Starting phenix.refine on Mon May 20 17:17:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4xcr.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4xcr/4xcr.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4xcr/4xcr.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4xcr/4xcr.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4xcr.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4xcr.pdb" } 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 None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Time building chain proxies: 1.19, per 1000 atoms: 0.39 Number of scatterers: 3086 At special positions: 0 Unit cell: (70.8199, 70.8199, 70.01, 90, 90, 120) Space group: P 65 (No. 170) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 308 8.00 N 280 7.00 C 954 6.00 H 1544 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: 2.18 Conformation dependent library (CDL) restraints added in 231.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing sheet with id= A, first strand: chain 'A' and resid 64 through 71 removed outlier: 5.403A pdb=" N VAL A 5 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE A 108 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.804A pdb=" N GLY A 41 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A 43 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= D, first strand: chain 'B' and resid 3 through 9 removed outlier: 3.564A pdb=" N GLY B 33 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 42 through 44 Processing sheet with id= F, first strand: chain 'B' and resid 45 through 47 59 hydrogen bonds defined for protein. 162 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: 1.63 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.10: 1544 1.10 - 1.21: 0 1.21 - 1.33: 308 1.33 - 1.44: 336 1.44 - 1.56: 918 Bond restraints: 3106 Sorted by residual: bond pdb=" N GLY A 104 " pdb=" H GLY A 104 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA A 93 " pdb=" H ALA A 93 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS B 48 " pdb=" H HIS B 48 " 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 10 " pdb=" H GLY A 10 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N SER B 103 " pdb=" H SER B 103 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3101 not shown) Histogram of bond angle deviations from ideal: 102.64 - 108.90: 1201 108.90 - 115.16: 2931 115.16 - 121.42: 737 121.42 - 127.67: 747 127.67 - 133.93: 16 Bond angle restraints: 5632 Sorted by residual: angle pdb=" N HIS A 46 " pdb=" CA HIS A 46 " pdb=" C HIS A 46 " ideal model delta sigma weight residual 108.79 114.62 -5.83 1.53e+00 4.27e-01 1.45e+01 angle pdb=" N ALA B 50 " pdb=" CA ALA B 50 " pdb=" C ALA B 50 " ideal model delta sigma weight residual 108.13 114.63 -6.50 1.72e+00 3.38e-01 1.43e+01 angle pdb=" N HIS B 46 " pdb=" CA HIS B 46 " pdb=" C HIS B 46 " ideal model delta sigma weight residual 109.07 115.09 -6.02 1.61e+00 3.86e-01 1.40e+01 angle pdb=" N THR A 86 " pdb=" CA THR A 86 " pdb=" C THR A 86 " ideal model delta sigma weight residual 108.96 114.59 -5.63 1.59e+00 3.96e-01 1.26e+01 angle pdb=" N ALA A 109 " pdb=" CA ALA A 109 " pdb=" C ALA A 109 " ideal model delta sigma weight residual 112.93 108.80 4.13 1.33e+00 5.65e-01 9.65e+00 ... (remaining 5627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1281 17.29 - 34.57: 82 34.57 - 51.86: 49 51.86 - 69.15: 16 69.15 - 86.44: 2 Dihedral angle restraints: 1430 sinusoidal: 788 harmonic: 642 Sorted by residual: dihedral pdb=" CA HIS B 46 " pdb=" C HIS B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU B 101 " pdb=" C LEU B 101 " pdb=" N ALA B 102 " pdb=" CA ALA B 102 