Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_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 amber.topology_file_name=4amber_2fdq.prmtop amber.coordinate_file_name=4amber_2fdq.rst7 amber.order_file_name=4amber_2fdq.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_2fdq.prmtop 4amber_2fdq.rst7 4amber_2fdq.order Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_2fdq.pdb" } default_model = "4phenix_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 } amber { use_amber = True topology_file_name = 4amber_2fdq.prmtop coordinate_file_name = 4amber_2fdq.rst7 order_file_name = 4amber_2fdq.order } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/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: 0.50, per 1000 atoms: 0.12 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: 0.76 Conformation dependent library (CDL) restraints added in 85.0 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: 1.15 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: 0.78 Time building geometry restraints manager: 0.87 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: 548 1.33 - 1.50: 697 1.50 - 1.68: 864 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 VAL A 12 " pdb=" H VAL A 12 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+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: 1739 17.57 - 35.13: 119 35.13 - 52.70: 64 52.70 - 70.26: 20 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: 0.62 - 1.42: 12 1.42 - 2.21: 606 2.21 - 3.01: 12393 3.01 - 3.80: 18471 3.80 - 4.60: 29612 Warning: very small nonbonded interaction distances. Nonbonded interactions: 61094 Sorted by model distance: nonbonded pdb=" HD2 HIS B 30 " pdb=" HG SER B 72 " model vdw 0.622 2.100 nonbonded pdb=" HD2 HIS C 30 " pdb=" HG SER C 72 " model vdw 0.911 2.100 nonbonded pdb=" HD2 HIS A 30 " pdb=" HG SER A 72 " model vdw 0.930 2.100 nonbonded pdb=" HG1 THR B 35 " pdb=" H VAL B 36 " model vdw 1.096 2.100 nonbonded pdb=" HG SER A 65 " pdb=" H ASP A 68 " model vdw 1.134 2.100 ... (remaining 61089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_2fdq.prmtop atom order : 4amber_2fdq.order coordinates : 4amber_2fdq.rst7 ===================================== ... ===================================== ============================== 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 } amber { use_amber = True topology_file_name = "4amber_2fdq.prmtop" coordinate_file_name = "4amber_2fdq.rst7" order_file_name = "4amber_2fdq.order" } } output { prefix = "4phenix_2fdq_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== WARNING: failed to analyze molecule topology. Atomic model may be wrong. ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 24.56 A, n_refl.=3901 (all), 4.54 % free)-------------| | | | r_work= 0.3364 r_free= 0.3847 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 5.412919 | | target function (ml) not normalized (work): 20157.708773 | | target function (ml) not normalized (free): 955.492546 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3364 0.3847 5.4129 5.3983| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 27.33 1.00 0.42 10642.75| |alpha: min = 0.23 max = 0.54 mean = 0.42| |beta: min = 3829.30 max = 48370.26 mean = 10642.75| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.72 mean = 27.33| |phase err.