Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_3fm7.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.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_3fm7.prmtop amber.coordinate_file_name=4amber_3fm7.rst7 amber.order_file_name=4amber_3fm7.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_3fm7.order 4amber_3fm7.prmtop 4amber_3fm7.rst7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_3fm7.pdb" } default_model = "4phenix_3fm7.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.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_3fm7.prmtop coordinate_file_name = 4amber_3fm7.rst7 order_file_name = 4amber_3fm7.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: 6837 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1598 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1609 Classifications: {'peptide': 104} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 23} Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain: "E" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1380 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1380 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Time building chain proxies: 0.78, per 1000 atoms: 0.11 Number of scatterers: 6837 At special positions: 0 Unit cell: (115.79, 115.79, 90.5004, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 666 8.00 N 569 7.00 C 2187 6.00 H 3393 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: 1.18 Conformation dependent library (CDL) restraints added in 138.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 4 sheets defined 28.5% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.750A pdb=" N LYS A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 53 removed outlier: 5.803A pdb=" N ASN A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR A 41 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 42 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS A 48 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 51 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 53 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 removed outlier: 4.854A pdb=" N THR B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 48 removed outlier: 4.661A pdb=" N ASN B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASN B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.637A pdb=" N GLU E 30 " --> pdb=" O THR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 50 Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.603A pdb=" N GLN F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 49 Processing sheet with id= A, first strand: chain 'A' and resid 60 through 69 removed outlier: 3.531A pdb=" N MET A 68 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 101 " --> pdb=" O MET A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 59 through 69 Processing sheet with id= C, first strand: chain 'E' and resid 54 through 59 removed outlier: 6.114A pdb=" N TYR E 77 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE E 8 " --> pdb=" O TYR E 77 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 54 through 59 removed outlier: 6.889A pdb=" N TYR F 77 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE F 8 " --> pdb=" O TYR F 77 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 366 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: 1.10 Time building geometry restraints manager: 1.35 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: 3381 1.15 - 1.31: 591 1.31 - 1.48: 1393 1.48 - 1.64: 1508 1.64 - 1.81: 32 Bond restraints: 6905 Sorted by residual: bond pdb=" NE2 GLN F 27 " pdb="HE21 GLN F 27 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N SER B 80 " pdb=" H SER B 80 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG