Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_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 amber.topology_file_name=4amber_4xcr.prmtop amber.coordinate_file_name=4amber_4xcr.rst7 amber.order_file_name=4amber_4xcr.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_4xcr.rst7 4amber_4xcr.prmtop 4amber_4xcr.order 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 = "4phenix_4xcr.pdb" } default_model = "4phenix_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 } amber { use_amber = True topology_file_name = 4amber_4xcr.prmtop coordinate_file_name = 4amber_4xcr.rst7 order_file_name = 4amber_4xcr.order } } Starting job =============================================================================== Symmetric amino acids flipped None 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: 3084 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1542 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "B" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1542 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Time building chain proxies: 0.42, per 1000 atoms: 0.14 Number of scatterers: 3084 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 1542 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: 0.56 Conformation dependent library (CDL) restraints added in 70.8 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: 0.18 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: 0.47 Time building geometry restraints manager: 0.66 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: 1542 1.10 - 1.21: 0 1.21 - 1.33: 308 1.33 - 1.44: 336 1.44 - 1.56: 918 Bond restraints: 3104 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 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 bond pdb=" NE ARG A 85 " pdb=" HE ARG A 85 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N VAL B 67 " pdb=" H VAL B 67 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3099 not shown) Histogram of bond angle deviations from ideal: 102.64 - 108.90: 1205 108.90 - 115.16: 2927 115.16 - 121.42: 737 121.42 - 127.67: 743 127.67 - 133.93: 16 Bond angle restraints: 5628 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 5623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1277 17.29 - 34.57: 85 34.57 - 51.86: 48 51.86 - 69.15: 16 69.15 - 86.44: 2 Dihedral angle restraints: 1428 sinusoidal: 788 harmonic: 640 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 1425 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: 1.03 - 1.73: 11 1.73 - 2.42: 1180 2.42 - 3.11: 9247 3.11 - 3.81: 11416 3.81 - 4.50: 18069 Nonbonded interactions: 39923 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 30 " pdb=" HG SER A 68 " model vdw 1.035 2.100 nonbonded pdb=" HZ1 LYS B 3 " pdb=" O GLN B 110 " model vdw 1.332 2.450 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 2.450 nonbonded pdb=" O LEU B 42 " pdb=" H GLY B 94 " model vdw 1.609 2.450 ... (remaining 39918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_4xcr.prmtop atom order : 4amber_4xcr.order coordinates : 4amber_4xcr.rst7 ===================================== ... ===================================== ============================== 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 1542 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: 1542 of 3084 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3084 n_use_u_iso = 1542 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 = 3084 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3084 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1542 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 } amber { use_amber = True topology_file_name = "4amber_4xcr.prmtop" coordinate_file_name = "4amber_4xcr.rst7" order_file_name = "4amber_4xcr.order" } } output { prefix = "4phenix_4xcr_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: 3.60 - 46.13 A, n_refl.