(test): min = 0.00 max = 88.17 mean = 26.62| |-----------------------------------------------------------------------------| ----------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= 0.3364 r_free= 0.3847 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 5.412919 | | target function (ml) not normalized (work): 20157.708773 | | target function (ml) not normalized (free): 955.492546 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3387 0.3364 0.3847 n_refl.: 3901 re-set all scales: r(all,work,free)=0.3387 0.3364 0.3847 n_refl.: 3901 remove outliers: r(all,work,free)=0.3388 0.3366 0.3847 n_refl.: 3900 overall B=0.00 to atoms: r(all,work,free)=0.3388 0.3366 0.3847 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.2170 0.2183 0.1907 n_refl.: 3900 remove outliers: r(all,work,free)=0.2170 0.2183 0.1907 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 0.1720 879.157 869.565 1.115 1.055 0.340 11.543-9.422 100.00 94 5 0.1521 860.008 839.050 1.163 1.046 0.340 9.405-7.656 100.00 172 7 0.1529 693.097 680.303 1.121 1.036 0.346 7.645-6.234 100.00 300 18 0.2171 507.617 491.478 1.040 1.023 0.343 6.230-5.074 100.00 574 24 0.2378 440.655 420.498 0.985 1.002 0.336 5.067-4.130 100.00 1040 46 0.2183 487.975 469.656 1.043 0.971 0.290 4.129-3.498 99.54 1446 73 0.2393 390.824 370.689 1.046 0.931 0.160 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.9168 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.733636 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.471414 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 0.1538 0.2361 0.0823 0.019 2.5 2.4 1.2 3.7 1 1.867 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.38 23.61 8.23 1.305 29.588 0.471 0.027 15.31 23.88 8.57 1.861 29.732 0.014 0.027 14.77 23.59 8.82 1.864 29.768 0.059 0.025 13.88 23.10 9.22 2.986 29.994 0.236 0.023 13.05 22.86 9.80 5.029 30.274 0.471 0.020 12.67 22.73 10.06 6.161 30.607 0.707 0.019 12.50 22.71 10.21 6.821 30.782 0.943 0.018 12.19 22.62 10.43 8.131 31.239 1.179 0.018 12.09 22.63 10.54 8.646 31.383 1.414 0.017 11.84 22.59 10.75 10.006 31.896 1.650 0.017 11.72 22.62 10.90 10.793 32.149 1.886 0.016 11.63 22.63 11.00 11.428 32.351 2.121 0.016 11.61 22.64 11.02 11.649 32.392 2.357 0.016 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.014 Accepted refinement result: 15.31 23.88 8.57 1.861 29.732 0.014 0.027 Individual atomic B min max mean iso aniso Overall: 20.55 53.34 29.64 1.26 2088 0 Protein: 20.55 53.34 29.64 1.26 2088 0 Chain A: 22.43 50.73 31.94 N/A 696 0 Chain B: 21.13 50.43 29.03 N/A 696 0 Chain C: 20.55 53.34 27.96 N/A 696 0 Histogram: Values Number of atoms 20.55 - 23.83 292 23.83 - 27.11 484 27.11 - 30.39 510 30.39 - 33.67 383 33.67 - 36.95 199 36.95 - 40.23 117 40.23 - 43.50 53 43.50 - 46.78 32 46.78 - 50.06 15 50.06 - 53.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.1531 r_free=0.2388 r_work=0.1528 r_free=0.2377 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1528 r_free= 0.2377 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ls_wunit_k1) (work): 0.027212 | | target function (ls_wunit_k1) not normalized (work): 101.310021 | | target function (ls_wunit_k1) not normalized (free): 11.254090 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1567 0.1528 0.2377 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3092 0.3034 0.4041 