879 0.452 0.033 16.66 20.58 3.93 1.852 31.018 0.014 0.032 16.11 20.35 4.24 1.825 31.029 0.056 0.030 15.27 19.96 4.69 2.868 31.180 0.226 0.027 14.23 19.64 5.41 5.538 31.602 0.452 0.024 13.83 19.57 5.74 6.884 32.002 0.678 0.022 13.60 19.59 5.99 7.771 32.263 0.904 0.022 13.43 19.59 6.16 8.520 32.487 1.129 0.021 13.15 19.64 6.49 9.912 32.969 1.355 0.020 13.04 19.71 6.67 10.568 33.178 1.581 0.020 12.97 19.76 6.79 11.015 33.305 1.807 0.020 12.91 19.82 6.90 11.419 33.423 2.033 0.019 12.89 19.85 6.96 11.589 33.455 2.259 0.019 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.678 Accepted refinement result: 13.83 19.57 5.74 6.884 32.002 0.678 0.022 Individual atomic B min max mean iso aniso Overall: 16.74 111.63 32.89 6.19 2088 0 Protein: 16.74 111.63 32.89 6.19 2088 0 Chain A: 17.77 85.61 37.47 N/A 696 0 Chain B: 16.74 70.43 31.25 N/A 696 0 Chain C: 16.74 111.63 29.95 N/A 696 0 Histogram: Values Number of atoms 16.74 - 26.23 649 26.23 - 35.72 748 35.72 - 45.21 411 45.21 - 54.70 183 54.70 - 64.19 81 64.19 - 73.67 13 73.67 - 83.16 1 83.16 - 92.65 1 92.65 - 102.14 0 102.14 - 111.63 1 =========================== Idealize ADP of riding H ========================== r_work=0.1383 r_free=0.1957 r_work=0.1356 r_free=0.1951 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1356 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.23 A | | | | normalized target function (ls_wunit_k1) (work): 0.021452 | | target function (ls_wunit_k1) not normalized (work): 79.865630 | | target function (ls_wunit_k1) not normalized (free): 8.456068 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1384 0.1356 0.1951 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3071 0.3020 0.3990 n_refl.: 3900 remove outliers: r(all,work,free)=0.3071 0.3020 0.3990 n_refl.: 3900 overall B=1.29 to atoms: r(all,work,free)=0.3118 0.3067 0.4034 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1386 0.1359 0.1946 n_refl.: 3900 remove outliers: r(all,work,free)=0.1386 0.1359 0.1946 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1135 603.090 598.829 1.082 1.070 0.339 11.543-9.422 100.00 94 5 0.0957 589.954 582.029 1.161 1.059 0.349 9.405-7.656 100.00 172 7 0.0989 475.455 472.061 1.118 1.048 0.348 7.645-6.234 100.00 300 18 0.1415 348.218 345.464 1.050 1.033 0.348 6.230-5.074 100.00 574 24 0.1516 302.284 298.631 0.995 1.007 0.346 5.067-4.130 100.00 1040 46 0.1302 334.744 331.982 1.044 0.971 0.285 4.129-3.498 99.54 1446 73 0.1494 268.100 263.683 1.081 0.923 0.147 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.8039 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.462684 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.043840 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 0.1468 0.1959 0.0491 0.004 0.5 3.8 0.0 0.5 0 0.073 0.1326 0.2024 0.0698 0.008 0.8 7.4 1.2 2.3 0 0.219 0.1242 0.2112 0.0870 0.013 1.2 11.0 2.8 4.1 0 0.439 0.1197 0.2116 0.0918 0.017 1.4 12.2 3.2 5.0 0 0.658 0.1166 0.2146 0.0980 0.020 1.6 14.6 3.6 5.0 0 0.878 0.1144 0.2142 0.0997 0.023 1.8 16.3 4.0 5.0 0 1.097 0.1128 0.2140 0.1012 0.025 1.9 15.9 4.0 5.0 0 1.316 0.1114 0.2153 0.1040 0.028 2.1 20.2 4.8 5.5 0 1.536 0.1186 0.2123 0.0937 0.018 1.5 13.0 3.2 5.0 0 0.731 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1468 0.1959 0.0491 0.004 0.5 3.8 0.0 0.5 0 0.073 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.68 19.59 4.91 6.713 38.324 0.044 5.466 16.74 19.85 3.11 6.429 41.335 0.001 5.597 15.35 19.44 4.09 6.138 39.509 0.005 5.508 13.62 19.00 5.39 7.039 39.455 0.022 5.379 12.90 18.98 6.08 8.938 39.880 0.044 5.320 12.75 19.18 6.43 9.335 39.744 0.066 5.307 12.63 19.35 6.72 9.975 39.858 0.088 5.297 12.51 19.47 6.96 10.694 40.050 0.110 5.286 12.43 19.55 7.12 11.237 40.192 0.132 5.280 12.38 19.64 7.26 11.654 40.301 0.153 5.276 12.33 19.71 7.38 12.066 40.411 0.175 5.272 12.30 19.77 7.46 12.310 40.474 0.197 5.270 12.26 19.83 7.57 12.703 40.581 0.219 5.267 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.022 Accepted