E 60 " pdb="HH22 ARG E 60 " 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 E 66 " pdb=" H VAL E 66 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU A 55 " pdb=" H GLU A 55 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6900 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 230 107.50 - 114.12: 8500 114.12 - 120.73: 1545 120.73 - 127.35: 2142 127.35 - 133.97: 26 Bond angle restraints: 12443 Sorted by residual: angle pdb=" C ASN F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta sigma weight residual 119.89 122.75 -2.86 1.02e+00 9.61e-01 7.84e+00 angle pdb=" N VAL E 7 " pdb=" CA VAL E 7 " pdb=" C VAL E 7 " ideal model delta sigma weight residual 106.72 111.14 -4.42 1.59e+00 3.96e-01 7.74e+00 angle pdb=" N ASN C 119 " pdb=" CA ASN C 119 " pdb=" C ASN C 119 " ideal model delta sigma weight residual 107.61 112.16 -4.55 1.74e+00 3.30e-01 6.84e+00 angle pdb=" N ASN E 10 " pdb=" CA ASN E 10 " pdb=" C ASN E 10 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.71e+00 angle pdb=" CA GLY A 72 " pdb=" C GLY A 72 " pdb=" N ALA A 73 " ideal model delta sigma weight residual 118.67 116.19 2.48 9.80e-01 1.04e+00 6.40e+00 ... (remaining 12438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 2913 26.78 - 53.56: 281 53.56 - 80.34: 52 80.34 - 107.12: 4 107.12 - 133.91: 2 Dihedral angle restraints: 3252 sinusoidal: 1731 harmonic: 1521 Sorted by residual: dihedral pdb=" CA MET F 13 " pdb=" C MET F 13 " pdb=" N SER F 14 " pdb=" CA SER F 14 " ideal model delta harmonic sigma weight residual 180.00 46.09 133.91 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" CA ASN C 114 " pdb=" C ASN C 114 " pdb=" N VAL C 115 " pdb=" CA VAL C 115 " ideal model delta harmonic sigma weight residual 180.00 52.83 127.17 0 5.00e+00 4.00e-02 6.47e+02 dihedral pdb=" CA MET E 13 " pdb=" C MET E 13 " pdb=" N SER E 14 " pdb=" CA SER E 14 " ideal model delta harmonic sigma weight residual -180.00 -75.18 -104.82 0 5.00e+00 4.00e-02 4.39e+02 ... (remaining 3249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 437 0.022 - 0.043: 11 0.043 - 0.065: 19 0.065 - 0.087: 59 0.087 - 0.108: 13 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA ASN D 114 " pdb=" N ASN D 114 " pdb=" C ASN D 114 " pdb=" CB ASN D 114 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.93e-01 chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.09 2.00e-01 2.50e+01 2.10e-01 chirality pdb=" CA ILE B 23 " pdb=" N ILE B 23 " pdb=" C ILE B 23 " pdb=" CB ILE B 23 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.04e-01 ... (remaining 536 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 46 " 0.000 2.00e-02 2.50e+03 8.24e-04 2.04e-02 pdb=" CG PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE F 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 40 " -0.000 2.00e-02 2.50e+03 7.01e-04 1.97e-02 pdb=" CG TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP B 40 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 40 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 54 " -0.000 2.00e-02 2.50e+03 6.55e-04 1.72e-02 pdb=" CG TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP E 54 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP E 54 " 0.000 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 0.66 - 1.45: 47 1.45 - 2.23: 1219 2.23 - 3.02: 19441 3.02 - 3.81: 30456 3.81 - 4.60: 48178 Warning: very small nonbonded interaction distances. Nonbonded interactions: 99341 Sorted by model distance: nonbonded pdb=" HG1 THR E 67 " pdb=" HZ1 LYS F 43 " model vdw 0.657 2.100 nonbonded pdb=" HA ASN C 114 " pdb="HG23 VAL C 115 " model vdw 0.746 2.440 nonbonded pdb=" HG1 THR B 92 " pdb=" HG SER B 105 " model vdw 0.788 2.100 nonbonded pdb=" HG1 THR A 77 " pdb=" HG1 THR C 118 " model vdw 0.814 2.100 nonbonded pdb=" HG3 GLN C 133 " pdb=" HB3 LYS F 36 " model vdw 0.848 2.440 ... (remaining 99336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_3fm7.prmtop atom order : 4amber_3fm7.order coordinates : 4amber_3fm7.