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE B 69 " pdb=" C ILE B 69 " pdb=" N GLU B 70 " pdb=" CA GLU B 70 " ideal model delta harmonic sigma weight residual 180.00 163.32 16.68 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 1427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 152 0.034 - 0.067: 46 0.067 - 0.101: 23 0.101 - 0.135: 17 0.135 - 0.168: 6 Chirality restraints: 244 Sorted by residual: chirality pdb=" CA VAL B 47 " pdb=" N VAL B 47 " pdb=" C VAL B 47 " pdb=" CB VAL B 47 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ILE A 18 " pdb=" N ILE A 18 " pdb=" C ILE A 18 " pdb=" CB ILE A 18 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 241 not shown) Planarity restraints: 494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " -0.000 2.00e-02 2.50e+03 4.94e-03 7.31e-01 pdb=" CG PHE B 20 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 20 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE B 20 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE B 20 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 45 " 0.004 2.00e-02 2.50e+03 4.84e-03 7.02e-01 pdb=" CG PHE A 45 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 45 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 45 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 45 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 45 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 45 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " 0.003 2.00e-02 2.50e+03 3.91e-03 4.58e-01 pdb=" CG PHE A 20 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 20 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 20 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 20 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 20 " -0.001 2.00e-02 2.50e+03 ... (remaining 491 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.08: 144 2.08 - 2.69: 4346 2.69 - 3.29: 8486 3.29 - 3.90: 10882 3.90 - 4.50: 16220 Nonbonded interactions: 40078 Sorted by model distance: nonbonded pdb=" H GLY A 96 " pdb="HD21 ASN B 26 " model vdw sym.op. 1.477 2.100 -x+1,-y+1,z+1/2 nonbonded pdb=" OE2 GLU A 21 " pdb=" HE1 TRP A 32 " model vdw 1.545 1.850 nonbonded pdb=" O LEU B 42 " pdb=" H GLY B 94 " model vdw 1.609 1.850 nonbonded pdb=" H VAL A 47 " pdb=" O GLY A 52 " model vdw 1.623 1.850 nonbonded pdb=" O ASP A 60 " pdb=" H GLY A 63 " model vdw 1.652 1.850 ... (remaining 40073 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: 4 Type Number sf(0) Gaussians O 308 7.97 1 N 280 6.97 1 C 954 5.97 1 H 1544 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: 1544 of 3086 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3086 n_use_u_iso = 1544 n_use_u_aniso = 1542 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 = 3086 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3086 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1544 aniso = 1542) 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 { sheet { first_strand = chain 'A' and resid 64 through 71 sheet_id = " A" strand { selection = chain 'A' and resid 29 through 36 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 35 and name N bond_start_previous = chain 'A' and resid 65 and name O } strand { selection = chain 'A' and resid 15 through 21 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 19 and name N bond_start_previous = chain 'A' and resid 32 and name O } strand { selection = chain 'A' and resid 3 through 9 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 8 and name N bond_start_previous = chain 'A' and resid 16 and name O } strand { selection = chain 'A' and resid 107 through 110 