Starting qr.refine on Sun May 19 16:30:55 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dq0_27645.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dq0_27645.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/8dq0_27645.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dq0_27645.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dq0_27645.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dq0_27645.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 276": "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: 4753 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4753 Classifications: {'peptide': 298} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Time building chain proxies: 0.60, per 1000 atoms: 0.13 Number of scatterers: 4753 At special positions: 0 Unit cell: (63.21, 67.08, 63.21, 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 14 16.00 O 430 8.00 N 440 7.00 C 1507 6.00 H 2362 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: 0.92 Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Time building geometry restraints manager: 1.06 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: 2353 1.14 - 1.31: 412 1.31 - 1.48: 1000 1.48 - 1.64: 1024 1.64 - 1.81: 19 Bond restraints: 4808 Sorted by residual: bond pdb=" N PRO A 133 " pdb=" CA PRO A 133 " ideal model delta sigma weight residual 1.466 1.482 -0.016 1.50e-02 4.44e+03 1.10e+00 bond pdb=" C ASP A 275 " pdb=" N PHE A 276 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.15e-01 bond pdb=" C VAL A 22 " pdb=" N PRO A 23 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.56e-01 bond pdb=" C LEU A 211 " pdb=" N PRO A 212 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.51e-01 bond pdb=" C SER A 93 " pdb=" N GLU A 94 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 4.45e-01 ... (remaining 4803 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.73: 95 106.73 - 113.54: 5546 113.54 - 120.34: 1581 120.34 - 127.14: 1407 127.14 - 133.95: 46 Bond angle restraints: 8675 Sorted by residual: angle pdb=" C VAL A 37 " pdb=" N GLU A 38 " pdb=" CA GLU A 38 " ideal model delta sigma weight residual 121.70 128.37 -6.67 1.80e+00 3.09e-01 1.37e+01 angle pdb=" CA CYS A 82 " pdb=" C CYS A 82 " pdb=" N PRO A 83 " ideal model delta sigma weight residual 116.90 121.26 -4.36 1.50e+00 4.44e-01 8.43e+00 angle pdb=" CA LEU A 85 " pdb=" C LEU A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 116.90 119.71 -2.81 1.50e+00 4.44e-01 3.50e+00 angle pdb=" C VAL A 24 " pdb=" N PHE A 25 " pdb=" CA PHE A 25 " ideal model delta sigma weight residual 121.70 118.34 3.36 1.80e+00 3.09e-01 3.48e+00 angle pdb=" CA GLU A 38 " pdb=" C GLU A 38 " pdb=" N GLY A 39 " ideal model delta sigma weight residual 116.20 119.91 -3.71 2.00e+00 2.50e-01 3.44e+00 ... (remaining 8670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 2037 17.70 - 35.39: 131 35.39 - 53.09: 44 53.09 - 70.79: 16 70.79 - 88.49: 2 Dihedral angle restraints: 2230 sinusoidal: 1224 harmonic: 1006 Sorted by residual: dihedral pdb=" CA THR A 68 " pdb=" C THR A 68 " pdb=" N HIS A 69 " pdb=" CA HIS A 69 " ideal model delta harmonic sigma weight residual -180.00 -164.33 -15.67 0 5.00e+00 4.00e-02 9.83e+00 dihedral pdb=" CA GLN A 121 " pdb=" C GLN A 121 " pdb=" N ARG A 122 " pdb=" CA ARG A 122 " ideal model delta harmonic sigma weight residual 180.00 165.01 14.99 0 5.00e+00 4.00e-02 8.99e+00 dihedral pdb=" CA LEU A 4 " pdb=" C LEU A 4 " pdb=" N SER A 5 " pdb=" CA SER A 5 " ideal model delta harmonic sigma weight residual -180.00 -165.10 -14.90 0 5.00e+00 4.00e-02 8.89e+00 ... (remaining 2227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 223 0.027 - 0.055: 92 0.055 - 0.082: 23 0.082 - 0.109: 15 0.109 - 0.136: 5 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ILE A 154 " pdb=" N ILE A 154 " pdb=" C ILE A 154 " pdb=" CB ILE A 154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL A 24 " pdb=" N VAL A 24 " pdb=" C VAL A 24 " pdb=" CB VAL A 24 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 67 " pdb=" N