Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_1m10.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.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_1m10.prmtop amber.coordinate_file_name=4amber_1m10.rst7 amber.order_file_name=4amber_1m10.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_1m10.order 4amber_1m10.prmtop 4amber_1m10.rst7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.mtz" model { file = "4phenix_1m10.pdb" } default_model = "4phenix_1m10.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_1m10.prmtop coordinate_file_name = 4amber_1m10.rst7 order_file_name = 4amber_1m10.order } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 7468 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3250 Classifications: {'peptide': 199} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "B" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 4218 Classifications: {'peptide': 267} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 246} Time building chain proxies: 0.85, per 1000 atoms: 0.11 Number of scatterers: 7468 At special positions: 0 Unit cell: (89.84, 89.84, 124.63, 90, 90, 120) Space group: P 61 (No. 169) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 682 8.00 N 628 7.00 C 2366 6.00 H 3778 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 695 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 17 " distance=2.03 Simple disulfide: pdb=" SG CYS B 209 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 211 " - pdb=" SG CYS B 264 " distance=2.04 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: 1.32 Conformation dependent library (CDL) restraints added in 154.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 886 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 5 sheets defined 21.7% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 527 through 542 removed outlier: 3.711A pdb=" N VAL A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 628 through 644 removed outlier: 4.322A pdb=" N ARG A 632 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN A 633 " --> pdb=" O MET A 630 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 635 " --> pdb=" O ARG A 632 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 641 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'A' and resid 680 through 695 removed outlier: 4.470A pdb=" N GLU A 684 " --> pdb=" O ASP A 681 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP A 688 " --> pdb=" O GLN A 685 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 694 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 214 through 226 removed outlier: 6.240A pdb=" N GLU B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing sheet with id= A, first strand: chain 'A' and resid 646 through 650 removed outlier: 6.410A pdb=" N ARG A 616 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE A 649 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA A 618 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A 559 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.355A pdb=" N PHE A 675 " --> pdb=" O GLY A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 5 through 9 removed outlier: 6.610A pdb=" N ILE B 35 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN B 59 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR B 81 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 104 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU B 128 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS B 152 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR B 176 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE B 199 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 45 through 47 removed outlier: 6.794A pdb=" N LYS B 69 " --> pdb=" O PHE B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 228 through 232 82 hydrogen bonds defined for protein. 