n_refl.: 3900 remove outliers: r(all,work,free)=0.3092 0.3034 0.4041 n_refl.: 3900 overall B=16.54 to atoms: r(all,work,free)=0.3689 0.3635 0.4589 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1543 0.1506 0.2292 n_refl.: 3900 remove outliers: r(all,work,free)=0.1543 0.1506 0.2292 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 0.1051 600.628 603.335 1.023 1.014 0.345 11.543-9.422 100.00 94 5 0.1005 587.547 570.394 1.046 1.011 0.340 9.405-7.656 100.00 172 7 0.1059 473.515 467.588 1.048 1.008 0.349 7.645-6.234 100.00 300 18 0.1471 346.797 343.767 1.007 1.004 0.347 6.230-5.074 100.00 574 24 0.1649 301.050 296.827 0.945 0.996 0.332 5.067-4.130 100.00 1040 46 0.1491 333.378 330.977 1.001 0.987 0.253 4.129-3.498 99.54 1446 73 0.1702 267.006 261.016 1.042 0.974 0.135 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-3.1801 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.611471 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.029916 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 0.1718 0.2256 0.0538 0.014 2.0 0.5 0.8 1.8 0 0.031 0.1470 0.2293 0.0823 0.019 2.5 1.9 1.2 3.7 1 0.092 0.1493 0.2296 0.0802 0.020 2.6 2.6 1.2 3.7 1 0.183 0.1498 0.2296 0.0797 0.020 2.5 2.6 1.2 3.7 1 0.275 0.1466 0.2297 0.0831 0.023 2.6 3.1 1.2 3.7 1 0.367 0.1441 0.2304 0.0863 0.025 2.7 3.1 1.2 3.7 2 0.459 0.1411 0.2300 0.0889 0.028 2.9 3.4 1.2 3.7 2 0.550 0.1418 0.2304 0.0886 0.032 2.8 3.4 1.2 3.7 2 0.642 0.1482 0.2294 0.0812 0.021 2.6 2.9 1.2 3.7 1 0.306 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1718 0.2256 0.0538 0.014 2.0 0.5 0.8 1.8 0 0.031 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.18 22.56 5.38 4.387 49.336 0.030 5.611 17.33 22.98 5.65 4.663 49.924 0.001 5.620 16.07 22.25 6.18 4.597 49.578 0.004 5.543 14.70 21.68 6.98 5.951 49.991 0.015 5.455 14.22 21.62 7.40 7.019 50.311 0.030 5.423 13.98 21.63 7.65 7.798 50.550 0.045 5.406 13.81 21.64 7.83 8.487 50.762 0.060 5.394 13.70 21.67 7.97 9.065 50.927 0.075 5.385 13.61 21.67 8.06 9.582 51.071 0.090 5.378 13.56 21.68 8.12 9.916 51.158 0.105 5.374 13.52 21.71 8.19 10.223 51.241 0.120 5.371 13.38 21.73 8.35 11.342 51.554 0.135 5.359 13.28 21.76 8.48 12.475 51.867 0.150 5.350 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.001 Accepted refinement result: 17.33 22.98 5.65 4.663 49.924 0.001 5.620 Individual atomic B min max mean iso aniso Overall: 38.43 64.88 47.35 0.99 2088 0 Protein: 38.43 64.88 47.35 0.99 2088 0 Chain A: 42.57 62.26 51.56 N/A 696 0 Chain B: 39.04 61.97 45.90 N/A 696 0 Chain C: 38.43 64.88 44.59 N/A 696 0 Histogram: Values Number of atoms 38.43 - 41.07 191 41.07 - 43.72 357 43.72 - 46.36 460 46.36 - 49.01 469 49.01 - 51.65 179 51.65 - 54.30 140 54.30 - 56.94 180 56.94 - 59.59 73 59.59 - 62.23 37 62.23 - 64.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1733 r_free=0.2298 r_work=0.1733 r_free=0.2293 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1733 r_free= 0.2293 coordinate error (max.