Starting qr.refine on Sun May 19 14:27:52 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjy_18454.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjy_18454.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/8qjy_18454.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjy_18454.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjy_18454.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjy_18454.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 318": "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: 3038 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3038 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Time building chain proxies: 0.42, per 1000 atoms: 0.14 Number of scatterers: 3038 At special positions: 0 Unit cell: (61.1, 57.2, 66.3, 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 310 8.00 N 258 7.00 C 971 6.00 H 1490 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: 0.57 Adding C-beta torsion restraints... Number of C-beta restraints generated: 376 Time building geometry restraints manager: 0.65 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: 1486 1.14 - 1.31: 262 1.31 - 1.48: 661 1.48 - 1.64: 648 1.64 - 1.81: 14 Bond restraints: 3071 Sorted by residual: bond pdb=" C ALA A 268 " pdb=" N PHE A 269 " ideal model delta sigma weight residual 1.329 1.344 -0.015 1.40e-02 5.10e+03 1.16e+00 bond pdb=" C TYR A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.341 1.328 0.013 1.60e-02 3.91e+03 7.03e-01 bond pdb=" C TYR A 242 " pdb=" O TYR A 242 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 5.18e-01 bond pdb=" C THR A 214 " pdb=" N PRO A 215 " ideal model delta sigma weight residual 1.341 1.331 0.010 1.60e-02 3.91e+03 3.61e-01 bond pdb=" C VAL A 138 " pdb=" N ASN A 139 " ideal model delta sigma weight residual 1.329 1.337 -0.008 1.40e-02 5.10e+03 3.60e-01 ... (remaining 3066 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.42: 101 107.42 - 114.05: 3582 114.05 - 120.68: 982 120.68 - 127.31: 825 127.31 - 133.94: 15 Bond angle restraints: 5505 Sorted by residual: angle pdb=" C ASN A 278 " pdb=" CA ASN A 278 " pdb=" CB ASN A 278 " ideal model delta sigma weight residual 110.10 114.64 -4.54 1.90e+00 2.77e-01 5.71e+00 angle pdb=" N PHE A 172 " pdb=" CA PHE A 172 " pdb=" C PHE A 172 " ideal model delta sigma weight residual 111.00 105.82 5.18 2.80e+00 1.28e-01 3.43e+00 angle pdb=" N SER A 220 " pdb=" CA SER A 220 " pdb=" C SER A 220 " ideal model delta sigma weight residual 111.00 105.95 5.05 2.80e+00 1.28e-01 3.26e+00 angle pdb=" N GLN A 146 " pdb=" CA GLN A 146 " pdb=" C GLN A 146 " ideal model delta sigma weight residual 111.00 105.97 5.03 2.80e+00 1.28e-01 3.22e+00 angle pdb=" N THR A 165 " pdb=" CA THR A 165 " pdb=" C THR A 165 " ideal model delta sigma weight residual 111.00 106.23 4.77 2.80e+00 1.28e-01 2.91e+00 ... (remaining 5500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 1362 14.79 - 29.58: 77 29.58 - 44.37: 23 44.37 - 59.16: 10 59.16 - 73.95: 3 Dihedral angle restraints: 1475 sinusoidal: 784 harmonic: 691 Sorted by residual: dihedral pdb=" CA PHE A 172 " pdb=" C PHE A 172 " pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta harmonic sigma weight residual -180.00 -164.58 -15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA ARG A 249 " pdb=" CB ARG A 249 " pdb=" CG ARG A 249 " pdb=" CD ARG A 249 " ideal model delta sinusoidal sigma weight residual -180.00 -125.55 -54.45 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CB MET A 236 " pdb=" CG MET A 236 " pdb=" SD MET A 236 " pdb=" CE MET A 236 " ideal model delta sinusoidal sigma weight residual 60.00 107.33 -47.33 3 1.50e+01 4.44e-03 8.48e+00 ... (remaining 1472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 152 0.031 - 0.061: 71 0.061 - 0.092: 12 0.092 - 0.123: 10 0.123 - 0.153: 6 Chirality restraints: 251 Sorted by residual: chirality pdb=" CA ILE A 176 " pdb=" N ILE A 176 " pdb=" C ILE A 176 " pdb=" CB ILE A 176 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE A 292 " pdb=" N ILE A 292 " pdb=" C ILE A 292 " pdb=" CB ILE A 292 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 248 not shown) Planarity restraints: 467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 139 