177 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: 1.23 Time building geometry restraints manager: 1.52 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: 3777 1.15 - 1.32: 695 1.32 - 1.49: 1423 1.49 - 1.67: 1630 1.67 - 1.84: 19 Bond restraints: 7544 Sorted by residual: bond pdb=" N GLU A 700 " pdb=" H GLU A 700 " 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 A 632 " pdb="HH22 ARG A 632 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE B 199 " pdb=" H PHE B 199 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND2 ASN B 158 " pdb="HD22 ASN B 158 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU B 136 " pdb=" H LEU B 136 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 7539 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.21: 392 106.21 - 113.18: 8799 113.18 - 120.15: 2310 120.15 - 127.12: 2204 127.12 - 134.09: 31 Bond angle restraints: 13736 Sorted by residual: angle pdb=" N VAL B 78 " pdb=" CA VAL B 78 " pdb=" C VAL B 78 " ideal model delta sigma weight residual 112.43 120.71 -8.28 9.20e-01 1.18e+00 8.10e+01 angle pdb=" C LEU B 76 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " ideal model delta sigma weight residual 119.84 130.41 -10.57 1.25e+00 6.40e-01 7.15e+01 angle pdb=" C LEU B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.56 127.99 -8.43 1.02e+00 9.61e-01 6.83e+01 angle pdb=" N ILE B 213 " pdb=" CA ILE B 213 " pdb=" C ILE B 213 " ideal model delta sigma weight residual 112.90 105.33 7.57 9.60e-01 1.09e+00 6.21e+01 angle pdb=" N ARG A 511 " pdb=" CA ARG A 511 " pdb=" C ARG A 511 " ideal model delta sigma weight residual 108.45 118.26 -9.81 1.26e+00 6.30e-01 6.06e+01 ... (remaining 13731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3177 17.57 - 35.14: 229 35.14 - 52.71: 106 52.71 - 70.28: 26 70.28 - 87.84: 3 Dihedral angle restraints: 3541 sinusoidal: 1982 harmonic: 1559 Sorted by residual: dihedral pdb=" CA LYS A 585 " pdb=" CB LYS A 585 " pdb=" CG LYS A 585 " pdb=" CD LYS A 585 " ideal model delta sinusoidal sigma weight residual -60.00 -118.49 58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN B 159 " pdb=" CB GLN B 159 " pdb=" CG GLN B 159 " pdb=" CD GLN B 159 " ideal model delta sinusoidal sigma weight residual 60.00 113.33 -53.33 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" C HIS B 195 " pdb=" N HIS B 195 " pdb=" CA HIS B 195 " pdb=" CB HIS B 195 " ideal model delta harmonic sigma weight residual -122.60 -115.04 -7.56 0 2.50e+00 1.60e-01 9.15e+00 ... (remaining 3538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 349 0.080 - 0.160: 177 0.160 - 0.240: 54 0.240 - 0.320: 12 0.320 - 0.400: 4 Chirality restraints: 596 Sorted by residual: chirality pdb=" CA PRO B 2 " pdb=" N PRO B 2 " pdb=" C PRO B 2 " pdb=" CB PRO B 2 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLN B 21 " pdb=" N GLN B 21 " pdb=" C GLN B 21 " pdb=" CB GLN B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA HIS B 195 " pdb=" N HIS B 195 " pdb=" C HIS B 195 " pdb=" CB HIS B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 593 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 44 " -0.125 2.00e-02 2.50e+03 5.17e-02 8.01e+01 pdb=" CG TYR B 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 44 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 44 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 44 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 44 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 44 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 44 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 TYR B 44 " 0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 44 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR B 44 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR B 44 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 600 " 0.122 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" CG TYR A 600 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 