-lik. estimate): 0.36 A | | | | normalized target function (ml) (work): 5.619696 | | target function (ml) not normalized (work): 20922.128083 | | target function (ml) not normalized (free): 1070.269542 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1759 0.1733 0.2293 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3822 0.3785 0.4394 n_refl.: 3900 remove outliers: r(all,work,free)=0.3822 0.3785 0.4394 n_refl.: 3900 overall B=0.00 to atoms: r(all,work,free)=0.3822 0.3785 0.4394 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1725 0.1700 0.2226 n_refl.: 3900 remove outliers: r(all,work,free)=0.1725 0.1700 0.2226 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 0.1164 473.777 475.411 1.011 1.032 0.345 11.543-9.422 100.00 94 5 0.0967 463.458 457.085 1.070 1.025 0.350 9.405-7.656 100.00 172 7 0.1126 373.510 369.878 1.080 1.019 0.370 7.645-6.234 100.00 300 18 0.1470 273.555 269.526 1.017 1.012 0.370 6.230-5.074 100.00 574 24 0.1796 237.469 233.978 0.957 0.998 0.360 5.067-4.130 100.00 1040 46 0.1725 262.970 258.021 0.997 0.979 0.300 4.129-3.498 99.54 1446 73 0.2000 210.615 204.122 1.034 0.954 0.170 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.8164 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.670994 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.030926 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 0.1749 0.2280 0.0531 0.014 2.0 0.5 0.8 2.3 0 0.034 0.1700 0.2226 0.0526 0.014 2.0 0.5 0.8 1.8 0 0.101 0.1693 0.2231 0.0538 0.015 2.0 0.7 0.8 1.8 0 0.201 0.1633 0.2203 0.0569 0.018 2.1 0.5 0.8 1.8 0 0.302 0.1594 0.2196 0.0602 0.021 2.2 0.5 0.8 1.8 0 0.403 0.1551 0.2203 0.0652 0.025 2.4 0.7 0.8 1.4 0 0.503 0.1597 0.2195 0.0598 0.026 2.2 0.5 0.8 1.8 0 0.604 0.1478 0.2216 0.0739 0.034 2.8 1.4 0.8 1.4 1 0.705 0.1611 0.2204 0.0593 0.019 2.2 0.5 0.8 1.8 0 0.335 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1700 0.2226 0.0526 0.014 2.0 0.5 0.8 1.8 0 0.101 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.00 22.26 5.26 6.755 52.171 0.031 5.367 16.71 21.59 4.88 6.280 52.862 0.001 5.347 15.99 21.94 5.95 6.910 52.219 0.004 5.307 14.37 20.92 6.55 8.105 53.011 0.015 5.196 14.03 21.08 7.05 8.766 53.225 0.031 5.172 13.90 21.24 7.34 9.187 53.340 0.046 5.162 13.79 21.30 7.51 9.624 53.493 0.062 5.154 13.60 21.27 7.67 10.628 53.854 0.077 5.138 13.47 21.29 7.81 11.634 54.176 0.093 5.127 13.43 21.32 7.89 12.036 54.289 0.108 5.124 13.40 21.34 7.94 12.348 54.376 0.124 5.121 13.38 21.38 8.00 12.643 54.458 0.139 5.119 13.36 21.39 8.03 12.904 54.531 0.155 5.117 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.001 Accepted refinement result: 16.71 21.59 4.88 6.280 52.862 0.001 5.347 Individual atomic B min max mean iso aniso Overall: 36.80 80.27 48.73 0.95 2088 0 Protein: 36.80 80.27 48.73 0.95 2088 0 Chain A: 42.85 80.27 57.23 N/A 696 0 Chain B: 38.47 66.03 45.00 N/A 696 0 Chain C: 36.80 65.20 43.95 N/A 696 0 Histogram: Values Number of atoms 36.80 - 41.15 301 41.15 - 45.49 665 45.49 - 49.84 412 49.84 - 54.19 284 54.19 - 58.53 97 58.53 - 62.88 150 62.88 - 67.23 97 67.23 - 71.57 58 71.57 - 75.92 14 75.92 - 80.27 10 =========================== Idealize ADP of riding H ========================== r_work=0.1671 r_free=0.2159 r_work=0.1672 r_free=0.2156 ----------X-ray data---------- |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1672 r_free= 0.2156 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.347651 | | target function (ml) not normalized (work): 19909.305003 | | target function (ml) not normalized (free): 1020.442807 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1672 0.2156 5.3477 5.7652| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 14.77 1.00 1.00 5723.51| |alpha: min = 0.95 max = 1.06 mean = 1.00| |beta: min = 4889.73 max = 7111.41 mean = 5723.51| |figures of merit: min = 0.02 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 88.42 mean = 14.77| |phase err.