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 140 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 172 " 0.010 2.00e-02 2.50e+03 5.36e-03 8.62e-01 pdb=" CG PHE A 172 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE A 172 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 172 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 172 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 172 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 172 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 172 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 172 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 318 " -0.009 2.00e-02 2.50e+03 4.31e-03 5.57e-01 pdb=" CG PHE A 318 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 318 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 318 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 318 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 318 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 318 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 318 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 318 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 318 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 318 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 318 " -0.001 2.00e-02 2.50e+03 ... (remaining 464 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 226 2.14 - 2.76: 5337 2.76 - 3.37: 8255 3.37 - 3.99: 11611 3.99 - 4.60: 16639 Nonbonded interactions: 42068 Sorted by model distance: nonbonded pdb=" H SER A 264 " pdb=" OE2 GLU A 303 " model vdw 1.530 1.800 nonbonded pdb=" O PHE A 235 " pdb=" HH TYR A 320 " model vdw 1.582 1.800 nonbonded pdb=" O MET A 236 " pdb=" H GLU A 323 " model vdw 1.664 1.800 nonbonded pdb=" H ASN A 278 " pdb=" O CYS A 289 " model vdw 1.671 1.800 nonbonded pdb=" HZ2 LYS A 219 " pdb=" O GLY A 221 " model vdw 1.676 1.800 ... (remaining 42063 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 310 7.97 2 N 258 6.97 2 C 971 5.97 2 H 1490 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 : 0.003 0.015 1581 Z= 0.171 ANGLE : 0.958 5.183 2158 Z= 0.440 CHIRALITY : 0.043 0.153 251 PLANARITY : 0.003 0.030 278 DIHEDRAL : 10.786 73.952 559 MIN NONBONDED DISTANCE : 2.300 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 3.95 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 6.67 % FAVORED : 93.33 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 5.14 % FAVORED : 94.86 % 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: -1.34 (0.62), RESIDUES: 195 HELIX: -0.35 (1.76), RESIDUES: 6 SHEET: -0.65 (0.57), RESIDUES: 77 LOOP : -1.06 (0.65), RESIDUES: 112 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG A 280 TYR 0.010 0.001 TYR A 320 PHE 0.015 0.002 PHE A 172 TRP 0.008 0.001 TRP A 296 HIS 0.002 0.001 HIS A 188 Resolution of map is: 3.8955 Map-model correlation coefficient (CC) CC_mask : 0.8202 weight= None bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 Initial weight estimate from ratio of grad norms: 0.5886573505616123 cycle: 0 start: weight= 0.5887 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.5887 bond: 0.030 angle: 2.50 clash: 22.7 rota: 1.71 rama: f: 88.72 o: 0.51 Z: -4.22 cb: 1.06 shift=0.3818 cc_mask=0.8678 cycle: 1 start: weight= 0.4121 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.4121 bond: 0.024 angle: 2.13 clash: 13.2 rota: 1.14 rama: f: 92.82 o: 0.00 Z: -3.24 cb: 0.53 shift=0.3418 cc_mask=0.8615 cycle: 2 start: weight= 0.2884 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.2884 bond: 0.019 angle: 1.87 clash: 8.9 rota: 0.57 rama: f: 94.87 o: 0.00 Z: -2.53 cb: 0.00 shift=0.3077 cc_mask=0.8557 cycle: 3 start: weight= 0.1442 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.1442 bond: 0.014 angle: 1.62 clash: 3.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -1.40 cb: 0.00 shift=0.2409 cc_mask=0.8439 cycle: 4 start: weight= 0.1010 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.1010 bond: 0.012 angle: 1.58 clash: 2.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -1.06 cb: 0.00 shift=0.2196 cc_mask=0.8387 cycle: 5 start: weight= 0.0707 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.0707 bond: 0.011 angle: 1.56 clash: 2.0 rota: 0.00 rama: f: 98.46 o: 0.00 Z: -0.98 cb: 0.00 shift=0.2120 cc_mask=0.8343 cycle: 6 start: weight= 0.0353 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.0353 bond: 0.010 angle: 1.55 clash: 1.3 rota: 0.00 rama: f: 97.