Starting qr.refine on Sun May 19 13:41:24 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7kzn_23083.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7kzn_23083.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- mode=refine restraints=qm engine=aimnet2 clustering=false minimizer=lbfgsb max_bond_rmsd=0.0001 gradient_only=false Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7kzn_23083.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7kzn_23083.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7kzn_23083.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7kzn_23083.map" } cluster { clustering = false } quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { max_bond_rmsd = 0.0001 minimizer = lbfgs *lbfgsb } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = False debug = False scattering_table = wk1995 it1992 *n_gaussian electron neutron use_reduce = True cluster { charge_cutoff = 8 clustering = False charge_embedding = False two_buffers = False maxnum_residues_in_cluster = 15 bcc_threshold = 9 select_within_radius = 10 clustering_method = gnc *bcc altloc_method = average *subtract save_clusters = True bond_with_altloc = True re_calculate_rmsd_tolerance = 0.5 } restraints = cctbx *qm expansion = False quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server basis = Auto charge = None method = Auto memory = None nproc = 1 server_url = "http://127.0.0.1:8000" qm_addon = gcp dftd3 gcp-d3 qm_addon_method = None } refine { dry_run = False sf_algorithm = *direct fft refinement_target_name = *ml ls_wunit_k1 mode = opt *refine gtest number_of_macro_cycles = 1 number_of_weight_search_cycles = 50 number_of_refine_cycles = 5 number_of_micro_cycles = 50 data_weight = None skip_weight_search = False adjust_restraints_weight_scale_value = 2 max_iterations_weight = 50 max_iterations_refine = 50 use_ase_lbfgs = False line_search = True stpmax = 0.2 gradient_only = False refine_sites = True refine_adp = False restraints_weight_scale = 1 shake_sites = False use_convergence_test = True max_bond_rmsd = 0.0001 max_angle_rmsd = 1.7 stop_one_found_first_good_weight = True max_r_work_r_free_gap = 5 r_tolerance = 0.001 rmsd_tolerance = 0.01 opt_log = False pre_opt = False pre_opt_stpmax = 0.1 pre_opt_iter = 10 pre_opt_switch = 2 pre_opt_gconv = 3000 minimizer = lbfgs *lbfgsb shift_evaluation = max *mean } parallel { method = *multiprocessing slurm pbs sge lsf threading nproc = 1 qsub_command = None } output_file_name_prefix = None output_folder_name = "pdb" rst_file = None dump_gradients = None output { filename = None file_name = None prefix = None suffix = None serial = 0 serial_format = "%03d" target_output_format = None *pdb mmcif overwrite = False } ------------------------------------------------------------------------------- Extracting model **************** Symmetric amino acids flipped Residue "K ASP 14": "OD1" <-> "OD2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "K PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib" Total number of atoms: 1324 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1324 Inner-chain residues flagged as termini: ['pdbres="GLU K 71 "'] Classifications: {'peptide': 82} Modifications used: {'NH3': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Time building chain proxies: 0.26, per 1000 atoms: 0.20 Number of scatterers: 1324 At special positions: 0 Unit cell: (46.24, 51.68, 48.