600 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 600 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 600 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 600 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 600 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 600 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 54 " 0.112 2.00e-02 2.50e+03 4.13e-02 5.13e+01 pdb=" CG TYR B 54 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 54 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 54 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 54 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 54 " 0.042 2.00e-02 2.50e+03 pdb=" HD1 TYR B 54 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR B 54 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR B 54 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 54 " 0.006 2.00e-02 2.50e+03 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.62: 61 1.62 - 2.36: 2594 2.36 - 3.11: 24648 3.11 - 3.85: 32923 3.85 - 4.60: 52324 Warning: very small nonbonded interaction distances. Nonbonded interactions: 112550 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 599 " pdb=" HH TYR B 228 " model vdw 0.875 2.100 nonbonded pdb=" H PHE B 192 " pdb=" HH TYR B 215 " model vdw 0.878 2.100 nonbonded pdb=" HG SER A 526 " pdb=" H GLU A 529 " model vdw 0.931 2.100 nonbonded pdb=" HG SER A 593 " pdb=" H GLU A 596 " model vdw 0.994 2.100 nonbonded pdb=" HA HIS A 559 " pdb=" HA ALA A 592 " model vdw 1.014 2.440 ... (remaining 112545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1m10.prmtop atom order : 4amber_1m10.order coordinates : 4amber_1m10.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 14 15.96 2 O 682 7.97 1 N 628 6.97 1 C 2366 5.97 2 H 3778 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: 3778 of 7468 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7468 n_use_u_iso = 7468 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 = 7468 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7468 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7468 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 527 through 542 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 574 through 583 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 594 through 604 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 628 through 644 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 659 through 666 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 680 through 695 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 48 through 51 helix_type = alpha pi *3_10 unknown } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 214 through 226 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 243 through 245 helix_type = alpha pi *3_10 unknown } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 256 through 258 helix_type = alpha pi *3_10 unknown } sheet { first_strand = chain 'A' and resid 646 through 650 sheet_id = " A" strand { selection = chain 'A' and resid 615 through 621 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 616 and name N bond_start_previous = chain 'A' and resid 647 and name O } strand { selection = chain 'A' and resid 513 through 520 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 514 and name N bond_start_previous = chain 'A' and resid 615 and name O } strand { selection = chain 'A' and resid 551 through 559 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 552 and name N bond_start_previous = chain 'A' and resid 513 and name O } strand { selection = chain 'A' and resid 561 through 564 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 563 and name N bond_start_previous = chain 'A' and resid 557 and name O } } sheet { first_strand = chain 'A' and resid 651 through 653 sheet_id = " B" strand { selection = chain 'A' and resid 675 through 677 