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 22 15.91 1 O 666 7.97 1 N 569 6.97 1 C 2187 5.97 1 H 3393 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: 3393 of 6837 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6837 n_use_u_iso = 6837 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 = 6837 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6837 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 6837 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 12 through 22 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 34 through 53 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'B' and resid 13 through 26 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'B' and resid 34 through 48 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'E' and resid 16 through 31 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'E' and resid 35 through 50 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'F' and resid 16 through 31 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'F' and resid 35 through 49 } sheet { first_strand = chain 'A' and resid 60 through 69 sheet_id = " A" strand { selection = chain 'A' and resid 100 through 109 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 109 and name N bond_start_previous = chain 'A' and resid 60 and name O } strand { selection = chain 'A' and resid 89 through 96 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 95 and name N bond_start_previous = chain 'A' and resid 102 and name O } } sheet { first_strand = chain 'B' and resid 59 through 69 sheet_id = " B" strand { selection = chain 'B' and resid 100 through 110 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 109 and name N bond_start_previous = chain 'B' and resid 60 and name O } strand { selection = chain 'B' and resid 89 through 94 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 93 and name N bond_start_previous = chain 'B' and resid 104 and name O } } sheet { first_strand = chain 'E' and resid 54 through 59 sheet_id = " C" strand { selection = chain 'E' and resid 81 through 87 sense = parallel *antiparallel unknown bond_start_current = chain 'E' and resid 86 and name N bond_start_previous = chain 'E' and resid 55 and name O } strand { selection = chain 'E' and resid 73 through 78 sense = parallel *antiparallel unknown bond_start_current = chain 'E' and resid 78 and name N bond_start_previous = chain 'E' and resid 81 and name O } strand { selection = chain 'E' and resid 6 through 12 sense = parallel *antiparallel unknown bond_start_current = chain 'E' and resid 12 and name N bond_start_previous = chain 'E' and resid 73 and name O } } sheet { first_strand = chain 'F' and resid 54 through 59 sheet_id = " D" strand { selection = chain 'F' and resid 81 through 87 sense = parallel *antiparallel unknown bond_start_current = chain 'F' and resid 86 and name N bond_start_previous = chain 'F' and resid 55 and name O } strand { selection = chain 'F' and resid 73 through 78 sense = parallel *antiparallel unknown bond_start_current = chain 'F' and resid 78 and name N bond_start_previous = chain 'F' and resid 81 and name O } strand { selection = chain 'F' and resid 6 through 12 sense = parallel *antiparallel unknown bond_start_current = chain 'F' and resid 12 and name N bond_start_previous = chain 'F' and resid 73 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_3fm7.prmtop" coordinate_file_name = "4amber_3fm7.rst7" order_file_name = "4amber_3fm7.order" } } output { prefix = "4phenix_3fm7_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 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3572 r_free= 0.3827 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431399 | | target function (ml) not normalized (work): 50647.270436 | | target function (ml) not normalized (free): 5712.577760 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1358 142 0.4106 0.4304 7.4386 7.4069| | 2: 6.35 - 5.05 1.00 1326 136 0.3187 0.3413 6.6875 6.7641| | 3: 5.04 - 4.41 1.00 1320 143 0.3184 0.3219 6.3284 6.4624| | 4: 4.41 - 4.01 0.99 1291 153 0.3398 0.3700 6.1287 6.4147| | 5: 4.01 - 3.72 0.99 1285 148 0.3352 0.4070 5.9733 6.2415| | 6: 3.72 - 3.50 0.99 1295 148 0.3850 0.4163 5.9743 6.1592| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1358 142 0.52 50.28 0.82 0.72 438474.05| | 2: 6.35 - 5.05 1326 136 0.56 47.26 1.23 0.89 199272.70| | 3: 5.04 - 4.41 1320 143 0.78 29.05 1.38 1.01 71169.56| | 4: 4.41 - 4.01 1291 153 0.71 34.64 1.41 1.00 52684.75| | 5: 4.01 - 3.72 1285 148 0.62 42.31 1.34 0.96 45102.05| | 6: 3.72 - 3.50 1295 148 0.64 41.12 1.46 0.94 40619.02| |alpha: min = 0.72 max = 1.01 mean = 0.92| |beta: min = 40619.02 max = 438474.05 mean = 143771.55| |figures of merit: min = 0.00 max = 1.00 mean = 0.64| |phase err.(work): min = 0.00 max = 89.98 mean = 40.84| |phase err.(test): min = 0.00 max = 89.52 mean = 40.45| |-----------------------------------------------------------------------------| ----------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 : 0.003 0.016 3512 Z= 0.194 Angle : 0.846 4.753 4762 Z= 0.586 Chirality : 0.032 0.108 539 Planarity : 0.000 0.001 601 Dihedral : 23.554 133.906 1264 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 44.43 Ramachandran Plot: Outliers : 4.77 % Allowed : 13.60 % Favored : 81.62 % Rotamer: Outliers : 25.33 % Allowed : 17.15 % Favored : 57.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 2.64 % 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: -5.75 (0.30), residues: 419 helix: -4.63 (0.19), residues: 131 sheet: -1.47 (0.57), residues: 92 loop : -4.46 (0.27), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 60 TYR 0.001 0.000 TYR F 65 PHE 0.001 0.000 PHE F 46 TRP 0.001 0.000 TRP B 40 HIS 0.000 0.000 HIS A 76 Individual atomic B min max mean iso aniso Overall: 2.00 500.00 94.66 89.80 3444 0 Protein: 2.00 500.00 94.66 89.80 3444 0 Chain A: 2.00 500.00 114.65 N/A 807 0 Chain B: 2.00 458.88 97.81 N/A 813 0 Chain C: 2.00 495.15 104.99 N/A 215 0 Chain D: 2.00 500.00 119.77 N/A 215 0 Chain E: 2.00 478.28 71.82 N/A 697 0 Chain F: 2.00 403.25 79.76 N/A 697 0 Histogram: Values Number of atoms 2.00 - 51.80 934 51.80 - 101.60 1312 101.60 - 151.40 657 151.40 - 201.20 310 201.20 - 251.00 111 251.00 - 300.80 57 300.80 - 350.60 34 350.60 - 400.40 17 400.40 - 450.20 6 450.20 - 500.00 6 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3572 r_free= 0.3827 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431399 | | target function (ml) not normalized (work): 50647.270436 | | target function (ml) not normalized (free): 5712.577760 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3588 0.3572 0.3827 n_refl.: 8745 re-set all scales: r(all,work,free)=0.3588 0.3572 0.3827 n_refl.: 8745 remove outliers: r(all,work,free)=0.3584 0.3569 0.3813 n_refl.: 8739 overall B=16.89 to atoms: r(all,work,free)=0.4188 0.4198 0.4170 n_refl.: 8739 bulk-solvent and scaling: r(all,work,free)=0.2235 0.2135 0.3142 n_refl.: 8739 remove outliers: r(all,work,free)=0.2229 0.2129 0.3142 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3558 1472.214 1327.718 1.202 0.994 0.325 15.490-12.512 99.01 89 11 0.2182 1305.894 1249.161 1.075 0.993 0.284 12.419-9.967 