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 122 8.00 N 112 7.00 C 433 6.00 H 653 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Adding C-beta torsion restraints... Number of C-beta restraints generated: 158 Time building geometry restraints manager: 0.27 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: 652 1.15 - 1.32: 112 1.32 - 1.48: 281 1.48 - 1.65: 289 1.65 - 1.82: 6 Bond restraints: 1340 Sorted by residual: bond pdb=" CA TYR K 77 " pdb=" CB TYR K 77 " ideal model delta sigma weight residual 1.530 1.581 -0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" N GLU K 71 " pdb=" CA GLU K 71 " ideal model delta sigma weight residual 1.491 1.455 0.036 2.10e-02 2.27e+03 2.92e+00 bond pdb=" CD1 PHE K 75 " pdb=" CE1 PHE K 75 " ideal model delta sigma weight residual 1.382 1.349 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" C LYS K 73 " pdb=" N HIS K 74 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 8.36e-01 bond pdb=" CG LEU K 86 " pdb=" CD2 LEU K 86 " ideal model delta sigma weight residual 1.521 1.547 -0.026 3.30e-02 9.18e+02 6.45e-01 ... (remaining 1335 not shown) Histogram of bond angle deviations from ideal: 101.13 - 107.69: 123 107.69 - 114.26: 1502 114.26 - 120.82: 444 120.82 - 127.39: 339 127.39 - 133.95: 6 Bond angle restraints: 2414 Sorted by residual: angle pdb=" CA PHE K 78 " pdb=" CB PHE K 78 " pdb=" CG PHE K 78 " ideal model delta sigma weight residual 113.80 116.02 -2.22 1.00e+00 1.00e+00 4.94e+00 angle pdb=" N PHE K 78 " pdb=" CA PHE K 78 " pdb=" CB PHE K 78 " ideal model delta sigma weight residual 110.50 113.66 -3.16 1.70e+00 3.46e-01 3.46e+00 angle pdb=" N GLU K 71 " pdb=" CA GLU K 71 " pdb=" C GLU K 71 " ideal model delta sigma weight residual 111.00 105.90 5.10 2.80e+00 1.28e-01 3.31e+00 angle pdb=" N VAL K 83 " pdb=" CA VAL K 83 " pdb=" C VAL K 83 " ideal model delta sigma weight residual 111.00 105.95 5.05 2.80e+00 1.28e-01 3.25e+00 angle pdb=" N GLU K 71 " pdb=" CA GLU K 71 " pdb=" CB GLU K 71 " ideal model delta sigma weight residual 110.50 113.47 -2.97 1.70e+00 3.46e-01 3.04e+00 ... (remaining 2409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 545 11.87 - 23.73: 51 23.73 - 35.60: 13 35.60 - 47.46: 9 47.46 - 59.33: 8 Dihedral angle restraints: 626 sinusoidal: 320 harmonic: 306 Sorted by residual: dihedral pdb=" CA GLU K 37 " pdb=" C GLU K 37 " pdb=" N LYS K 38 " pdb=" CA LYS K 38 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE K 44 " pdb=" C ILE K 44 " pdb=" N LYS K 45 " pdb=" CA LYS K 45 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ILE K 36 " pdb=" C ILE K 36 " pdb=" N GLU K 37 " pdb=" CA GLU K 37 " ideal model delta harmonic sigma weight residual -180.00 -164.08 -15.92 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 52 0.028 - 0.056: 32 0.056 - 0.085: 3 0.085 - 0.113: 9 0.113 - 0.141: 3 Chirality restraints: 99 Sorted by residual: chirality pdb=" CA TYR K 77 " pdb=" N TYR K 77 " pdb=" C TYR K 77 " pdb=" CB TYR K 77 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE K 10 " pdb=" N ILE K 10 " pdb=" C ILE K 10 " pdb=" CB ILE K 10 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA VAL K 83 " pdb=" N VAL K 83 " pdb=" C VAL K 83 " pdb=" CB VAL K 83 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 96 not shown) Planarity restraints: 196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 53 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO K 54 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO K 54 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 54 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 75 " 0.017 2.00e-02 2.50e+03 8.41e-03 2.12e+00 pdb=" CG PHE K 75 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE K 75 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE K 75 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE K 75 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE K 75 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE K 75 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE K 75 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE K 75 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE K 75 