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 675 and name N bond_start_previous = chain 'A' and resid 652 and name O } } sheet { first_strand = chain 'B' and resid 5 through 9 sheet_id = " C" strand { selection = chain 'B' and resid 12 through 16 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 16 and name N bond_start_previous = chain 'B' and resid 5 and name O } strand { selection = chain 'B' and resid 35 through 37 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 35 and name N bond_start_previous = chain 'B' and resid 15 and name O } strand { selection = chain 'B' and resid 59 through 61 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 59 and name N bond_start_previous = chain 'B' and resid 36 and name O } strand { selection = chain 'B' and resid 81 through 83 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 81 and name N bond_start_previous = chain 'B' and resid 60 and name O } strand { selection = chain 'B' and resid 104 through 106 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 104 and name N bond_start_previous = chain 'B' and resid 82 and name O } strand { selection = chain 'B' and resid 128 through 130 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 128 and name N bond_start_previous = chain 'B' and resid 105 and name O } strand { selection = chain 'B' and resid 152 through 154 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 152 and name N bond_start_previous = chain 'B' and resid 129 and name O } strand { selection = chain 'B' and resid 176 through 178 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 176 and name N bond_start_previous = chain 'B' and resid 153 and name O } strand { selection = chain 'B' and resid 199 through 201 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 199 and name N bond_start_previous = chain 'B' and resid 177 and name O } } sheet { first_strand = chain 'B' and resid 45 through 47 sheet_id = " D" strand { selection = chain 'B' and resid 69 through 71 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 69 and name N bond_start_previous = chain 'B' and resid 46 and name O } } sheet { first_strand = chain 'B' and resid 228 through 232 sheet_id = " E" strand { selection = chain 'B' and resid 237 through 241 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 240 and name N bond_start_previous = chain 'B' and resid 229 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_1m10.prmtop" coordinate_file_name = "4amber_1m10.rst7" order_file_name = "4amber_1m10.order" } } output { prefix = "4phenix_1m10_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: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3803 r_free= 0.4309 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 5.437703 | | target function (ml) not normalized (work): 53942.017433 | | target function (ml) not normalized (free): 2943.717609 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.3658 0.4500 6.0034 5.8552| | 2: 4.90 - 3.90 1.00 2453 134 0.3746 0.3976 5.6046 5.831| | 3: 3.89 - 3.40 1.00 2476 150 0.4078 0.4337 5.2699 5.4052| | 4: 3.40 - 3.09 1.00 2461 127 0.3903 0.4701 4.8586 4.9716| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.59 44.89 0.82 0.19 23817.59| | 2: 4.90 - 3.90 2453 134 0.66 39.71 1.40 0.30 15628.07| | 3: 3.89 - 3.40 2476 150 0.61 43.78 1.52 0.32 9102.41| | 4: 3.40 - 3.09 2461 127 0.53 49.82 1.29 0.25 4240.62| |alpha: min = 0.19 max = 0.32 mean = 0.27| |beta: min = 4240.62 max = 23817.59 mean = 13262.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.60| |phase err.(work): min = 0.00 max = 89.81 mean = 44.56| |phase err.