99.48 175 15 0.1807 1475.876 1427.569 1.143 0.995 0.280 9.933-7.985 99.73 337 34 0.1933 1108.105 1067.433 1.155 0.992 0.265 7.976-6.403 100.00 631 64 0.2451 609.743 573.187 1.078 0.989 0.230 6.399-5.132 99.93 1234 135 0.2163 578.003 550.253 0.978 0.983 0.184 5.129-4.115 99.81 2357 259 0.1734 559.459 548.538 0.999 0.973 0.114 4.114-3.501 98.83 2959 341 0.2470 337.934 327.523 1.066 0.960 0.037 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0046 b_overall=-0.2698 ============================ 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 = 4.351057 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.128878 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 0.2372 0.3328 0.0955 0.014 2.2 1.3 2.9 14.0 1 0.125 0.2208 0.3301 0.1093 0.013 2.1 1.3 3.1 15.6 1 0.250 0.2077 0.3280 0.1203 0.014 2.2 2.6 2.6 17.4 1 0.500 0.1948 0.3250 0.1302 0.015 2.4 4.8 3.3 16.1 1 1.000 0.1840 0.3252 0.1412 0.019 2.8 8.2 4.3 22.2 2 2.000 0.1786 0.3255 0.1469 0.022 3.1 12.2 4.8 23.2 4 3.000 0.1750 0.3261 0.1511 0.024 3.4 15.3 5.5 23.7 8 4.000 0.1719 0.3275 0.1555 0.027 3.7 18.6 6.0 25.1 10 5.000 0.1699 0.3283 0.1585 0.029 4.0 19.8 6.0 25.1 13 6.000 0.1682 0.3297 0.1614 0.032 4.4 23.6 7.4 27.7 19 7.000 0.1661 0.3319 0.1659 0.034 4.5 24.1 6.9 25.9 19 8.000 0.1650 0.3308 0.1659 0.036 4.8 27.0 8.1 29.3 27 9.000 0.1638 0.3325 0.1687 0.038 5.0 27.9 8.1 29.8 29 10.000 0.1831 0.3248 0.1417 0.019 2.8 9.8 4.1 22.2 3 2.176 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1831 0.3248 0.1417 0.019 2.8 9.8 4.1 22.2 3 2.176 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.31 32.48 14.17 64.045 110.129 0.129 0.041 24.62 32.60 7.99 46.529 119.620 0.004 0.067 24.28 32.46 8.18 46.596 119.462 0.016 0.065 23.27 32.06 8.78 46.830 119.099 0.064 0.061 22.11 31.65 9.54 47.359 118.390 0.129 0.056 21.31 31.41 10.10 47.830 117.975 0.193 0.052 20.68 31.26 10.59 48.333 117.557 0.258 0.049 20.14 31.15 11.01 48.850 117.144 0.322 0.047 19.71 31.06 11.35 49.344 116.776 0.387 0.046 19.28 30.98 11.70 49.976 116.215 0.451 0.044 19.57 31.07 11.49 49.644 117.470 0.516 0.045 19.23 31.02 11.79 50.097 117.066 0.580 0.044 18.95 31.01 12.06 50.501 116.756 0.644 0.043 max suggested for this run: 22.03 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.004 Accepted refinement result: 24.62 32.60 7.99 46.529 119.620 0.004 0.067 Individual atomic B min max mean iso aniso Overall: 64.76 511.89 130.39 57.12 3444 0 Protein: 64.76 511.89 130.39 57.12 3444 0 Chain A: 79.91 511.89 151.79 N/A 807 0 Chain B: 79.71 470.77 133.27 N/A 813 0 Chain C: 75.61 507.04 143.92 N/A 215 0 Chain D: 80.07 511.89 154.78 N/A 215 0 Chain E: 64.76 490.17 106.29 N/A 697 0 Chain F: 73.23 415.14 114.66 N/A 697 0 Histogram: Values Number of atoms 64.76 - 109.47 1487 109.47 - 154.19 1268 154.19 - 198.90 399 198.90 - 243.61 144 243.61 - 288.32 61 288.32 - 333.04 36 333.04 - 377.75 26 377.75 - 422.46 14 422.46 - 467.17 3 467.17 - 511.89 6 =========================== Idealize ADP of riding H ========================== r_work=0.2462 r_free=0.3260 r_work=0.2551 r_free=0.3235 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2551 r_free= 0.3235 coordinate error (max.-lik. estimate): 0.16 A | | | | normalized target function (ls_wunit_k1) (work): 0.071062 | | target function (ls_wunit_k1) not normalized (work): 559.187483 | | target function (ls_wunit_k1) not normalized (free): 109.190671 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2619 0.2551 0.3235 n_refl.: 8738 re-set all scales: r(all,work,free)=0.5204 0.5230 0.4978 n_refl.: 8738 remove outliers: r(all,work,free)=0.5204 0.5230 0.4978 n_refl.: 8738 overall B=-31.10 to atoms: r(all,work,free)=0.4095 0.4104 0.4082 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2295 