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.2022 cc_mask=0.8285 cycle: 7 start: weight= 0.0247 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.0247 bond: 0.010 angle: 1.54 clash: 1.3 rota: 0.00 rama: f: 97.95 o: 0.00 Z: -0.72 cb: 0.00 shift=0.2014 cc_mask=0.8264 cycle: 8 start: weight= 0.0173 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.0173 bond: 0.010 angle: 1.54 clash: 1.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.71 cb: 0.00 shift=0.1989 cc_mask=0.8252 cycle: 9 start: weight= 0.0087 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.0087 bond: 0.009 angle: 1.54 clash: 1.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.74 cb: 0.00 shift=0.1991 cc_mask=0.8235 cycle: 10 start: weight= 0.0061 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.0061 bond: 0.009 angle: 1.55 clash: 1.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.74 cb: 0.00 shift=0.1996 cc_mask=0.8230 cycle: 11 start: weight= 0.0042 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.0042 bond: 0.009 angle: 1.55 clash: 1.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.75 cb: 0.00 shift=0.2003 cc_mask=0.8226 cycle: 12 start: weight= 0.0021 bond: 0.003 angle: 0.96 clash: 4.0 rota: 0.00 rama: f: 93.33 o: 0.00 Z: -1.34 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 1.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.76 cb: 0.00 shift=0.2009 cc_mask=0.8221 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.002120932801984334 start: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 1.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.76 cb: 0.00 shift=0.0000 cc_mask=0.8202 final: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 1.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.77 cb: 0.00 shift=0.2015 cc_mask=0.8221 start: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 1.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.77 cb: 0.00 shift=0.2015 cc_mask=0.8221 final: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 1.0 rota: 0.00 rama: f: 97.95 o: 0.00 Z: -0.67 cb: 0.00 shift=0.2799 cc_mask=0.8205 start: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 1.0 rota: 0.00 rama: f: 97.95 o: 0.00 Z: -0.67 cb: 0.00 shift=0.2799 cc_mask=0.8205 final: weight= 0.0021 bond: 0.009 angle: 1.54 clash: 0.3 rota: 0.00 rama: f: 98.46 o: 0.00 Z: -0.92 cb: 0.00 shift=0.3343 cc_mask=0.8180 start: weight= 0.0021 bond: 0.009 angle: 1.54 clash: 0.3 rota: 0.00 rama: f: 98.46 o: 0.00 Z: -0.92 cb: 0.00 shift=0.3343 cc_mask=0.8180 final: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 0.7 rota: 0.00 rama: f: 97.95 o: 0.00 Z: -1.23 cb: 0.53 shift=0.3716 cc_mask=0.8166 start: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 0.7 rota: 0.00 rama: f: 97.95 o: 0.00 Z: -1.23 cb: 0.53 shift=0.3716 cc_mask=0.8166 final: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 0.3 rota: 0.57 rama: f: 97.44 o: 0.00 Z: -1.20 cb: 0.00 shift=0.4131 cc_mask=0.8142 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.032 1581 Z= 0.480 ANGLE : 1.552 9.076 2158 Z= 0.815 CHIRALITY : 0.114 0.430 251 PLANARITY : 0.018 0.144 278 DIHEDRAL : 11.889 88.931 559 MIN NONBONDED DISTANCE : 2.616 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.33 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.56 % FAVORED : 97.44 % ROTAMER: OUTLIERS : 0.57 % ALLOWED : 1.71 % FAVORED : 97.71 % 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: -1.20 (0.60), RESIDUES: 195 HELIX: -3.09 (0.84), RESIDUES: 12 SHEET: -1.22 (0.52), RESIDUES: 70 LOOP : -0.09 (0.66), RESIDUES: 113 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.010 0.003 ARG A 266 TYR 0.061 0.015 TYR A 320 PHE 0.047 0.013 PHE A 172 TRP 0.099 0.025 TRP A 296 HIS 0.002 0.001 HIS A 218 Resolution of map is: 3.8955 Map-model correlation coefficient (CC) CC_mask : 0.8142 =============================================================================== Job complete usr+sys time: 351.26 seconds wall clock time: 6 minutes 38.21 seconds (398.21 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)