(test): min = 0.00 max = 89.17 mean = 44.87| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.119 3766 Z= 0.613 Angle : 1.710 10.944 5117 Z= 1.081 Chirality : 0.104 0.400 596 Planarity : 0.010 0.086 656 Dihedral : 15.487 87.844 1425 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 35.77 Ramachandran Plot: Outliers : 4.98 % Allowed : 12.77 % Favored : 82.25 % Rotamer: Outliers : 5.28 % Allowed : 6.24 % Favored : 88.49 % 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: -5.24 (0.31), residues: 462 helix: -4.51 (0.29), residues: 98 sheet: -2.23 (0.51), residues: 89 loop : -3.68 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 545 TYR 0.104 0.022 TYR B 44 PHE 0.051 0.010 PHE B 201 TRP 0.058 0.016 TRP B 219 HIS 0.003 0.001 HIS B 86 Individual atomic B min max mean iso aniso Overall: 15.65 95.55 52.24 1.37 3690 0 Protein: 15.65 95.55 52.24 1.37 3690 0 Chain A: 21.62 95.55 60.64 N/A 1602 0 Chain B: 15.65 77.97 45.80 N/A 2088 0 Histogram: Values Number of atoms 15.65 - 23.64 14 23.64 - 31.63 190 31.63 - 39.62 520 39.62 - 47.61 817 47.61 - 55.60 852 55.60 - 63.59 530 63.59 - 71.58 302 71.58 - 79.57 236 79.57 - 87.56 164 87.56 - 95.55 65 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3803 r_free= 0.4309 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 5.437703 | | target function (ml) not normalized (work): 53942.017433 | | target function (ml) not normalized (free): 2943.717609 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3827 0.3803 0.4309 n_refl.: 10454 re-set all scales: r(all,work,free)=0.3827 0.3803 0.4309 n_refl.: 10454 remove outliers: r(all,work,free)=0.3827 0.3803 0.4301 n_refl.: 10449 overall B=15.40 to atoms: r(all,work,free)=0.4409 0.4389 0.4796 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2295 0.2267 0.2830 n_refl.: 10449 remove outliers: r(all,work,free)=0.2295 0.2267 0.2830 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2304 1395.880 1346.219 1.089 1.182 0.395 14.512-11.594 100.00 95 5 0.1555 1328.501 1304.310 0.949 1.171 0.369 11.568-9.227 100.00 193 11 0.1408 1283.695 1251.033 0.958 1.155 0.360 9.162-7.352 100.00 368 15 0.2074 850.444 821.762 0.943 1.127 0.349 7.349-5.862 100.00 740 33 0.2221 628.796 612.170 0.868 1.088 0.328 5.858-4.671 100.00 1425 79 0.1951 673.674 650.770 0.914 1.022 0.277 4.669-3.723 99.86 2790 156 0.2268 618.903 593.517 1.183 0.920 0.183 3.723-3.092 99.93 4210 230 0.2746 337.939 316.561 1.437 0.781 0.057 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-5.4500 ============================ 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 = 4.140215 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.204244 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2466 0.2728 0.0262 0.014 2.0 0.3 0.6 3.8 1 0.125 0.2325 0.2701 0.0376 0.013 2.0 0.8 1.1 4.1 0 0.250 0.2176 0.2723 0.0547 0.014 2.1 1.2 1.5 3.6 1 0.500 0.2053 0.2747 0.0694 0.015 2.3 3.1 1.3 4.3 1 1.000 0.1943 0.2787 0.0844 0.019 2.9 5.9 3.0 7.0 2 2.000 0.1872 0.2813 0.0940 0.023 3.3 7.6 3.5 9.1 6 3.000 0.1832 0.2848 0.1015 0.027 3.7 11.1 5.2 9.4 10 4.000 0.1795 0.2881 0.1086 0.030 4.2 14.1 6.1 12.9 15 5.000 0.1771 0.2900 0.1129 0.034 4.5 16.1 7.4 13.7 19 6.000 0.1748 0.2932 0.1184 0.037 4.8 18.6 7.8 14.6 22 7.000 0.1833 0.2776 0.0942 0.039 4.2 18.8 4.8 7.9 6 8.000 0.1825 0.2778 0.0953 0.041 4.4 20.4 5.2 8.2 7 9.000 0.1858 0.2763 0.0905 0.041 4.1 21.3 5.4 8.2 4 10.000 0.1944 0.2767 0.0823 0.020 2.9 6.0 3.0 5.5 3 2.070 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2325 0.2701 0.0376 0.013 2.0 0.8 1.1 4.1 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.25 27.01 3.76 0.970 67.376 0.204 0.058 23.38 26.87 3.48 2.051 67.504 0.006 0.059 22.92 26.77 3.85 2.084 67.587 0.026 0.057 21.50 26.61 5.11 4.699 68.079 0.102 0.050 20.89 26.72 5.83 6.297 68.457 0.204 0.047 20.49 26.79 6.30 7.695 68.906 0.306 0.045 20.29 26.86 6.56 8.545 69.152 0.408 0.045 20.14 26.92 6.78 9.275 69.377 0.511 0.044 20.00 26.98 6.98 9.988 69.611 0.613 0.043 19.93 27.02 7.10 10.433 69.739 0.715 0.043 19.65 27.11 7.46 12.070 70.342 0.817 0.042 19.58 27.16 7.58 12.599 70.507 0.919 0.042 19.50 27.20 7.71 13.174 70.695 1.021 0.041 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.102 Accepted refinement