=2197 (all), 9.97 % free)-------------| | | | r_work= 0.4855 r_free= 0.4509 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ml) (work): 6.419256 | | target function (ml) not normalized (work): 12697.287881 | | target function (ml) not normalized (free): 1443.258192 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.4371 0.4488 6.6466 6.7465| | 2: 4.53 - 3.60 0.94 993 110 0.5449 0.4533 6.1937 6.4354| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 37.90 0.84 0.99 176771.07| | 2: 4.53 - 3.60 993 110 0.87 20.55 2.00 1.79 35012.13| |alpha: min = 0.37 max = 2.03 mean = 1.39| |beta: min = 27384.49 max = 448290.27 mean = 105604.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 90.00 mean = 29.19| |phase err.(test): min = 0.00 max = 89.79 mean = 29.32| |-----------------------------------------------------------------------------| ----------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 : 2.92 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 76 47.80 - 53.23 306 53.23 - 58.65 307 58.65 - 64.08 257 64.08 - 69.50 240 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= 0.4855 r_free= 0.4509 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ml) (work): 6.419256 | | target function (ml) not normalized (work): 12697.287881 | | target function (ml) not normalized (free): 1443.258192 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3123 percent. r_work = 0.4986 r_free = 0.4703 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4959 0.4986 0.4703 n_refl.: 2197 re-set all scales: r(all,work,free)=0.4959 0.4986 0.4703 n_refl.: 2197 remove outliers: r(all,work,free)=0.4920 0.4944 0.4703 n_refl.: 2192 overall B=-12.47 to atoms: r(all,work,free)=0.4438 0.4454 0.4343 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2090 0.2033 0.2615 n_refl.: 2192 remove outliers: r(all,work,free)=0.2090 0.2033 0.2615 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 0.1862 812.492 780.517 1.253 1.025 0.366 10.083-8.012 89.47 92 10 0.2093 541.003 522.255 1.185 1.015 0.364 8.010-6.369 94.31 180 19 0.2311 513.402 486.435 1.060 1.008 0.362 6.360-5.059 92.00 354 37 0.1960 502.797 476.901 0.938 1.002 0.365 5.057-4.020 93.59 707 82 0.1974 525.069 501.945 0.991 0.990 0.281 4.017-3.602 94.20 556 61 0.2114 381.422 353.353 1.012 0.981 0.247 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.6763 ============================ 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 = 3.425674 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.259974 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 0.2198 0.2796 0.0598 0.013 2.0 0.3 0.9 3.8 0 0.125 0.2027 0.2841 0.0814 0.014 2.1 0.3 0.9 3.2 0 0.250 0.1881 0.2886 0.1005 0.014 2.2 0.6 1.9 3.8 0 0.500 0.1705 0.2927 0.1222 0.017 2.5 1.6 1.9 5.8 0 1.000 0.1572 0.2897 0.1324 0.021 3.1 3.6 1.9 5.1 3 2.000 0.1631 0.2712 0.1082 0.024 2.7 3.2 1.4 3.8 0 3.000 0.1566 0.2750 0.1185 0.028 3.2 4.9 1.4 4.5 0 4.000 0.1573 0.2718 0.1145 0.031 3.1 4.9 0.9 3.8 0 5.000 0.1556 0.2735 0.1179 0.033 3.3 5.2 0.9 3.8 0 6.000 0.1534 0.2743 0.1208 0.036 3.5 5.8 0.9 4.5 1 7.000 0.1584 0.2700 0.1116 0.035 3.0 5.5 0.9 3.8 0 8.000 0.1622 0.2702 0.1079 0.036 2.8 5.5 0.9 3.8 0 9.000 0.1555 0.2712 0.1156 0.039 3.3 6.2 0.9 3.8 0 10.000 0.1604 0.2926 0.1322 0.020 2.9 3.2 1.9 8.3 2 1.713 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1584 0.2700 0.1116 0.035 3.0 5.5 0.9 3.8 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.84 27.00 11.16 1.320 49.073 0.260 0.033 15.92 27.32 11.40 1.797 49.188 0.008 0.033 15.40 27.21 11.81 1.953 49.214 0.032 0.031 14.67 26.94 12.27 2.552 49.175 0.130 0.029 13.88 26.74 12.86 4.471 49.429 0.260 0.026 13.64 26.71 13.07 