refinement result: 13.62 19.00 5.39 7.039 39.455 0.022 5.379 Individual atomic B min max mean iso aniso Overall: 13.03 149.44 36.43 7.17 2088 0 Protein: 13.03 149.44 36.43 7.17 2088 0 Chain A: 18.81 109.90 44.37 N/A 696 0 Chain B: 14.33 84.19 33.03 N/A 696 0 Chain C: 13.03 149.44 31.89 N/A 696 0 Histogram: Values Number of atoms 13.03 - 26.67 585 26.67 - 40.31 852 40.31 - 53.95 390 53.95 - 67.60 166 67.60 - 81.24 83 81.24 - 94.88 8 94.88 - 108.52 2 108.52 - 122.16 1 122.16 - 135.80 0 135.80 - 149.44 1 =========================== Idealize ADP of riding H ========================== r_work=0.1362 r_free=0.1900 r_work=0.1357 r_free=0.1895 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1357 r_free= 0.1895 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.375939 | | target function (ml) not normalized (work): 20014.621341 | | target function (ml) not normalized (free): 1073.577421 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1382 0.1357 0.1895 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3123 0.3076 0.3962 n_refl.: 3900 remove outliers: r(all,work,free)=0.3123 0.3076 0.3962 n_refl.: 3900 overall B=6.42 to atoms: r(all,work,free)=0.3362 0.3315 0.4209 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1384 0.1360 0.1883 n_refl.: 3900 remove outliers: r(all,work,free)=0.1384 0.1360 0.1883 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1269 603.090 604.484 1.081 1.009 0.337 11.543-9.422 100.00 94 5 0.1032 589.954 579.914 1.153 1.007 0.340 9.405-7.656 100.00 172 7 0.0994 475.455 471.401 1.133 1.004 0.347 7.645-6.234 100.00 300 18 0.1388 348.218 345.632 1.067 1.001 0.348 6.230-5.074 100.00 574 24 0.1453 302.284 298.866 0.982 0.995 0.342 5.067-4.130 100.00 1040 46 0.1299 334.744 331.202 1.011 0.986 0.277 4.129-3.498 99.54 1446 73 0.1503 268.100 261.411 1.028 0.974 0.143 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0417 b_overall=2.4065 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1360 r_free=0.1883 After: r_work=0.1360 r_free=0.1883 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.391308 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.034523 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 0.1363 0.1894 0.0531 0.003 0.5 4.3 0.0 0.5 0 0.070 0.1299 0.1888 0.0590 0.008 0.7 4.3 0.0 0.5 0 0.209 0.1196 0.1946 0.0751 0.011 1.3 7.7 0.4 0.5 0 0.417 0.1171 0.1974 0.0803 0.013 1.3 9.4 0.4 1.4 0 0.626 0.1134 0.2010 0.0875 0.016 1.6 10.8 1.2 1.8 0 0.835 0.1141 0.2010 0.0869 0.017 1.6 12.5 0.8 2.3 0 1.043 0.1124 0.2022 0.0898 0.021 1.7 13.7 1.2 3.2 0 1.252 0.1105 0.2040 0.0935 0.022 2.0 13.9 1.6 3.7 0 1.461 0.1159 0.1989 0.0830 0.014 1.4 8.4 0.8 1.4 0 0.696 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1299 0.1888 0.0590 0.008 0.7 4.3 0.0 0.5 0 0.209 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.99 18.88 5.90 7.694 47.456 0.035 5.333 15.92 19.37 3.45 7.784 50.422 0.001 5.531 14.30 19.11 4.81 7.505 48.433 0.004 5.437 12.61 19.31 6.71 7.599 48.132 0.017 5.300 11.97 19.37 7.40 9.310 48.175 0.035 5.238 11.86 19.44 7.58 9.925 48.182 0.052 5.227 11.72 19.56 7.84 10.699 48.377 0.069 5.211 11.69 19.61 7.92 10.981 48.440 0.086 5.208 11.71 19.59 7.89 10.967 48.419 0.104 5.209 11.66 19.70 8.04 11.369 48.547 0.121 5.204 11.62 19.79 8.17 11.763 48.672 0.138 5.201 11.63 19.79 8.16 11.806 48.683 0.155 5.201 11.63 19.79 8.16 11.867 48.702 0.173 5.201 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.004 Accepted refinement result: 14.30 19.11 4.81 7.505 48.433 0.004 5.437 Individual atomic B min max mean iso aniso Overall: 21.88 150.86 44.80 4.67 2088 0 Protein: 21.88 150.86 44.80 4.67 2088 0 Chain A: 31.49 111.32 54.28 N/A 696 0 Chain B: 25.04 85.61 40.66 N/A 696 0 Chain C: 21.88 150.86 39.45 N/A 696 0 Histogram: Values Number of atoms 21.88 - 34.77 497 34.77 - 47.67 938 47.67 - 60.57 352 60.57 - 73.47 223 73.47 - 86.37 68 86.37 - 99.27 6 99.27 - 112.17 3 112.17 - 125.06 0 125.06 - 137.96 0 137.96 - 150.86 1 =========================== Idealize ADP of riding H ========================== r_work=0.1430 r_free=0.1911 r_work=0.1447 r_free=0.1904 ----------X-ray data---------- |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1447 r_free= 0.1904 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.448026 | | target function (ml) not normalized (work): 20283.000305 | | target function (ml) not normalized (free): 1053.301814 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 24.56 - 3.50 1.00 3723 177 0.1447 0.1904 5.448 5.9509| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 24.56 - 3.50 3723 177 0.94 11.91 1.00 1.14 7091.01| |alpha: min = 1.07 max = 1.22 mean = 1.14| |beta: min = 5093.12 max = 13899.10 mean = 7091.01| |figures of merit: min = 0.03 max = 1.00 mean = 0.94| |phase err.(work): min = 0.00 max = 87.61 mean = 11.91| |phase err.(test): min = 0.00 max = 87.24 mean = 11.67| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1468 0.1447 0.1904 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3489 0.3445 0.4296 n_refl.: 3900 remove outliers: r(all,work,free)=0.3489 0.3445 0.4296 n_refl.: 3900 overall B=0.00 to atoms: r(all,work,free)=0.3489 0.3445 0.4296 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1457 0.1435 0.1890 n_refl.: 3900 remove outliers: r(all,work,free)=0.1457 0.1435 0.1890 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1283 524.575 522.752 1.001 1.065 0.340 11.543-9.422 100.00 94 5 0.1002 513.150 506.404 1.081 1.056 0.340 9.405-7.656 100.00 172 7 0.0977 413.557 411.264 1.079 1.045 0.350 7.645-6.234 100.00 300 18 0.1397 302.885 300.508 1.018 1.030 0.350 6.230-5.074 100.00 574 24 0.1499 262.930 259.801 0.964 1.006 0.350 5.067-4.130 100.00 1040 46 0.1403 291.165 287.153 1.017 0.971 0.287 4.129-3.498 99.54 1446 73 0.1627 233.197 227.667 1.081 0.925 0.152 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.8886 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3367 0.3847 0.009 1.450 20.4 55.4 29.4 0 0.000 1_bss: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_settarget: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_weight: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_xyzrec: 0.1675 0.2051 0.014 1.249 21.7 56.7 30.6 0 0.260 1_adp: 0.1383 0.1957 0.014 1.249 16.7 111.6 32.9 0 0.260 1_regHadp: 0.1356 0.1951 0.014 1.249 16.7 111.6 32.9 0 0.260 2_bss: 0.1359 0.1946 0.014 1.249 18.0 112.9 34.2 0 0.260 2_settarget: 0.1359 0.1946 0.014 1.249 18.0 112.9 34.2 0 0.260 2_updatecdl: 0.1359 0.1946 0.014 1.282 18.0 112.9 34.2 0 0.260 2_weight: 0.1359 0.1946 0.014 1.282 18.0 112.9 34.2 0 0.260 2_xyzrec: 0.1468 0.1959 0.004 0.539 18.0 112.9 34.2 0 0.318 2_adp: 0.1362 0.1900 0.004 0.539 13.0 149.4 36.4 0 0.318 2_regHadp: 0.1357 0.1895 0.004 0.539 13.0 149.4 36.4 0 0.318 3_bss: 0.1360 0.1883 0.004 0.539 19.4 155.9 42.8 0 0.318 3_settarget: 0.1360 0.1883 0.004 0.539 19.4 155.9 42.8 0 0.318 3_updatecdl: 0.1360 0.1883 0.004 0.582 19.4 155.9 42.8 0 0.318 3_setrh: 0.1360 0.1883 0.004 0.582 19.4 155.9 42.8 0 0.318 3_weight: 0.1360 0.1883 0.004 0.582 19.4 155.9 42.8 0 0.318 3_xyzrec: 0.1299 0.1888 0.008 0.711 19.4 155.9 42.8 0 0.322 3_adp: 0.1430 0.1911 0.008 0.711 21.9 150.9 44.8 0 0.322 3_regHadp: 0.1447 0.1904 0.008 0.711 21.9 150.9 44.8 0 0.322 end: 0.1435 0.1890 0.008 0.711 21.9 150.9 44.8 0 0.322 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2fdq_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2fdq_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.2900 Refinement macro-cycles (run) : 145.4600 Write final files (write_after_run_outputs) : 15.7300 Total : 167.4800 Total CPU time: 3.29 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:28:55 PDT -0700 (1716251335.18 s) Start R-work = 0.2170, R-free = 0.1921 Final R-work = 0.1435, R-free = 0.1890 =============================================================================== Job complete usr+sys time: 208.99 seconds wall clock time: 11 minutes 50.31 seconds (710.31 seconds total)