result: 21.50 26.61 5.11 4.699 68.079 0.102 0.050 Individual atomic B min max mean iso aniso Overall: 35.36 115.57 69.07 4.46 3690 0 Protein: 35.36 115.57 69.07 4.46 3690 0 Chain A: 37.09 115.57 76.86 N/A 1602 0 Chain B: 35.36 104.03 63.09 N/A 2088 0 Histogram: Values Number of atoms 35.36 - 43.38 30 43.38 - 51.40 304 51.40 - 59.42 667 59.42 - 67.44 934 67.44 - 75.47 703 75.47 - 83.49 411 83.49 - 91.51 290 91.51 - 99.53 234 99.53 - 107.55 97 107.55 - 115.57 20 =========================== Idealize ADP of riding H ========================== r_work=0.2150 r_free=0.2661 r_work=0.2136 r_free=0.2649 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2136 r_free= 0.2649 coordinate error (max.-lik. estimate): 0.52 A | | | | normalized target function (ls_wunit_k1) (work): 0.049170 | | target function (ls_wunit_k1) not normalized (work): 487.567897 | | target function (ls_wunit_k1) not normalized (free): 44.036465 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2161 0.2136 0.2649 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4397 0.4384 0.4648 n_refl.: 10449 remove outliers: r(all,work,free)=0.4397 0.4384 0.4648 n_refl.: 10449 overall B=-5.36 to atoms: r(all,work,free)=0.4184 0.4171 0.4449 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2162 0.2135 0.2661 n_refl.: 10449 remove outliers: r(all,work,free)=0.2162 0.2135 0.2661 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2052 759.914 736.407 1.276 1.112 0.389 14.512-11.594 100.00 95 5 0.1123 723.233 721.182 1.118 1.106 0.366 11.568-9.227 100.00 193 11 0.1368 698.841 686.012 1.114 1.095 0.365 9.162-7.352 100.00 368 15 0.1700 462.980 456.767 1.092 1.077 0.367 7.349-5.862 100.00 740 33 0.1987 342.315 336.837 0.963 1.051 0.341 5.858-4.671 100.00 1425 79 0.1853 366.747 357.458 0.968 1.008 0.295 4.669-3.723 99.93 2790 156 0.2042 336.929 329.814 1.149 0.939 0.217 3.723-3.092 100.00 4210 230 0.2819 183.973 174.535 1.255 0.846 0.056 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=1.1730 ============================ 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 = 0.852405 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.041192 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2198 0.2683 0.0485 0.013 2.0 0.4 0.6 3.8 0 0.043 0.2134 0.2661 0.0526 0.013 2.0 0.8 1.1 4.1 0 0.128 0.2133 0.2661 0.0528 0.013 2.0 0.8 1.1 4.1 0 0.256 0.2123 0.2660 0.0537 0.014 2.0 0.8 1.1 4.1 0 0.384 0.2118 0.2658 0.0540 0.014 2.0 0.8 1.1 4.1 0 0.511 0.2113 0.2655 0.0543 0.014 2.0 0.8 1.1 4.1 0 0.639 0.2087 0.2647 0.0560 0.016 2.1 0.8 1.1 4.1 1 0.767 0.2125 0.2661 0.0536 0.014 2.0 0.8 1.1 4.1 0 0.895 0.2122 0.2658 0.0536 0.014 2.0 0.8 1.1 4.1 0 0.426 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2087 0.2647 0.0560 0.016 2.1 0.8 1.1 4.1 1 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.87 26.47 5.60 10.438 70.553 0.041 5.734 23.80 27.93 4.13 8.988 73.790 0.001 5.804 21.92 26.43 4.51 10.617 70.389 0.005 5.751 20.86 26.47 5.60 10.440 70.551 0.021 5.734 20.65 26.36 5.71 10.866 70.309 0.041 5.721 19.85 26.55 6.70 12.307 70.616 0.062 5.694 19.64 26.80 7.16 13.102 71.137 0.082 5.690 19.50 26.79 7.28 13.422 71.258 0.103 5.687 19.70 26.66 6.96 12.668 70.686 0.124 5.692 19.65 26.71 7.06 12.792 70.778 0.144 5.692 19.61 26.75 7.14 12.903 70.854 0.165 5.691 19.57 26.78 7.20 13.001 70.919 0.185 5.691 19.55 26.80 7.25 13.088 70.973 0.206 5.690 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.041 Accepted refinement result: 20.65 26.36 5.71 10.866 70.309 0.041 5.721 Individual atomic B min max mean iso aniso Overall: 25.00 110.52 63.21 5.12 3690 0 Protein: 25.00 110.52 63.21 5.12 3690 0 Chain A: 30.67 110.52 71.02 N/A 1602 0 Chain B: 25.00 101.19 57.22 N/A 2088 0 Histogram: Values Number of atoms 25.00 - 33.55 12 33.55 - 42.10 185 42.10 - 50.66 562 50.66 - 59.21 902 59.21 - 67.76 807 67.76 - 76.31 493 76.31 - 84.86 338 84.86 - 93.42 259 93.42 - 101.97 107 