(test): min = 0.00 max = 83.15 mean = 14.06| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1695 0.1672 0.2156 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3837 0.3799 0.4421 n_refl.: 3900 remove outliers: r(all,work,free)=0.3837 0.3799 0.4421 n_refl.: 3900 overall B=-0.03 to atoms: r(all,work,free)=0.3836 0.3798 0.4420 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1684 0.1661 0.2150 n_refl.: 3900 remove outliers: r(all,work,free)=0.1684 0.1661 0.2150 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 0.1174 473.777 474.579 0.933 1.094 0.340 11.543-9.422 100.00 94 5 0.0958 463.458 456.542 0.997 1.079 0.340 9.405-7.656 100.00 172 7 0.1127 373.510 369.240 1.021 1.064 0.357 7.645-6.234 100.00 300 18 0.1471 273.555 269.488 0.979 1.042 0.360 6.230-5.074 100.00 574 24 0.1755 237.469 234.103 0.955 1.008 0.360 5.067-4.130 100.00 1040 46 0.1687 262.970 258.237 1.023 0.958 0.290 4.129-3.498 99.54 1446 73 0.1931 210.615 204.654 1.116 0.893 0.190 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0072 ================= 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 : 0.3364 0.3847 0.009 1.450 20.4 55.4 29.4 0 0.000 1_bss: 0.2183 0.1907 0.009 1.450 20.4 55.4 29.4 0 0.000 1_settarget: 0.2183 0.1907 0.009 1.450 20.4 55.4 29.4 0 0.000 1_weight: 0.2183 0.1907 0.009 1.450 20.4 55.4 29.4 0 0.000 1_xyzrec: 0.1538 0.2361 0.019 2.533 20.4 55.4 29.4 0 0.420 1_adp: 0.1531 0.2388 0.019 2.533 20.6 53.3 29.6 0 0.420 1_regHadp: 0.1528 0.2377 0.019 2.533 20.6 53.3 29.6 0 0.420 2_bss: 0.1506 0.2292 0.019 2.533 37.1 69.9 46.2 0 0.420 2_settarget: 0.1506 0.2292 0.019 2.533 37.1 69.9 46.2 0 0.420 2_updatecdl: 0.1506 0.2292 0.019 2.526 37.1 69.9 46.2 0 0.420 2_weight: 0.1506 0.2292 0.019 2.526 37.1 69.9 46.2 0 0.420 2_xyzrec: 0.1718 0.2256 0.014 1.960 37.1 69.9 46.2 0 0.482 2_adp: 0.1733 0.2298 0.014 1.960 38.4 64.9 47.3 0 0.482 2_regHadp: 0.1733 0.2293 0.014 1.960 38.4 64.9 47.3 0 0.482 3_bss: 0.1700 0.2226 0.014 1.960 38.4 64.9 47.3 0 0.482 3_settarget: 0.1700 0.2226 0.014 1.960 38.4 64.9 47.3 0 0.482 3_updatecdl: 0.1700 0.2226 0.014 1.965 38.4 64.9 47.3 0 0.482 3_setrh: 0.1700 0.2226 0.014 1.965 38.4 64.9 47.3 0 0.482 3_weight: 0.1700 0.2226 0.014 1.965 38.4 64.9 47.3 0 0.482 3_xyzrec: 0.1700 0.2226 0.014 1.965 38.4 64.9 47.3 0 0.482 3_adp: 0.1671 0.2159 0.014 1.965 36.8 80.3 48.7 0 0.482 3_regHadp: 0.1672 0.2156 0.014 1.965 36.8 80.3 48.7 0 0.482 end: 0.1661 0.2150 0.014 1.965 36.8 80.2 48.7 0 0.482 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2fdq_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2fdq_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.7500 Refinement macro-cycles (run) : 124.5700 Write final files (write_after_run_outputs) : 8.5500 Total : 135.8700 Total CPU time: 2.60 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:35:38 PDT -0700 (1723221338.27 s) Start R-work = 0.2183, R-free = 0.1907 Final R-work = 0.1661, R-free = 0.2150 =============================================================================== Job complete usr+sys time: 161.09 seconds wall clock time: 4 minutes 6.63 seconds (246.63 seconds total)