0.2206 0.3113 n_refl.: 8738 remove outliers: r(all,work,free)=0.2295 0.2206 0.3113 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.2792 635.426 606.829 1.320 0.951 0.325 15.490-12.512 99.01 89 11 0.1531 563.640 557.852 1.211 0.953 0.292 12.419-9.967 99.48 175 15 0.1373 637.006 624.022 1.247 0.958 0.277 9.933-7.985 99.73 337 34 0.1410 478.272 468.558 1.261 0.962 0.266 7.976-6.403 100.00 631 64 0.2138 263.173 253.717 1.120 0.968 0.222 6.399-5.132 99.93 1234 135 0.2100 249.473 240.890 0.995 0.977 0.179 5.129-4.115 99.81 2357 259 0.2023 241.469 236.299 1.006 0.990 0.132 4.114-3.501 98.83 2959 341 0.3057 145.857 138.904 0.995 1.007 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.3319 ============================ 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 = 1.568364 wxc_scale = 0.051 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.038114 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 0.2840 0.3296 0.0456 0.014 2.1 0.7 2.9 13.5 1 0.008 0.2634 0.3188 0.0554 0.014 2.2 1.3 2.9 14.8 1 0.024 0.2507 0.3123 0.0616 0.014 2.2 1.3 3.1 14.8 1 0.048 0.2405 0.3115 0.0710 0.014 2.2 1.8 3.1 15.0 1 0.072 0.2319 0.3075 0.0756 0.014 2.2 1.8 2.9 17.7 1 0.096 0.2263 0.3063 0.0800 0.014 2.3 2.5 3.1 17.4 1 0.120 0.2245 0.3056 0.0811 0.014 2.3 2.8 3.1 17.7 2 0.143 0.2212 0.3050 0.0837 0.014 2.4 3.2 3.3 17.2 2 0.167 0.2361 0.3081 0.0719 0.014 2.2 1.8 2.6 17.2 1 0.080 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2212 0.3050 0.0837 0.014 2.4 3.2 3.3 17.2 2 0.167 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.12 30.50 8.37 45.156 110.870 0.038 5.607 28.13 31.31 3.19 33.246 126.656 0.001 5.651 26.65 30.55 3.90 32.909 125.402 0.005 5.640 23.91 29.35 5.44 33.919 122.120 0.019 5.621 22.24 28.89 6.64 36.315 119.627 0.038 5.582 21.30 28.84 7.54 38.386 117.563 0.057 5.559 20.82 28.94 8.12 39.828 116.214 0.076 5.549 20.52 29.05 8.53 40.623 114.767 0.095 5.544 20.39 29.10 8.71 41.327 114.211 0.114 5.542 20.32 29.19 8.87 41.842 113.871 0.133 5.542 20.26 29.24 8.97 42.240 113.664 0.152 5.542 20.24 29.29 9.05 42.555 113.505 0.172 5.542 20.22 29.33 9.11 42.806 113.413 0.191 5.543 max suggested for this run: 22.17 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 26.65 30.55 3.90 32.909 125.402 0.005 5.640 Individual atomic B min max mean iso aniso Overall: 58.62 475.79 128.14 34.51 3444 0 Protein: 58.62 475.79 128.14 34.51 3444 0 Chain A: 92.01 475.79 153.78 N/A 807 0 Chain B: 75.72 434.67 131.73 N/A 813 0 Chain C: 71.40 470.94 144.56 N/A 215 0 Chain D: 73.00 475.79 154.08 N/A 215 0 Chain E: 58.80 454.07 100.17 N/A 697 0 Chain F: 58.62 379.04 109.17 N/A 697 0 Histogram: Values Number of atoms 58.62 - 100.33 1000 100.33 - 142.05 1429 142.05 - 183.77 710 183.77 - 225.49 177 225.49 - 267.20 58 267.20 - 308.92 28 308.92 - 350.64 20 350.64 - 392.35 14 392.35 - 434.07 3 434.07 - 475.79 5 =========================== Idealize ADP of riding H ========================== r_work=0.2665 r_free=0.3055 r_work=0.2702 r_free=0.3008 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2702 r_free= 0.3008 coordinate error (max.-lik. estimate): 0.13 A | | | | normalized target function (ml) (work): 5.648686 | | target function (ml) not normalized (work): 44449.511656 | | target function (ml) not normalized (free): 4990.721131 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2732 0.2702 0.3008 n_refl.: 8738 re-set all scales: r(all,work,free)=0.5210 0.5249 0.4873 n_refl.: 8738 remove outliers: r(all,work,free)=0.5210 0.5249 0.4873 n_refl.: 8738 overall B=-19.84 to atoms: r(all,work,free)=0.4501 0.4532 0.4251 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2496 0.2446 0.2960 n_refl.: 8738 remove outliers: r(all,work,free)=0.2496 0.2446 0.2960 