101.97 - 110.52 25 =========================== Idealize ADP of riding H ========================== r_work=0.2065 r_free=0.2636 r_work=0.2064 r_free=0.2638 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2064 r_free= 0.2638 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ml) (work): 5.720238 | | target function (ml) not normalized (work): 56721.875454 | | target function (ml) not normalized (free): 3145.431426 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2093 0.2064 0.2638 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4117 0.4102 0.4410 n_refl.: 10449 remove outliers: r(all,work,free)=0.4117 0.4102 0.4410 n_refl.: 10449 overall B=0.00 to atoms: r(all,work,free)=0.4117 0.4102 0.4410 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2102 0.2073 0.2653 n_refl.: 10449 remove outliers: r(all,work,free)=0.2102 0.2073 0.2653 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.1981 759.914 743.364 1.329 1.065 0.386 14.512-11.594 100.00 95 5 0.1126 723.233 722.917 1.189 1.062 0.373 11.568-9.227 100.00 193 11 0.1344 698.841 687.902 1.171 1.056 0.370 9.162-7.352 100.00 368 15 0.1646 462.980 458.170 1.127 1.044 0.370 7.349-5.862 100.00 740 33 0.1958 342.315 336.743 0.993 1.028 0.350 5.858-4.671 100.00 1425 79 0.1805 366.747 357.144 0.968 1.001 0.290 4.669-3.723 99.93 2790 156 0.1964 336.929 329.708 1.122 0.958 0.220 3.723-3.092 100.00 4210 230 0.2739 183.973 174.516 1.164 0.899 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=1.5143 ============================ 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 = 0.878501 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.042719 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2184 0.2687 0.0503 0.013 2.0 0.4 0.6 3.6 0 0.044 0.2080 0.2644 0.0563 0.013 2.1 0.8 1.1 4.1 0 0.132 0.2068 0.2646 0.0578 0.015 2.1 0.8 1.1 4.1 1 0.264 0.2073 0.2653 0.0581 0.016 2.1 0.8 1.1 4.1 1 0.395 0.2073 0.2653 0.0581 0.016 2.1 0.8 1.1 4.1 1 0.527 0.2073 0.2653 0.0581 0.016 2.1 0.8 1.1 4.1 1 0.659 0.2073 0.2653 0.0581 0.016 2.1 0.8 1.1 4.1 1 0.791 0.2073 0.2653 0.0581 0.016 2.1 0.8 1.1 4.1 1 0.922 0.2073 0.2653 0.0581 0.016 2.1 0.8 1.1 4.1 1 0.439 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2080 0.2644 0.0563 0.013 2.1 0.8 1.1 4.1 0 0.132 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.80 26.44 5.63 9.845 69.488 0.043 5.725 23.83 27.86 4.04 8.522 72.782 0.001 5.803 21.99 26.47 4.48 9.927 69.341 0.005 5.751 20.80 26.44 5.63 9.845 69.488 0.021 5.725 20.79 26.43 5.64 9.865 69.476 0.043 5.725 20.39 26.43 6.04 10.812 69.087 0.064 5.708 19.72 26.80 7.09 12.469 69.599 0.085 5.690 19.66 26.85 7.20 12.589 69.669 0.107 5.689 19.62 26.90 7.28 12.697 69.728 0.128 5.689 19.56 26.96 7.41 12.934 69.864 0.150 5.688 19.52 27.01 7.49 13.103 69.954 0.171 5.688 19.48 27.05 7.57 13.269 70.036 0.192 5.688 19.45 27.10 7.66 13.477 70.138 0.214 5.687 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.043 Accepted refinement result: 20.79 26.43 5.64 9.865 69.476 0.043 5.725 Individual atomic B min max mean iso aniso Overall: 24.82 110.53 63.19 5.15 3690 0 Protein: 24.82 110.53 63.19 5.15 3690 0 Chain A: 30.59 110.53 71.00 N/A 1602 0 Chain B: 24.82 101.29 57.19 N/A 2088 0 Histogram: Values Number of atoms 24.82 - 33.39 12 33.39 - 41.96 182 41.96 - 50.53 555 50.53 - 59.10 900 59.10 - 67.67 814 67.67 - 76.24 495 76.24 - 84.81 341 84.81 - 93.39 257 93.39 - 101.96 109 101.96 - 110.53 25 =========================== Idealize ADP of riding H ========================== r_work=0.2079 r_free=0.2643 r_work=0.2079 r_free=0.2643 ----------X-ray data---------- |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2079 r_free= 0.2643 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ml) (work): 5.724611 | | target function (ml) not normalized (work): 56765.242226 | | target function (ml) not normalized (free): 3147.075053 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.1735 