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 110 and name N bond_start_previous = chain 'A' and resid 3 and name O } } sheet { first_strand = chain 'A' and resid 41 through 44 sheet_id = " B" strand { selection = chain 'A' and resid 56 through 59 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 59 and name N bond_start_previous = chain 'A' and resid 41 and name O } } sheet { first_strand = chain 'A' and resid 45 through 47 sheet_id = " C" strand { selection = chain 'A' and resid 86 through 90 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 88 and name N bond_start_previous = chain 'A' and resid 46 and name O } strand { selection = chain 'A' and resid 101 through 105 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 104 and name N bond_start_previous = chain 'A' and resid 87 and name O } } sheet { first_strand = chain 'B' and resid 3 through 9 sheet_id = " D" strand { selection = chain 'B' and resid 15 through 22 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 20 and name N bond_start_previous = chain 'B' and resid 4 and name O } strand { selection = chain 'B' and resid 29 through 36 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 36 and name N bond_start_previous = chain 'B' and resid 15 and name O } strand { selection = chain 'B' and resid 66 through 71 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 71 and name N bond_start_previous = chain 'B' and resid 29 and name O } } sheet { first_strand = chain 'B' and resid 42 through 44 sheet_id = " E" strand { selection = chain 'B' and resid 56 through 58 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 57 and name N bond_start_previous = chain 'B' and resid 43 and name O } } sheet { first_strand = chain 'B' and resid 45 through 47 sheet_id = " F" strand { selection = chain 'B' and resid 86 through 90 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 88 and name N bond_start_previous = chain 'B' and resid 46 and name O } strand { selection = chain 'B' and resid 101 through 105 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 104 and name N bond_start_previous = chain 'B' and resid 87 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "4xcr_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1544 occupancy sum: 1544.00 (% of total atoms 50.09) Rotatable: count: 506 occupancy sum: 506.00 (% of total atoms 16.41) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.60 - 46.13 A, n_refl.=2197 (all), 9.97 % free)-------------| | | | r_work= 0.4859 r_free= 0.4533 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 6.422387 | | target function (ml) not normalized (work): 12703.482032 | | target function (ml) not normalized (free): 1443.643012 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 46.13 - 4.54 0.92 985 109 0.4372 0.4517 6.651 6.749| | 2: 4.53 - 3.60 0.94 993 110 0.5457 0.4551 6.1956 6.4364| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 46.13 - 4.54 985 109 0.66 38.01 0.84 0.99 177349.34| | 2: 4.53 - 3.60 993 110 0.87 20.59 2.01 1.79 35225.25| |alpha: min = 0.37 max = 2.03 mean = 1.39| |beta: min = 27468.29 max = 448438.04 mean = 105999.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 90.00 mean = 29.26| |phase err.