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3254 635.426 581.768 1.225 0.983 0.336 15.490-12.512 99.01 89 11 0.1696 563.640 551.604 1.218 0.983 0.318 12.419-9.967 99.48 175 15 0.1513 637.006 618.498 1.155 0.987 0.281 9.933-7.985 99.73 337 34 0.1625 478.272 463.817 1.186 0.988 0.267 7.976-6.403 100.00 631 64 0.2699 263.173 246.520 1.111 0.989 0.232 6.399-5.132 99.93 1234 135 0.2518 249.473 236.231 0.986 0.991 0.175 5.129-4.115 99.81 2357 259 0.2148 241.469 234.996 0.994 0.992 0.102 4.114-3.501 98.83 2959 341 0.3220 145.857 136.984 1.021 0.994 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0393 b_overall=1.8639 ============================ 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 = 1.466844 wxc_scale = 0.285 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.034950 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 0.2597 0.3004 0.0408 0.014 2.2 1.0 2.9 14.5 2 0.042 0.2385 0.2984 0.0599 0.014 2.3 2.2 3.6 15.3 2 0.126 0.2445 0.2960 0.0515 0.014 2.3 3.2 3.3 17.2 2 0.251 0.2446 0.2960 0.0514 0.014 2.3 3.2 3.3 17.2 2 0.377 0.2446 0.2960 0.0514 0.014 2.3 3.2 3.3 17.2 2 0.502 0.2442 0.2960 0.0518 0.014 2.4 3.2 3.3 17.2 2 0.628 0.2441 0.2960 0.0519 0.014 2.4 3.2 3.3 17.2 2 0.753 0.2437 0.2957 0.0519 0.015 2.4 3.2 3.3 17.2 2 0.879 0.2446 0.2960 0.0514 0.014 2.3 3.2 3.3 17.2 2 0.419 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2437 0.2957 0.0519 0.015 2.4 3.2 3.3 17.2 2 0.879 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.37 29.57 5.19 31.192 120.974 0.035 5.648 29.75 31.50 1.75 25.345 134.501 0.001 5.675 27.80 30.42 2.61 25.201 133.015 0.004 5.638 23.01 28.74 5.73 28.764 127.149 0.017 5.572 22.10 28.70 6.61 30.218 123.850 0.035 5.571 22.06 28.76 6.71 30.757 123.055 0.052 5.572 22.05 28.83 6.78 31.047 122.756 0.070 5.574 22.02 28.89 6.86 31.257 122.685 0.087 5.574 22.03 28.91 6.88 31.385 122.581 0.105 5.574 22.00 28.92 6.92 31.516 122.614 0.122 5.574 21.98 28.93 6.95 31.627 122.654 0.140 5.574 22.01 28.95 6.93 31.642 122.524 0.157 5.575 21.99 28.96 6.96 31.734 122.590 0.175 5.574 max suggested for this run: 24.19 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.017 Accepted refinement result: 23.01 28.74 5.73 28.764 127.149 0.017 5.572 Individual atomic B min max mean iso aniso Overall: 44.85 450.95 120.56 32.29 3444 0 Protein: 44.85 450.95 120.56 32.29 3444 0 Chain A: 70.03 450.95 146.89 N/A 807 0 Chain B: 57.89 409.83 124.87 N/A 813 0 Chain C: 51.57 446.10 133.94 N/A 215 0 Chain D: 68.46 450.95 148.15 N/A 215 0 Chain E: 44.85 429.23 92.90 N/A 697 0 Chain F: 54.81 354.20 100.05 N/A 697 0 Histogram: Values Number of atoms 44.85 - 85.46 701 85.46 - 126.07 1450 126.07 - 166.68 904 166.68 - 207.29 253 207.29 - 247.90 71 247.90 - 288.51 26 288.51 - 329.12 18 329.12 - 369.73 13 369.73 - 410.34 4 410.34 - 450.95 4 =========================== Idealize ADP of riding H ========================== r_work=0.2301 r_free=0.2874 r_work=0.2292 r_free=0.2869 ----------X-ray data---------- |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2292 r_free= 0.2869 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.571039 | | target function (ml) not normalized (work): 43838.504883 | | target function (ml) not normalized (free): 4969.802487 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1354 141 0.2143 0.2708 6.1569 6.4012| | 2: 6.35 - 5.05 1.00 1326 136 0.2260 0.2813 5.7553 5.8898| | 3: 5.04 - 4.41 1.00 1320 143 0.1826 0.2403 5.5101 5.6501| | 4: 4.41 - 4.01 0.99 1291 153 0.2220 0.2831 5.3676 5.6034| | 5: 4.01 - 3.72 0.99 1285 148 0.2839 0.3137 5.2746 5.3955| | 6: 3.72 - 3.50 0.99 1293 148 0.3238 0.4017 5.3286 5.4217| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1354 141 0.72 33.23 0.94 0.89 51315.66| | 2: 6.35 - 5.05 1326 136 0.70 35.43 1.03 0.90 26694.21| | 3: 5.04 - 4.41 1320 143 0.83 23.93 1.07 0.93 12666.63| | 4: 4.41 - 4.01 1291 153 0.78 28.62 1.07 0.94 9726.78| | 5: 4.01 - 3.72 1285 148 0.68 37.49 1.12 0.92 8995.44| | 6: 3.72 - 3.50 1293 148 0.67 38.62 1.16 0.90 9428.95| |alpha: min = 0.89 max = 0.94 mean = 0.91| |beta: min = 8995.44 max = 51315.66 mean = 20066.