Starting qr.refine on Sun May 19 14:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi5_43249.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi5_43249.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/8vi5_43249.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi5_43249.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi5_43249.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi5_43249.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 "A PHE 28": "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: 4942 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4942 Classifications: {'peptide': 308} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 0.63, per 1000 atoms: 0.13 Number of scatterers: 4942 At special positions: 0 Unit cell: (62.826, 60.562, 62.826, 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 9 16.00 O 402 8.00 N 380 7.00 C 1662 6.00 H 2489 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: 0.96 Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 2488 1.14 - 1.31: 356 1.31 - 1.48: 1110 1.48 - 1.64: 1052 1.64 - 1.81: 17 Bond restraints: 5023 Sorted by residual: bond pdb=" C LEU A 144 " pdb=" O LEU A 144 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 4.95e-01 bond pdb=" C ALA A 206 " pdb=" O ALA A 206 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 4.64e-01 bond pdb=" N PRO A 182 " pdb=" CA PRO A 182 " ideal model delta sigma weight residual 1.466 1.476 -0.010 1.50e-02 4.44e+03 4.33e-01 bond pdb=" C PHE A 245 " pdb=" O PHE A 245 " ideal model delta sigma weight residual 1.231 1.244 -0.013 2.00e-02 2.50e+03 4.22e-01 bond pdb=" N PRO A 87 " pdb=" CA PRO A 87 " ideal model delta sigma weight residual 1.466 1.475 -0.009 1.50e-02 4.44e+03 3.93e-01 ... (remaining 5018 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.35: 192 107.35 - 114.01: 5702 114.01 - 120.66: 1956 120.66 - 127.32: 1192 127.32 - 133.97: 38 Bond angle restraints: 9080 Sorted by residual: angle pdb=" CA GLU A 181 " pdb=" C GLU A 181 " pdb=" N PRO A 182 " ideal model delta sigma weight residual 116.90 121.31 -4.41 1.50e+00 4.44e-01 8.64e+00 angle pdb=" CA LEU A 144 " pdb=" C LEU A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 116.90 121.19 -4.29 1.50e+00 4.44e-01 8.16e+00 angle pdb=" CA PHE A 245 " pdb=" C PHE A 245 " pdb=" N PRO A 246 " ideal model delta sigma weight residual 116.90 121.12 -4.22 1.50e+00 4.44e-01 7.91e+00 angle pdb=" CA ALA A 206 " pdb=" C ALA A 206 " pdb=" N PRO A 207 " ideal model delta sigma weight residual 116.90 120.78 -3.88 1.50e+00 4.44e-01 6.68e+00 angle pdb=" C SER A 192 " pdb=" CA SER A 192 " pdb=" CB SER A 192 " ideal model delta sigma weight residual 110.10 114.54 -4.44 1.90e+00 2.77e-01 5.46e+00 ... (remaining 9075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 2158 14.32 - 28.64: 133 28.64 - 42.96: 44 42.96 - 57.28: 39 57.28 - 71.60: 3 Dihedral angle restraints: 2377 sinusoidal: 1211 harmonic: 1166 Sorted by residual: dihedral pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " pdb=" CE MET A 294 " ideal model delta sinusoidal sigma weight residual 180.00 128.76 51.24 3 1.50e+01 4.44e-03 8.99e+00 dihedral pdb=" CA GLN A 196 " pdb=" CB GLN A 196 " pdb=" CG GLN A 196 " pdb=" CD GLN A 196 " ideal model delta sinusoidal sigma weight residual -60.00 -108.31 48.31 3 1.50e+01 4.44e-03 8.62e+00 dihedral pdb=" N TRP A 231 " pdb=" CA TRP A 231 " pdb=" CB TRP A 231 " pdb=" CG TRP A 231 " ideal model delta sinusoidal sigma weight residual -60.00 -107.22 47.22 3 1.50e+01 4.44e-03 8.46e+00 ... (remaining 2374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 224 0.023 - 0.046: 102 0.046 - 0.070: 30 0.070 - 0.093: 25 0.093 - 0.116: 9 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA PRO A 207 " pdb=" N PRO A 207 " pdb=" C PRO A 207 " pdb=" CB PRO A 207 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.37e-01 chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA VAL A 43 " pdb=" N VAL A 43 " pdb=" C VAL A 43 " pdb=" CB VAL A 43 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 387 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 24 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C SER A 24 " -0.017 2.00e-02 2.50e+03 pdb=" O SER A 24 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU A 25 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 44 " -0.005 2.00e-02 2.50e+03 9.83e-03 9.67e-01 pdb=" C LEU A 44 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 44 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY A 45 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 22 " -0.005 2.00e-02 2.50e+03 9.66e-03 9.34e-01 pdb=" C ALA A 22 " 0.017 2.00e-02 2.50e+03 pdb=" O ALA A 22 " -0.006 2.00e-02 2.50e+03 pdb=" N LEU A 23 " -0.006 2.00e-02 2.50e+03 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 594 2.19 - 2.79: 9709 2.79 - 3.40: 14862 3.40 - 4.00: 19485 4.00 - 4.60: 29136 Nonbonded interactions: 73786 Sorted by model distance: nonbonded pdb=" O PHE A 197 " pdb=" HG1 THR A 200 " model vdw 1.592 1.800 nonbonded pdb=" O PRO A 17 " pdb=" H ALA A 21 " model vdw 1.601 1.800 nonbonded pdb=" HH TYR A 13 " pdb=" O PHE A 311 " model vdw 1.609 1.800 nonbonded pdb=" O MET A 267 " pdb=" HG SER A 270 " model vdw 1.612 1.800 nonbonded pdb=" O ASN A 269 " pdb=" HG1 THR A 272 " model vdw 1.613 1.800 ... (remaining 73781 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 9 15.96 2 O 402 7.97 2 N 380 6.97 2 C 1662 5.97 2 H 2489 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 : 0.004 0.016 2534 Z= 0.198 ANGLE : 0.883 4.552 3457 Z= 0.443 CHIRALITY : 0.036 0.116 390 PLANARITY : 0.004 0.023 420 DIHEDRAL : 11.997 71.595 856 MIN NONBONDED DISTANCE : 2.305 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 2.63 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 6.86 % FAVORED : 93.14 % ROTAMER: OUTLIERS : 0.78 % ALLOWED : 0.39 % FAVORED : 98.82 % 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: -0.75 (0.50), RESIDUES: 306 HELIX: -0.55 (0.34), RESIDUES: 241 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.49 (0.89), RESIDUES: 65 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.001 ARG A 198 TYR 0.005 0.001 TYR A 61 PHE 0.007 0.001 PHE A 260 TRP 0.006 0.001 TRP A 177 HIS 0.001 0.000 HIS A 75 Resolution of map is: 3.2996 Map-model correlation coefficient (CC) CC_mask : 0.8393 weight= None bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 Initial weight estimate from ratio of grad norms: 0.2861300715429796 cycle: 0 start: weight= 0.2861 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.2861 bond: 0.022 angle: 2.08 clash: 4.5 rota: 0.39 rama: f: 96.41 o: 0.00 Z: -5.28 cb: 0.00 shift=0.3106 cc_mask=0.8735 cycle: 1 start: weight= 0.2003 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.2003 bond: 0.018 angle: 1.80 clash: 2.4 rota: 0.39 rama: f: 97.39 o: 0.00 Z: -4.10 cb: 0.00 shift=0.2726 cc_mask=0.8688 cycle: 2 start: weight= 0.1402 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.1402 bond: 0.015 angle: 1.61 clash: 1.0 rota: 0.39 rama: f: 98.04 o: 0.00 Z: -2.93 cb: 0.00 shift=0.2437 cc_mask=0.8648 cycle: 3 start: weight= 0.0701 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0701 bond: 0.011 angle: 1.41 clash: 0.6 rota: 0.39 rama: f: 97.71 o: 0.00 Z: -1.52 cb: 0.00 shift=0.2072 cc_mask=0.8576 cycle: 4 start: weight= 0.0491 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0491 bond: 0.010 angle: 1.35 clash: 0.4 rota: 0.39 rama: f: 98.04 o: 0.00 Z: -1.14 cb: 0.00 shift=0.1934 cc_mask=0.8541 cycle: 5 start: weight= 0.0343 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0343 bond: 0.009 angle: 1.32 clash: 0.4 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -0.93 cb: 0.00 shift=0.1865 cc_mask=0.8511 cycle: 6 start: weight= 0.0172 