(test): min = 0.00 max = 89.63 mean = 29.40| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 1562 Z= 0.351 Angle : 1.074 6.499 2110 Z= 0.704 Chirality : 0.052 0.168 244 Planarity : 0.002 0.012 280 Dihedral : 14.220 86.435 540 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.33 % Favored : 90.74 % Rotamer: Outliers : 3.85 % Allowed : 7.69 % Favored : 88.46 % 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: -4.86 (0.40), residues: 216 helix: None (None), residues: 0 sheet: -2.78 (0.43), residues: 94 loop : -3.71 (0.33), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 100 PHE 0.009 0.003 PHE A 45 TRP 0.004 0.001 TRP B 32 HIS 0.002 0.001 HIS B 80 Individual atomic B min max mean iso aniso Overall: 42.38 96.62 61.74 1.86 1542 0 Protein: 42.38 96.62 61.74 1.86 1542 0 Chain A: 42.38 92.35 59.13 N/A 771 0 Chain B: 46.95 96.62 64.36 N/A 771 0 Histogram: Values Number of atoms 42.38 - 47.80 75 47.80 - 53.23 307 53.23 - 58.65 306 58.65 - 64.08 257 64.08 - 69.50 241 69.50 - 74.92 185 74.92 - 80.35 96 80.35 - 85.77 43 85.77 - 91.20 25 91.20 - 96.62 7 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2197 (all), 9.97 % free)-------------| | | | r_work= 0.4859 r_free= 0.4533 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 6.422387 | | target function (ml) not normalized (work): 12703.482032 | | target function (ml) not normalized (free): 1443.643012 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3070 percent. r_work = 0.4990 r_free = 0.4731 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4964 0.4990 0.4731 n_refl.: 2197 re-set all scales: r(all,work,free)=0.4964 0.4990 0.4731 n_refl.: 2197 remove outliers: r(all,work,free)=0.4926 0.4948 0.4731 n_refl.: 2192 overall B=-12.88 to atoms: r(all,work,free)=0.4430 0.4444 0.4361 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2094 0.2035 0.2627 n_refl.: 2192 remove outliers: r(all,work,free)=0.2094 0.2035 0.2627 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.1851 812.492 781.541 1.249 1.028 0.367 10.083-8.012 89.47 92 10 0.2086 541.003 524.203 1.179 1.018 0.365 8.010-6.369 94.31 180 19 0.2300 513.402 486.339 1.059 1.011 0.363 6.360-5.059 92.00 354 37 0.1977 502.797 476.188 0.934 1.003 0.366 5.057-4.020 93.59 707 82 0.1974 525.069 501.856 0.990 0.990 0.283 4.017-3.602 94.20 556 61 0.2122 381.422 353.384 1.010 0.980 0.255 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.8283 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.033042 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.265339 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2226 0.2722 0.0496 0.002 0.5 1.9 0.9 3.8 0 0.125 0.2186 0.2731 0.0544 0.002 0.5 1.6 0.9 4.5 0 0.250 0.2111 0.2727 0.0616 0.003 0.5 1.6 0.9 4.5 0 0.500 0.1997 0.2769 0.0773 0.004 0.6 3.9 0.9 4.5 0 1.000 0.1905 0.2853 0.0947 0.005 0.7 6.5 1.9 5.8 0 2.000 0.1856 0.2908 0.1052 0.007 0.9 8.4 1.9 7.7 0 3.000 0.1816 0.2950 0.1133 0.008 1.0 12.0 2.8 8.3 0 4.000 0.1776 0.2949 0.1173 0.010 1.1 13.3 3.7 8.3 0 5.000 0.1750 0.2983 0.1233 0.011 1.2 14.3 3.2 9.0 0 6.000 0.1735 0.2975 0.1240 0.012 1.2 17.5 3.2 9.6 0 7.000 0.1716 0.2985 0.1269 0.014 1.3 17.5 2.8 9.6 0 8.000 0.1694 0.2975 0.1281 0.015 1.4 18.2 3.2 10.9 0 9.000 0.1681 0.2986 0.1306 0.016 1.5 18.5 2.8 10.3 0 10.000 0.1740 0.2977 0.1236 0.012 1.2 15.6 3.2 9.0 0 6.517 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2226 0.2722 0.0496 0.002 0.5 1.9 0.9 3.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.26 27.22 4.96 8.919 45.386 0.265 0.065 22.42 27.62 5.20 8.151 45.911 0.008 0.065 21.41 27.40 5.99 8.654 45.640 0.033 0.060 20.77 27.15 6.38 9.252 45.527 0.133 0.057 19.95 27.01 7.06 10.107 45.845 0.265 0.053 18.61 26.88 8.28 12.607 46.814 0.398 0.047 18.33 26.88 8.55 13.353 47.096 0.531 0.046 18.13 26.88 8.75 13.931 47.311 0.663 0.045 17.87 26.90 9.03 14.736 47.664 0.796 0.044 17.36 27.01 9.65 16.551 48.505 0.929 0.041 17.23 27.06 9.83 17.092 48.709 1.061 0.041 17.08 27.11 10.04 17.682 48.942 1.194 0.040 16.90 27.18 10.28 18.426 49.250 1.327 0.039 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.033 Accepted refinement result: 21.41 27.40 