5.230 49.583 0.390 0.025 13.44 26.63 13.19 5.967 49.800 0.520 0.025 13.21 26.55 13.33 6.885 50.116 0.650 0.024 13.11 26.48 13.37 7.403 50.276 0.780 0.023 13.02 26.45 13.43 7.842 50.409 0.910 0.023 12.89 26.39 13.51 8.612 50.688 1.040 0.023 12.83 26.37 13.54 8.939 50.781 1.170 0.023 12.82 26.37 13.56 9.022 50.782 1.300 0.022 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.008 Accepted refinement result: 15.92 27.32 11.40 1.797 49.188 0.008 0.033 Individual atomic B min max mean iso aniso Overall: 32.42 81.49 49.50 1.38 1542 0 Protein: 32.42 81.49 49.50 1.38 1542 0 Chain A: 32.42 75.52 47.09 N/A 771 0 Chain B: 35.95 81.49 51.91 N/A 771 0 Histogram: Values Number of atoms 32.42 - 37.33 112 37.33 - 42.24 296 42.24 - 47.14 276 47.14 - 52.05 255 52.05 - 56.96 264 56.96 - 61.86 192 61.86 - 66.77 86 66.77 - 71.68 34 71.68 - 76.59 20 76.59 - 81.49 7 =========================== Idealize ADP of riding H ========================== r_work=0.1592 r_free=0.2732 r_work=0.1595 r_free=0.2726 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.1595 r_free= 0.2726 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.033476 | | target function (ls_wunit_k1) not normalized (work): 66.048394 | | target function (ls_wunit_k1) not normalized (free): 21.205831 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1709 0.1595 0.2726 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4366 0.4368 0.4421 n_refl.: 2192 remove outliers: r(all,work,free)=0.4366 0.4368 0.4421 n_refl.: 2192 overall B=0.00 to atoms: r(all,work,free)=0.4366 0.4368 0.4421 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.1712 0.1599 0.2724 n_refl.: 2192 remove outliers: r(all,work,free)=0.1712 0.1599 0.2724 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 0.1626 474.960 462.384 1.220 1.031 0.366 10.083-8.012 89.47 92 10 0.1549 316.255 311.388 1.170 1.019 0.370 8.010-6.369 93.43 180 19 0.1830 300.120 294.413 1.067 1.013 0.370 6.360-5.059 92.00 354 37 0.1528 293.921 286.053 0.922 1.007 0.360 5.057-4.020 93.48 707 82 0.1516 306.940 299.055 0.978 0.995 0.270 4.017-3.602 94.20 556 61 0.1690 222.968 208.292 0.984 0.987 0.240 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=5.6356 ============================ 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 = 0.719043 wxc_scale = 0.416 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.033957 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 0.1901 0.2918 0.1017 0.014 2.2 0.6 1.4 4.5 0 0.030 0.1632 0.2949 0.1316 0.017 2.7 1.3 1.9 6.4 1 0.090 0.1515 0.2840 0.1324 0.024 3.4 3.6 0.9 5.1 3 0.179 0.1419 0.2941 0.1522 0.027 3.9 8.4 3.2 10.3 8 0.269 0.1374 0.3008 0.1633 0.031 4.4 10.7 5.6 16.0 17 0.359 0.1547 0.2746 0.1199 0.037 3.4 5.8 1.4 3.8 0 0.448 0.1599 0.2724 0.1125 0.035 3.0 5.5 0.9 3.8 0 0.538 0.1599 0.2724 0.1125 0.035 3.0 5.5 0.9 3.8 0 0.627 0.1408 0.2991 0.1582 0.028 4.1 9.7 4.6 13.5 14 0.299 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1599 0.2724 0.1125 0.035 3.0 5.5 0.9 3.8 0 0.538 0.1599 0.2724 0.1125 0.035 3.0 5.5 0.9 3.8 0 0.627 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.99 27.24 11.25 7.108 54.168 0.034 5.415 16.88 28.05 11.17 7.032 55.667 0.001 5.461 15.07 27.16 12.09 7.162 55.081 0.004 5.353 13.60 26.68 13.08 8.539 54.972 0.017 5.244 13.42 26.73 13.32 9.041 54.985 0.034 5.228 13.20 26.70 13.50 9.650 55.229 0.051 5.209 13.09 26.68 13.60 10.067 55.381 0.068 5.199 13.11 26.72 13.61 10.011 55.355 0.085 5.201 13.06 26.72 13.65 10.217 55.435 0.102 5.196 13.03 26.71 13.68 10.383 55.498 0.119 5.193 13.00 26.71 13.71 10.518 55.548 0.136 5.190 12.98 26.71 13.73 10.630 55.590 0.153 5.188 12.97 26.70 13.74 10.724 55.624 0.170 5.187 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: 16.88 28.05 11.17 7.032 55.667 0.001 5.461 Individual atomic B min max mean iso aniso Overall: 43.23 76.49 52.50 1.18 1542 0 Protein: 43.23 76.49 52.50 1.18 1542 0 Chain A: 43.23 70.52 51.01 N/A 771 0 Chain B: 43.56 76.49 53.99 N/A 771 0 Histogram: Values Number of atoms 43.23 - 46.56 131 46.56 - 49.88 392 49.88 - 53.21 438 53.21 - 56.53 288 56.53 - 59.86 169 59.86 - 63.19 73 63.19 - 66.51 24 66.51 - 69.84 10 69.84 - 73.17 15 73.17 - 76.