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.73| |phase err.(work): min = 0.00 max = 89.89 mean = 32.87| |phase err.(test): min = 0.00 max = 88.00 mean = 32.30| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2348 0.2292 0.2869 n_refl.: 8738 re-set all scales: r(all,work,free)=0.4961 0.4997 0.4670 n_refl.: 8738 remove outliers: r(all,work,free)=0.4961 0.4997 0.4670 n_refl.: 8738 overall B=-14.57 to atoms: r(all,work,free)=0.4415 0.4443 0.4204 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2275 0.2205 0.2917 n_refl.: 8738 remove outliers: r(all,work,free)=0.2275 0.2205 0.2917 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3247 635.426 580.966 1.160 0.989 0.335 15.490-12.512 99.01 89 11 0.1611 563.640 549.999 1.161 0.989 0.316 12.419-9.967 99.48 175 15 0.1519 637.006 619.216 1.092 0.993 0.268 9.933-7.985 99.73 337 34 0.1603 478.272 463.163 1.159 0.992 0.262 7.976-6.403 100.00 631 64 0.2596 263.173 245.872 1.103 0.992 0.237 6.399-5.132 99.93 1234 135 0.2302 249.473 236.822 0.980 0.991 0.191 5.129-4.115 99.81 2357 259 0.1821 241.469 235.897 0.956 0.989 0.096 4.114-3.501 98.83 2959 341 0.2824 145.857 138.369 0.995 0.986 0.065 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=3.2779 ================= 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 : 0.3572 0.3827 0.003 0.846 2.0 500.0 94.7 0 0.000 1_bss: 0.2129 0.3142 0.003 0.846 18.9 516.9 111.5 0 0.000 1_settarget: 0.2129 0.3142 0.003 0.846 18.9 516.9 111.5 0 0.000 1_weight: 0.2129 0.3142 0.003 0.846 18.9 516.9 111.5 0 0.000 1_xyzrec: 0.1831 0.3248 0.019 2.813 18.9 516.9 111.5 0 0.437 1_adp: 0.2462 0.3260 0.019 2.813 64.8 511.9 130.4 0 0.437 1_regHadp: 0.2551 0.3235 0.019 2.813 64.8 511.9 130.4 0 0.437 2_bss: 0.2206 0.3113 0.019 2.813 33.7 480.8 99.3 0 0.437 2_settarget: 0.2206 0.3113 0.019 2.813 33.7 480.8 99.3 0 0.437 2_updatecdl: 0.2206 0.3113 0.019 2.816 33.7 480.8 99.3 0 0.437 2_weight: 0.2206 0.3113 0.019 2.816 33.7 480.8 99.3 0 0.437 2_xyzrec: 0.2212 0.3050 0.014 2.358 33.7 480.8 99.3 0 0.452 2_adp: 0.2665 0.3055 0.014 2.358 58.6 475.8 128.1 0 0.452 2_regHadp: 0.2702 0.3008 0.014 2.358 58.6 475.8 128.1 0 0.452 3_bss: 0.2446 0.2960 0.014 2.358 38.8 455.9 108.3 0 0.452 3_settarget: 0.2446 0.2960 0.014 2.358 38.8 455.9 108.3 0 0.452 3_updatecdl: 0.2446 0.2960 0.014 2.347 38.8 455.9 108.3 0 0.452 3_setrh: 0.2446 0.2960 0.014 2.347 38.8 455.9 108.3 0 0.452 3_weight: 0.2446 0.2960 0.014 2.347 38.8 455.9 108.3 0 0.452 3_xyzrec: 0.2437 0.2957 0.015 2.362 38.8 455.9 108.3 0 0.452 3_adp: 0.2301 0.2874 0.015 2.362 44.8 450.9 120.6 0 0.452 3_regHadp: 0.2292 0.2869 0.015 2.362 44.8 450.9 120.6 0 0.452 end: 0.2205 0.2917 0.015 2.362 30.3 436.4 106.0 0 0.452 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_3fm7_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_3fm7_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9000 Refinement macro-cycles (run) : 199.3100 Write final files (write_after_run_outputs) : 10.2200 Total : 213.4300 Total CPU time: 4.12 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:41:28 PDT -0700 (1723221688.93 s) Start R-work = 0.2129, R-free = 0.3142 Final R-work = 0.2205, R-free = 0.2917 =============================================================================== Job complete usr+sys time: 256.44 seconds wall clock time: 10 minutes 2.09 seconds (602.09 seconds total)