5.99 8.654 45.640 0.033 0.060 Individual atomic B min max mean iso aniso Overall: 28.96 81.55 49.38 1.98 1542 0 Protein: 28.96 81.55 49.38 1.98 1542 0 Chain A: 28.96 74.47 46.87 N/A 771 0 Chain B: 32.39 81.55 51.89 N/A 771 0 Histogram: Values Number of atoms 28.96 - 34.21 41 34.21 - 39.47 215 39.47 - 44.73 304 44.73 - 49.99 286 49.99 - 55.25 256 55.25 - 60.51 245 60.51 - 65.77 121 65.77 - 71.03 38 71.03 - 76.29 26 76.29 - 81.55 10 =========================== Idealize ADP of riding H ========================== r_work=0.2141 r_free=0.2740 r_work=0.2127 r_free=0.2697 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2127 r_free= 0.2697 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ls_wunit_k1) (work): 0.059435 | | target function (ls_wunit_k1) not normalized (work): 117.264278 | | target function (ls_wunit_k1) not normalized (free): 21.233489 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2183 0.2127 0.2697 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4464 0.4473 0.4424 n_refl.: 2192 remove outliers: r(all,work,free)=0.4464 0.4473 0.4424 n_refl.: 2192 overall B=3.53 to atoms: r(all,work,free)=0.4599 0.4611 0.4516 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2131 0.2081 0.2590 n_refl.: 2192 remove outliers: r(all,work,free)=0.2131 0.2081 0.2590 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.2049 491.709 474.504 1.112 1.198 0.374 10.083-8.012 89.47 92 10 0.2174 327.408 316.547 1.031 1.152 0.376 8.010-6.369 93.43 180 19 0.2443 310.704 296.440 0.987 1.109 0.373 6.360-5.059 92.00 354 37 0.1964 304.286 289.909 0.927 1.045 0.369 5.057-4.020 93.48 707 82 0.1966 317.764 303.687 1.068 0.943 0.291 4.017-3.602 94.20 556 61 0.2209 230.831 211.576 1.196 0.844 0.273 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.1854 ============================ 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 = 2.041573 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.043149 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2301 0.2804 0.0503 0.002 0.4 2.9 0.9 3.2 0 0.005 0.2216 0.2764 0.0548 0.002 0.4 2.6 1.4 3.2 0 0.014 0.2117 0.2710 0.0593 0.002 0.4 2.3 1.4 3.2 0 0.028 0.2022 0.2664 0.0641 0.002 0.4 2.6 1.4 3.8 0 0.043 0.1969 0.2659 0.0690 0.002 0.5 2.9 1.4 3.8 0 0.057 0.1932 0.2670 0.0737 0.002 0.5 2.9 1.4 3.8 0 0.071 0.1915 0.2682 0.0767 0.002 0.5 2.9 1.4 3.8 0 0.085 0.1906 0.2670 0.0765 0.002 0.5 3.6 0.9 3.8 0 0.099 0.2002 0.2651 0.0649 0.002 0.4 2.3 1.4 3.8 0 0.047 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2002 0.2651 0.0649 0.002 0.4 2.3 1.4 3.8 0 0.047 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.02 26.51 6.49 7.175 57.573 0.043 5.641 21.22 27.47 6.25 7.108 59.027 0.001 5.687 19.67 26.99 7.32 6.886 58.743 0.005 5.616 17.59 26.54 8.95 8.705 58.544 0.022 5.504 17.08 26.59 9.51 9.663 58.758 0.043 5.477 16.82 26.64 9.82 10.409 59.028 0.065 5.461 16.70 26.65 9.95 10.823 59.177 0.086 5.453 16.57 26.67 10.10 11.328 59.373 0.108 5.444 16.48 26.68 10.20 11.740 59.527 0.129 5.438 16.41 26.68 10.27 12.071 59.649 0.151 5.433 16.36 26.69 10.32 12.349 59.753 0.173 5.429 16.14 26.68 10.53 13.652 60.212 0.194 5.413 16.12 26.70 10.58 13.890 60.297 0.216 5.411 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 19.67 26.99 7.32 6.886 58.743 0.005 5.616 Individual atomic B min max mean iso aniso Overall: 32.53 91.16 55.25 2.45 1542 0 Protein: 32.53 91.16 55.25 2.45 1542 0 Chain A: 32.53 91.16 52.45 N/A 771 0 Chain B: 38.96 84.27 58.06 N/A 771 0 Histogram: Values Number of atoms 32.53 - 38.39 67 38.39 - 44.25 139 44.25 - 50.12 281 50.12 - 55.98 350 55.98 - 61.85 328 61.85 - 67.71 212 67.71 - 73.57 104 73.57 - 79.44 42 79.44 - 85.30 