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE K 75 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE K 75 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 78 " 0.013 2.00e-02 2.50e+03 8.07e-03 1.96e+00 pdb=" CG PHE K 78 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE K 78 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE K 78 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE K 78 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE K 78 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE K 78 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE K 78 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE K 78 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE K 78 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE K 78 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE K 78 " 0.001 2.00e-02 2.50e+03 ... (remaining 193 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 181 2.23 - 2.82: 2661 2.82 - 3.41: 3403 3.41 - 4.01: 4346 4.01 - 4.60: 6222 Nonbonded interactions: 16813 Sorted by model distance: nonbonded pdb=" H PHE K 78 " pdb=" HD1 PHE K 78 " model vdw 1.635 2.000 nonbonded pdb=" H ARG K 62 " pdb=" HE2 PHE K 64 " model vdw 1.707 2.000 nonbonded pdb=" O PHE K 48 " pdb=" H LYS K 51 " model vdw 1.715 1.800 nonbonded pdb=" O HIS K 70 " pdb=" H2 GLU K 71 " model vdw 1.726 1.920 nonbonded pdb=" H THR K 28 " pdb=" HG1 THR K 28 " model vdw 1.751 2.000 ... (remaining 16808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 4 15.96 2 O 122 7.97 2 N 112 6.97 2 C 433 5.97 2 H 653 1.00 3 sf(0) = scattering factor at diffraction angle 0. Setting QM defaults Setting QM method to HF Setting QM basis to 6-31g GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.006 0.051 687 Z= 0.255 ANGLE : 0.999 5.097 926 Z= 0.486 CHIRALITY : 0.048 0.141 99 PLANARITY : 0.005 0.042 117 DIHEDRAL : 10.462 58.376 247 MIN NONBONDED DISTANCE : 2.355 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 15.09 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 10.00 % FAVORED : 90.00 % ROTAMER: OUTLIERS : 2.86 % ALLOWED : 8.57 % FAVORED : 88.57 % 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: -3.48 (0.81), RESIDUES: 80 HELIX: -1.71 (0.83), RESIDUES: 32 SHEET: -3.23 (1.02), RESIDUES: 15 LOOP : -2.26 (0.97), RESIDUES: 33 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.001 0.000 ARG K 62 TYR 0.011 0.003 TYR K 34 PHE 0.023 0.004 PHE K 78 TRP 0.001 0.000 TRP K 56 HIS 0.003 0.001 HIS K 74 Resolution of map is: 2.8530 Map-model correlation coefficient (CC) CC_mask : 0.6287 weight= None bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 Initial weight estimate from ratio of grad norms: 0.5907004093887802 cycle: 0 start: weight= 0.5907 bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.5907 bond: 0.073 angle: 4.12 clash: 52.1 rota: 12.86 rama: f: 73.08 o: 6.41 Z: -6.63 cb: 16.46 shift=0.9266 cc_mask=0.6759 cycle: 1 start: weight= 0.2954 bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.2954 bond: 0.058 angle: 2.76 clash: 20.4 rota: 1.43 rama: f: 83.33 o: 3.85 Z: -5.57 cb: 3.80 shift=0.5843 cc_mask=0.6675 cycle: 2 start: weight= 0.1477 bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.1477 bond: 0.049 angle: 2.30 clash: 10.6 rota: 1.43 rama: f: 91.03 o: 0.00 Z: -5.22 cb: 0.00 shift=0.3924 cc_mask=0.6534 cycle: 3 start: weight= 0.0738 bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.0738 bond: 0.046 angle: 2.14 clash: 3.8 rota: 1.43 rama: f: 92.31 o: 0.00 Z: -4.32 cb: 0.00 shift=0.3187 cc_mask=0.6447 cycle: 4 start: weight= 0.0369 bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.0369 bond: 0.039 angle: 2.03 clash: 3.0 rota: 1.43 rama: f: 93.59 o: 0.00 Z: -3.84 cb: 0.00 shift=0.2764 cc_mask=0.6347 cycle: 5 start: weight= 0.0185 bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.0185 bond: 0.038 angle: 2.02 clash: 3.8 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.68 cb: 0.00 shift=0.2777 cc_mask=0.6282 cycle: 6 start: weight= 0.0092 bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.0092 bond: 0.039 angle: 1.99 clash: 3.0 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.66 cb: 0.00 shift=0.2866 cc_mask=0.6255 cycle: 7 start: weight= 0.0046 bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.0046 bond: 0.039 angle: 1.99 clash: 3.0 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.67 cb: 0.00 shift=0.2762 cc_mask=0.6236 cycle: 8 start: weight= 0.0023 bond: 0.006 angle: 1.00 clash: 15.1 rota: 2.86 rama: f: 90.00 o: 0.00 Z: -3.48 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.0023 bond: 0.039 angle: 1.98 clash: 3.0 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.67 cb: 0.00 shift=0.2820 cc_mask=0.6230 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0023074234741749227 start: weight= 0.0023 bond: 0.039 angle: 1.98 clash: 3.0 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.67 cb: 0.00 shift=0.0000 cc_mask=0.6287 final: weight= 0.0023 bond: 0.039 angle: 1.97 clash: 3.0 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.84 cb: 0.00 shift=0.2711 cc_mask=0.6233 start: weight= 0.0023 bond: 0.039 angle: 1.97 clash: 3.0 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.84 cb: 0.00 shift=0.2711 cc_mask=0.6233 final: weight= 0.0023 bond: 0.037 angle: 1.95 clash: 2.3 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.93 cb: 0.00 shift=0.3655 cc_mask=0.6228 start: weight= 0.0023 bond: 0.037 angle: 1.95 clash: 2.3 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.93 cb: 0.00 shift=0.3655 cc_mask=0.6228 final: weight= 0.0023 bond: 0.040 angle: 1.96 clash: 3.0 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.81 cb: 0.00 shift=0.4217 cc_mask=0.6224 start: weight= 0.0023 bond: 0.040 angle: 1.96 clash: 3.0 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.81 cb: 0.00 shift=0.4217 cc_mask=0.6224 final: weight= 0.0023 bond: 0.040 angle: 1.95 clash: 2.3 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.83 cb: 0.00 shift=0.4751 cc_mask=0.6211 start: weight= 0.0023 bond: 0.040 angle: 1.95 clash: 2.3 rota: 1.43 rama: f: 96.15 o: 0.00 Z: -3.83 cb: 0.00 shift=0.4751 cc_mask=0.6211 final: weight= 0.0023 bond: 0.041 angle: 1.95 clash: 1.5 rota: 1.43 rama: f: 94.87 o: 0.00 Z: -3.56 cb: 0.00 shift=0.5278 cc_mask=0.6192 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.041 1.022 687 Z= 2.845 ANGLE : 1.953 24.132 926 Z= 1.130 CHIRALITY : 0.120 0.297 99 PLANARITY : 0.031 0.232 117 DIHEDRAL : 13.854 82.492 247 MIN NONBONDED DISTANCE : 2.634 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.51 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 5.13 % FAVORED : 94.87 % ROTAMER: OUTLIERS : 1.43 % ALLOWED : 4.29 % FAVORED : 94.29 % 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: -3.56 (0.75), RESIDUES: 78 HELIX: -2.35 (0.66), RESIDUES: 31 SHEET: -3.11 (1.16), RESIDUES: 17 LOOP : -1.53 (0.88), RESIDUES: 30 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.007 0.002 ARG K 62 TYR 0.085 0.020 TYR K 43 PHE 0.081 0.014 PHE K 78 TRP 0.121 0.051 TRP K 56 HIS 0.006 0.001 HIS K 74 Resolution of map is: 2.8530 Map-model correlation coefficient (CC) CC_mask : 0.6192 =============================================================================== Job complete usr+sys time: 179.89 seconds wall clock time: 3 minutes 30.85 seconds (210.85 seconds total) /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/ase/__init__.py:21: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if LooseVersion(np.__version__) < '1.9': /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. other = LooseVersion(other)