0.2172 5.9726 6.0584| | 2: 4.90 - 3.90 1.00 2451 133 0.1883 0.2395 5.8731 6.1829| | 3: 3.89 - 3.40 1.00 2475 150 0.2426 0.3018 5.7033 5.9125| | 4: 3.40 - 3.09 1.00 2460 127 0.2978 0.3787 5.3431 5.4543| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.85 21.87 1.00 0.84 27123.53| | 2: 4.90 - 3.90 2451 133 0.84 22.92 1.01 0.87 23726.60| | 3: 3.89 - 3.40 2475 150 0.76 31.14 1.03 0.82 18167.21| | 4: 3.40 - 3.09 2460 127 0.68 37.80 0.91 0.70 10445.34| |alpha: min = 0.70 max = 0.87 mean = 0.81| |beta: min = 10445.34 max = 27123.53 mean = 19910.83| |figures of merit: min = 0.01 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 89.25 mean = 28.40| |phase err.(test): min = 0.00 max = 86.86 mean = 29.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2108 0.2079 0.2643 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4120 0.4105 0.4410 n_refl.: 10449 remove outliers: r(all,work,free)=0.4120 0.4105 0.4410 n_refl.: 10449 overall B=0.54 to atoms: r(all,work,free)=0.4141 0.4126 0.4429 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2090 0.2062 0.2621 n_refl.: 10449 remove outliers: r(all,work,free)=0.2090 0.2062 0.2621 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.1961 759.914 740.782 1.248 1.149 0.386 14.512-11.594 100.00 95 5 0.1117 723.233 718.953 1.124 1.140 0.372 11.568-9.227 100.00 193 11 0.1314 698.841 685.658 1.117 1.126 0.370 9.162-7.352 100.00 368 15 0.1640 462.980 456.575 1.087 1.103 0.369 7.349-5.862 100.00 740 33 0.1950 342.315 336.291 0.978 1.069 0.349 5.858-4.671 100.00 1425 79 0.1818 366.747 357.326 0.989 1.013 0.298 4.669-3.723 99.93 2790 156 0.1973 336.929 329.753 1.194 0.925 0.228 3.723-3.092 100.00 4210 230 0.2691 183.973 174.556 1.331 0.806 0.059 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=2.4124 ================= 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 : 0.3803 0.4309 0.010 1.710 15.7 95.5 52.2 0 0.000 1_bss: 0.2267 0.2830 0.010 1.710 31.1 111.0 67.6 0 0.000 1_settarget: 0.2267 0.2830 0.010 1.710 31.1 111.0 67.6 0 0.000 1_weight: 0.2267 0.2830 0.010 1.710 31.1 111.0 67.6 0 0.000 1_xyzrec: 0.2325 0.2701 0.013 2.021 31.1 111.0 67.6 0 0.377 1_adp: 0.2150 0.2661 0.013 2.021 35.4 115.6 69.1 0 0.377 1_regHadp: 0.2136 0.2649 0.013 2.021 35.4 115.6 69.1 0 0.377 2_bss: 0.2135 0.2661 0.013 2.021 30.0 110.2 63.7 0 0.377 2_settarget: 0.2135 0.2661 0.013 2.021 30.0 110.2 63.7 0 0.377 2_updatecdl: 0.2135 0.2661 0.013 2.014 30.0 110.2 63.7 0 0.377 2_weight: 0.2135 0.2661 0.013 2.014 30.0 110.2 63.7 0 0.377 2_xyzrec: 0.2087 0.2647 0.016 2.108 30.0 110.2 63.7 0 0.375 2_adp: 0.2065 0.2636 0.016 2.108 25.0 110.5 63.2 0 0.375 2_regHadp: 0.2064 0.2638 0.016 2.108 25.0 110.5 63.2 0 0.375 3_bss: 0.2073 0.2653 0.016 2.108 25.0 110.5 63.2 0 0.375 3_settarget: 0.2073 0.2653 0.016 2.108 25.0 110.5 63.2 0 0.375 3_updatecdl: 0.2073 0.2653 0.016 2.106 25.0 110.5 63.2 0 0.375 3_setrh: 0.2073 0.2653 0.016 2.106 25.0 110.5 63.2 0 0.375 3_weight: 0.2073 0.2653 0.016 2.106 25.0 110.5 63.2 0 0.375 3_xyzrec: 0.2080 0.2644 0.013 2.066 25.0 110.5 63.2 0 0.375 3_adp: 0.2079 0.2643 0.013 2.066 24.8 110.5 63.2 0 0.375 3_regHadp: 0.2079 0.2643 0.013 2.066 24.8 110.5 63.2 0 0.375 end: 0.2062 0.2621 0.013 2.066 25.4 111.1 63.7 0 0.375 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1m10_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1m10_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8800 Refinement macro-cycles (run) : 212.2600 Write final files (write_after_run_outputs) : 10.8900 Total : 228.0300 Total CPU time: 4.41 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:42:15 PDT -0700 (1723221735.69 s) Start R-work = 0.2267, R-free = 0.2830 Final R-work = 0.2062, R-free = 0.2621 =============================================================================== Job complete usr+sys time: 274.43 seconds wall clock time: 10 minutes 48.54 seconds (648.54 seconds total)