16 85.30 - 91.16 3 =========================== Idealize ADP of riding H ========================== r_work=0.1967 r_free=0.2699 r_work=0.1968 r_free=0.2701 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.1968 r_free= 0.2701 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.615872 | | target function (ml) not normalized (work): 11080.114490 | | target function (ml) not normalized (free): 1331.092388 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2040 0.1968 0.2701 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4684 0.4692 0.4650 n_refl.: 2192 remove outliers: r(all,work,free)=0.4684 0.4692 0.4650 n_refl.: 2192 overall B=0.00 to atoms: r(all,work,free)=0.4684 0.4692 0.4650 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2049 0.1977 0.2711 n_refl.: 2192 remove outliers: r(all,work,free)=0.2049 0.1977 0.2711 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.2030 491.709 473.253 1.159 1.117 0.376 10.083-8.012 89.47 92 10 0.2259 327.408 315.655 1.054 1.087 0.380 8.010-6.369 93.43 180 19 0.2436 310.704 296.924 1.023 1.060 0.380 6.360-5.059 92.00 354 37 0.1896 304.286 290.706 0.933 1.023 0.370 5.057-4.020 93.48 707 82 0.1868 317.764 304.489 1.040 0.962 0.280 4.017-3.602 94.20 556 61 0.1948 230.831 213.740 1.118 0.905 0.240 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.7134 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1977 r_free=0.2711 After: r_work=0.1978 r_free=0.2710 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.948661 wxc_scale = 0.034 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.037087 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1987 0.2710 0.0724 0.002 0.5 2.3 1.4 3.8 0 0.007 0.1983 0.2711 0.0727 0.002 0.5 2.3 1.4 3.8 0 0.020 0.1981 0.2713 0.0732 0.002 0.5 2.3 1.4 3.8 0 0.040 0.1979 0.2713 0.0734 0.002 0.5 2.3 1.4 3.8 0 0.059 0.1974 0.2709 0.0735 0.002 0.5 2.3 1.4 3.8 0 0.079 0.1970 0.2704 0.0733 0.002 0.5 2.3 1.4 3.8 0 0.099 0.1963 0.2696 0.0733 0.003 0.5 2.3 1.4 3.8 0 0.119 0.1956 0.2695 0.0739 0.003 0.5 2.3 1.4 3.8 0 0.139 0.1978 0.2712 0.0734 0.002 0.5 2.3 1.4 3.8 0 0.066 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1963 0.2696 0.0733 0.003 0.5 2.3 1.4 3.8 0 0.119 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.63 26.96 7.33 8.058 60.572 0.037 5.614 21.74 27.70 5.96 7.822 63.700 0.001 5.704 19.64 26.88 7.24 8.239 60.754 0.005 5.613 17.50 26.71 9.21 9.096 61.417 0.019 5.500 16.81 26.79 9.98 10.343 61.833 0.037 5.456 16.70 26.81 10.10 10.748 61.897 0.056 5.447 16.50 26.84 10.34 11.424 62.184 0.074 5.433 16.40 26.84 10.44 11.844 62.348 0.093 5.426 16.27 26.88 10.61 12.451 62.582 0.111 5.417 16.21 26.90 10.70 12.843 62.726 0.130 5.412 16.15 26.91 10.75 13.193 62.851 0.148 5.408 16.11 26.92 10.81 13.503 62.961 0.167 5.404 16.07 26.92 10.85 13.794 63.061 0.185 5.401 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: 21.74 27.70 5.96 7.822 63.700 0.001 5.704 Individual atomic B min max mean iso aniso Overall: 50.81 86.16 61.51 1.25 1542 0 Protein: 50.81 86.16 61.51 1.25 1542 0 Chain A: 51.16 86.16 60.40 N/A 771 0 Chain B: 50.81 79.27 62.63 N/A 771 0 Histogram: Values Number of atoms 50.81 - 54.35 41 54.35 - 57.88 352 57.88 - 61.42 507 61.42 - 64.95 274 64.95 - 68.49 187 68.49 - 72.02 136 72.02 - 75.56 31 75.56 - 79.09 9 79.09 - 82.63 3 82.63 - 86.