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1688 r_free=0.2805 r_work=0.1694 r_free=0.2803 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.1694 r_free= 0.2803 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 5.464078 | | target function (ml) not normalized (work): 10780.625243 | | target function (ml) not normalized (free): 1364.591294 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1805 0.1694 0.2803 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4555 0.4558 0.4594 n_refl.: 2192 remove outliers: r(all,work,free)=0.4555 0.4558 0.4594 n_refl.: 2192 overall B=-1.12 to atoms: r(all,work,free)=0.4512 0.4514 0.4566 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.1796 0.1682 0.2819 n_refl.: 2192 remove outliers: r(all,work,free)=0.1796 0.1682 0.2819 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 0.1628 474.960 460.629 1.162 1.028 0.362 10.083-8.012 89.47 92 10 0.1632 316.255 311.181 1.114 1.017 0.363 8.010-6.369 93.43 180 19 0.1918 300.120 291.537 1.020 1.010 0.360 6.360-5.059 92.00 354 37 0.1656 293.921 282.956 0.905 1.002 0.353 5.057-4.020 93.48 707 82 0.1595 306.940 299.474 0.996 0.989 0.274 4.017-3.602 94.20 556 61 0.1779 222.968 211.617 1.018 0.979 0.255 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.2449 ============================ 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 = 0.766893 wxc_scale = 0.319 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.032275 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 0.2024 0.2988 0.0965 0.014 2.1 0.3 0.9 3.8 0 0.025 0.1734 0.3113 0.1379 0.016 2.5 1.3 1.9 8.3 0 0.074 0.1630 0.2924 0.1294 0.021 3.0 1.9 0.9 4.5 1 0.147 0.1530 0.2976 0.1447 0.026 3.6 4.2 0.9 5.1 7 0.221 0.1436 0.3032 0.1596 0.028 3.9 8.4 3.2 9.0 11 0.294 0.1422 0.3059 0.1637 0.031 4.2 10.7 4.2 14.1 18 0.368 0.1592 0.2846 0.1254 0.036 3.5 4.9 1.4 3.8 0 0.441 0.1636 0.2825 0.1188 0.037 3.3 5.5 1.4 3.8 0 0.515 0.1518 0.2975 0.1456 0.027 3.7 4.5 0.9 5.1 6 0.245 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1636 0.2825 0.1188 0.037 3.3 5.5 1.4 3.8 0 0.515 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.36 28.25 11.88 7.500 56.696 0.032 5.432 16.29 28.19 11.90 7.561 56.715 0.001 5.426 15.41 28.11 12.70 7.835 56.750 0.004 5.369 13.58 27.09 13.51 9.089 57.865 0.016 5.237 13.50 27.37 13.87 9.399 57.594 0.032 5.229 13.13 27.24 14.11 10.294 58.034 0.048 5.197 13.05 27.28 14.23 10.619 58.122 0.065 5.190 13.12 27.33 14.21 10.470 58.020 0.081 5.196 13.07 27.33 14.26 10.664 58.093 0.097 5.191 13.03 27.32 14.29 10.823 58.150 0.113 5.188 13.01 27.32 14.31 10.949 58.196 0.129 5.185 12.99 27.32 14.33 11.056 58.234 0.145 5.183 12.97 27.32 14.35 11.146 58.266 0.161 5.181 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: 16.29 28.19 11.90 7.561 56.715 0.001 5.426 Individual atomic B min max mean iso aniso Overall: 42.87 74.25 51.42 0.86 1542 0 Protein: 42.87 74.25 51.42 0.86 1542 0 Chain A: 42.87 67.85 49.93 N/A 771 0 Chain B: 43.22 74.25 52.91 N/A 771 0 Histogram: Values Number of atoms 42.87 - 46.01 172 46.01 - 49.15 384 49.15 - 52.29 431 52.29 - 55.42 273 55.42 - 58.56 159 58.56 - 61.70 73 61.70 - 64.84 22 64.84 - 67.98 12 67.98 - 71.11 13 71.11 - 74.25 3 =========================== Idealize ADP of riding H ========================== r_work=0.1629 r_free=0.2819 r_work=0.1628 r_free=0.2819 ----------X-ray