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0172 bond: 0.009 angle: 1.29 clash: 0.4 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -0.74 cb: 0.00 shift=0.1813 cc_mask=0.8470 cycle: 7 start: weight= 0.0120 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0120 bond: 0.009 angle: 1.29 clash: 0.4 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -0.71 cb: 0.00 shift=0.1818 cc_mask=0.8455 cycle: 8 start: weight= 0.0084 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0084 bond: 0.008 angle: 1.28 clash: 0.4 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -0.68 cb: 0.00 shift=0.1815 cc_mask=0.8444 cycle: 9 start: weight= 0.0042 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0042 bond: 0.008 angle: 1.27 clash: 0.4 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -0.66 cb: 0.00 shift=0.1811 cc_mask=0.8430 cycle: 10 start: weight= 0.0029 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0029 bond: 0.008 angle: 1.27 clash: 0.4 rota: 0.00 rama: f: 98.69 o: 0.00 Z: -0.58 cb: 0.00 shift=0.1782 cc_mask=0.8427 cycle: 11 start: weight= 0.0021 bond: 0.004 angle: 0.88 clash: 2.6 rota: 0.78 rama: f: 93.14 o: 0.00 Z: -0.75 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0021 bond: 0.008 angle: 1.28 clash: 0.4 rota: 0.00 rama: f: 98.69 o: 0.00 Z: -0.67 cb: 0.00 shift=0.1822 cc_mask=0.8423 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.002061853653201301 start: weight= 0.0021 bond: 0.008 angle: 1.28 clash: 0.4 rota: 0.00 rama: f: 98.69 o: 0.00 Z: -0.67 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0021 bond: 0.008 angle: 1.27 clash: 0.4 rota: 0.00 rama: f: 98.69 o: 0.00 Z: -0.58 cb: 0.00 shift=0.1785 cc_mask=0.8424 start: weight= 0.0021 bond: 0.008 angle: 1.27 clash: 0.4 rota: 0.00 rama: f: 98.69 o: 0.00 Z: -0.58 cb: 0.00 shift=0.1785 cc_mask=0.8424 final: weight= 0.0021 bond: 0.008 angle: 1.26 clash: 0.2 rota: 0.00 rama: f: 97.71 o: 0.00 Z: -1.14 cb: 0.00 shift=0.2359 cc_mask=0.8400 start: weight= 0.0021 bond: 0.008 angle: 1.26 clash: 0.2 rota: 0.00 rama: f: 97.71 o: 0.00 Z: -1.14 cb: 0.00 shift=0.2359 cc_mask=0.8400 final: weight= 0.0021 bond: 0.008 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -1.28 cb: 0.00 shift=0.2880 cc_mask=0.8365 start: weight= 0.0021 bond: 0.008 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -1.28 cb: 0.00 shift=0.2880 cc_mask=0.8365 final: weight= 0.0021 bond: 0.008 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -1.30 cb: 0.00 shift=0.3150 cc_mask=0.8337 start: weight= 0.0021 bond: 0.008 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -1.30 cb: 0.00 shift=0.3150 cc_mask=0.8337 final: weight= 0.0021 bond: 0.008 angle: 1.29 clash: 0.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -1.24 cb: 0.00 shift=0.3414 cc_mask=0.8305 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.008 0.040 2534 Z= 0.439 ANGLE : 1.287 8.912 3457 Z= 0.692 CHIRALITY : 0.107 0.316 390 PLANARITY : 0.012 0.073 420 DIHEDRAL : 11.557 81.705 856 MIN NONBONDED DISTANCE : 2.618 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.20 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.96 % FAVORED : 98.04 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.78 % FAVORED : 99.22 % 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: -1.24 (0.44), RESIDUES: 306 HELIX: -1.06 (0.26), RESIDUES: 242 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 1.10 (1.00), RESIDUES: 64 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.018 0.004 ARG A 189 TYR 0.055 0.013 TYR A 275 PHE 0.056 0.010 PHE A 7 TRP 0.071 0.013 TRP A 231 HIS 0.006 0.002 HIS A 139 Resolution of map is: 3.2996 Map-model correlation coefficient (CC) CC_mask : 0.8305 =============================================================================== Job complete usr+sys time: 497.24 seconds wall clock time: 9 minutes 5.60 seconds (545.60 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)