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.2174 r_free=0.2770 r_work=0.2192 r_free=0.2753 ----------X-ray data---------- |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2192 r_free= 0.2753 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 5.711383 | | target function (ml) not normalized (work): 11268.557907 | | target function (ml) not normalized (free): 1316.115867 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 46.13 - 4.54 0.92 980 109 0.2180 0.2731 5.8187 6.0438| | 2: 4.53 - 3.60 0.94 993 110 0.2207 0.2778 5.6055 5.9759| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 46.13 - 4.54 980 109 0.86 20.47 0.98 1.10 17607.22| | 2: 4.53 - 3.60 993 110 0.90 18.15 1.03 1.15 10402.57| |alpha: min = 1.05 max = 1.22 mean = 1.13| |beta: min = 8014.64 max = 23853.75 mean = 13981.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.88| |phase err.(work): min = 0.00 max = 90.00 mean = 19.30| |phase err.(test): min = 0.00 max = 80.98 mean = 18.56| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2247 0.2192 0.2753 n_refl.: 2192 re-set all scales: r(all,work,free)=0.5021 0.5035 0.4878 n_refl.: 2192 remove outliers: r(all,work,free)=0.5021 0.5035 0.4878 n_refl.: 2192 overall B=-5.86 to atoms: r(all,work,free)=0.4800 0.4811 0.4715 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2248 0.2188 0.2804 n_refl.: 2192 remove outliers: r(all,work,free)=0.2248 0.2188 0.2804 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.2073 427.945 414.370 1.201 1.052 0.373 10.083-8.012 89.47 92 10 0.2238 284.950 276.278 1.093 1.035 0.387 8.010-6.369 94.31 180 19 0.2528 270.412 257.416 1.052 1.021 0.392 6.360-5.059 92.00 354 37 0.2150 264.827 250.129 0.919 1.004 0.356 5.057-4.020 93.59 707 82 0.2117 276.557 263.277 1.015 0.975 0.259 4.017-3.602 94.20 556 61 0.2212 200.897 183.630 1.057 0.950 0.244 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=2.1457 ================= 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 : 0.4859 0.4533 0.005 1.074 42.4 96.6 61.7 0 0.000 1_bss: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_settarget: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_weight: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_xyzrec: 0.2226 0.2722 0.002 0.490 29.5 83.7 48.9 0 0.163 1_adp: 0.2141 0.2740 0.002 0.490 29.0 81.6 49.4 0 0.163 1_regHadp: 0.2127 0.2697 0.002 0.490 29.0 81.6 49.4 0 0.163 2_bss: 0.2081 0.2590 0.002 0.490 32.5 85.1 52.9 0 0.163 2_settarget: 0.2081 0.2590 0.002 0.490 32.5 85.1 52.9 0 0.163 2_updatecdl: 0.2081 0.2590 0.003 0.568 32.5 85.1 52.9 0 0.163 2_weight: 0.2081 0.2590 0.003 0.568 32.5 85.1 52.9 0 0.163 2_xyzrec: 0.2002 0.2651 0.002 0.443 32.5 85.1 52.9 0 0.208 2_adp: 0.1967 0.2699 0.002 0.443 32.5 91.2 55.3 0 0.208 2_regHadp: 0.1968 0.2701 0.002 0.443 32.5 91.2 55.3 0 0.208 3_bss: 0.1977 0.2711 0.002 0.443 32.5 91.2 55.3 0 0.208 3_settarget: 0.1977 0.2711 0.002 0.443 32.5 91.2 55.3 0 0.208 3_updatecdl: 0.1977 0.2711 0.002 0.494 32.5 91.2 55.3 0 0.208 3_setrh: 0.1978 0.2710 0.002 0.494 32.5 91.2 55.3 0 0.208 3_weight: 0.1978 0.2710 0.002 0.494 32.5 91.2 55.3 0 0.208 3_xyzrec: 0.1963 0.2696 0.003 0.472 32.5 91.2 55.3 0 0.208 3_adp: 0.2174 0.2770 0.003 0.472 50.8 86.2 61.5 0 0.208 3_regHadp: 0.2192 0.2753 0.003 0.472 50.8 86.2 61.5 0 0.208 end: 0.2188 0.2804 0.003 0.472 44.9 80.3 55.6 0 0.208 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/4xcr_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/4xcr_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.5500 Refinement macro-cycles (run) : 98.6300 Write final files (write_after_run_outputs) : 13.2500 Total : 116.4300 Total CPU time: 2.39 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:26:22 PDT -0700 (1716251182.25 s) Start R-work = 0.2035, R-free = 0.2627 Final R-work = 0.2188, R-free = 0.2804 =============================================================================== Job complete usr+sys time: 151.39 seconds wall clock time: 9 minutes 13.28 seconds (553.28 seconds total)