data---------- |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.1628 r_free= 0.2819 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ml) (work): 5.425958 | | target function (ml) not normalized (work): 10705.415877 | | target function (ml) not normalized (free): 1380.796336 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1634 0.2917 5.5325 6.4263| | 2: 4.53 - 3.60 0.94 993 110 0.1622 0.2704 5.3209 6.1848| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 13.71 1.00 1.04 8898.81| | 2: 4.53 - 3.60 993 110 0.94 12.49 0.99 1.02 5371.87| |alpha: min = 0.97 max = 1.06 mean = 1.03| |beta: min = 4237.73 max = 12236.85 mean = 7123.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.09| |phase err.(test): min = 0.00 max = 78.92 mean = 13.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1748 0.1628 0.2819 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4506 0.4508 0.4563 n_refl.: 2192 remove outliers: r(all,work,free)=0.4506 0.4508 0.4563 n_refl.: 2192 overall B=0.00 to atoms: r(all,work,free)=0.4506 0.4508 0.4563 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.1743 0.1624 0.2804 n_refl.: 2192 remove outliers: r(all,work,free)=0.1743 0.1624 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 0.1634 474.960 458.097 1.248 1.025 0.370 10.083-8.012 89.47 92 10 0.1600 316.255 309.937 1.165 1.015 0.369 8.010-6.369 93.43 180 19 0.1880 300.120 291.520 1.065 1.009 0.367 6.360-5.059 92.00 354 37 0.1619 293.921 282.923 0.935 1.002 0.360 5.057-4.020 93.48 707 82 0.1530 306.940 299.550 1.025 0.990 0.270 4.017-3.602 94.20 556 61 0.1683 222.968 212.193 1.049 0.981 0.238 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0393 b_overall=1.3347 ================= 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 : 0.4855 0.4509 0.005 1.074 42.4 96.6 61.7 0 0.000 1_bss: 0.2033 0.2615 0.005 1.074 29.9 84.1 49.3 0 0.000 1_settarget: 0.2033 0.2615 0.005 1.074 29.9 84.1 49.3 0 0.000 1_weight: 0.2033 0.2615 0.005 1.074 29.9 84.1 49.3 0 0.000 1_xyzrec: 0.1584 0.2700 0.035 3.046 29.9 84.1 49.3 0 0.075 1_adp: 0.1592 0.2732 0.035 3.046 32.4 81.5 49.5 0 0.075 1_regHadp: 0.1595 0.2726 0.035 3.046 32.4 81.5 49.5 0 0.075 2_bss: 0.1599 0.2724 0.035 3.046 32.4 81.5 49.5 0 0.075 2_settarget: 0.1599 0.2724 0.035 3.046 32.4 81.5 49.5 0 0.075 2_updatecdl: 0.1599 0.2724 0.035 3.048 32.4 81.5 49.5 0 0.075 2_weight: 0.1599 0.2724 0.035 3.048 32.4 81.5 49.5 0 0.075 2_xyzrec: 0.1599 0.2724 0.035 3.048 32.4 81.5 49.5 0 0.075 2_adp: 0.1688 0.2805 0.035 3.048 43.2 76.5 52.5 0 0.075 2_regHadp: 0.1694 0.2803 0.035 3.048 43.2 76.5 52.5 0 0.075 3_bss: 0.1682 0.2819 0.035 3.048 42.1 75.4 51.4 0 0.075 3_settarget: 0.1682 0.2819 0.035 3.048 42.1 75.4 51.4 0 0.075 3_updatecdl: 0.1682 0.2819 0.035 3.048 42.1 75.4 51.4 0 0.075 3_setrh: 0.1682 0.2819 0.035 3.048 42.1 75.4 51.4 0 0.075 3_weight: 0.1682 0.2819 0.035 3.048 42.1 75.4 51.4 0 0.075 3_xyzrec: 0.1636 0.2825 0.037 3.279 42.1 75.4 51.4 0 0.082 3_adp: 0.1629 0.2819 0.037 3.279 42.9 74.3 51.4 0 0.082 3_regHadp: 0.1628 0.2819 0.037 3.279 42.9 74.3 51.4 0 0.082 end: 0.1624 0.2804 0.037 3.279 42.9 74.3 51.4 0 0.082 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_4xcr_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_4xcr_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 1.9800 Refinement macro-cycles (run) : 87.0800 Write final files (write_after_run_outputs) : 5.7500 Total : 94.8100 Total CPU time: 115.43 seconds =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:36:06 PDT -0700 (1723221366.71 s) Start R-work = 0.2033, R-free = 0.2615 Final R-work = 0.1624, R-free = 0.2804 =============================================================================== Job complete usr+sys time: 118.27 seconds wall clock time: 4 minutes 32.86 seconds (272.86 seconds total)