ILE A 67 " pdb=" C ILE A 67 " pdb=" CB ILE A 67 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 355 not shown) Planarity restraints: 719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 277 " 0.015 5.00e-02 4.00e+02 2.23e-02 7.93e-01 pdb=" N PRO A 278 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 278 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 278 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 82 " -0.013 5.00e-02 4.00e+02 2.00e-02 6.39e-01 pdb=" N PRO A 83 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 123 " 0.012 5.00e-02 4.00e+02 1.78e-02 5.09e-01 pdb=" N PRO A 124 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.010 5.00e-02 4.00e+02 ... (remaining 716 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 388 2.15 - 2.77: 8752 2.77 - 3.38: 13654 3.38 - 3.99: 18129 3.99 - 4.60: 27252 Nonbonded interactions: 68175 Sorted by model distance: nonbonded pdb="HH11 ARG A 251 " pdb=" OE2 GLU A 256 " model vdw 1.542 1.800 nonbonded pdb=" O ARG A 148 " pdb="HH12 ARG A 171 " model vdw 1.562 1.800 nonbonded pdb=" H LEU A 143 " pdb=" O LEU A 151 " model vdw 1.585 1.800 nonbonded pdb=" O ASP A 44 " pdb=" H VAL A 48 " model vdw 1.591 1.800 nonbonded pdb=" HH TYR A 72 " pdb=" O PHE A 276 " model vdw 1.593 1.800 ... (remaining 68170 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 14 15.96 2 O 430 7.97 2 N 440 6.97 2 C 1507 5.97 2 H 2362 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 2446 Z= 0.187 ANGLE : 0.959 6.668 3320 Z= 0.453 CHIRALITY : 0.038 0.136 358 PLANARITY : 0.003 0.022 435 DIHEDRAL : 13.085 70.891 909 MIN NONBONDED DISTANCE : 2.250 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 3.37 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.05 % FAVORED : 95.95 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 3.19 % FAVORED : 96.81 % 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: -1.84 (0.45), RESIDUES: 296 HELIX: -0.22 (0.46), RESIDUES: 104 SHEET: -3.05 (0.65), RESIDUES: 41 LOOP : -1.33 (0.48), RESIDUES: 151 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG A 84 TYR 0.009 0.001 TYR A 238 PHE 0.006 0.001 PHE A 276 TRP 0.003 0.000 TRP A 65 HIS 0.002 0.001 HIS A 69 Resolution of map is: 3.5299 Map-model correlation coefficient (CC) CC_mask : 0.7545 weight= None bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 Initial weight estimate from ratio of grad norms: 0.3188193661901707 cycle: 0 start: weight= 0.3188 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.3188 bond: 0.024 angle: 2.49 clash: 14.1 rota: 1.99 rama: f: 88.51 o: 1.01 Z: -5.06 cb: 1.45 shift=0.3402 cc_mask=0.8015 cycle: 1 start: weight= 0.2232 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.2232 bond: 0.019 angle: 2.14 clash: 8.0 rota: 1.20 rama: f: 90.88 o: 0.34 Z: -4.38 cb: 1.09 shift=0.3177 cc_mask=0.7955 cycle: 2 start: weight= 0.1562 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.1562 bond: 0.016 angle: 1.92 clash: 4.6 rota: 0.80 rama: f: 93.24 o: 0.00 Z: -3.69 cb: 0.72 shift=0.3018 cc_mask=0.7896 cycle: 3 start: weight= 0.0781 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.0781 bond: 0.012 angle: 1.67 clash: 2.1 rota: 0.80 rama: f: 95.61 o: 0.00 Z: -2.66 cb: 0.00 shift=0.2556 cc_mask=0.7772 cycle: 4 start: weight= 0.0547 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.0547 bond: 0.011 angle: 1.62 clash: 1.1 rota: 0.80 rama: f: 96.28 o: 0.00 Z: -2.75 cb: 0.00 shift=0.2423 cc_mask=0.7721 cycle: 5 start: weight= 0.0383 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.0383 bond: 0.010 angle: 1.58 clash: 0.4 rota: 0.80 rama: f: 97.30 o: 0.00 Z: -2.69 cb: 0.00 shift=0.2318 cc_mask=0.7670 cycle: 6 start: weight= 0.0191 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.0191 bond: 0.009 angle: 1.56 clash: 0.4 rota: 0.80 rama: f: 97.97 o: 0.00 Z: -2.47 cb: 0.00 shift=0.2271 cc_mask=0.7595 cycle: 7 start: weight= 0.0134 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.0134 bond: 0.009 angle: 1.55 clash: 0.4 rota: 0.80 rama: f: 97.97 o: 0.00 Z: -2.39 cb: 0.00 shift=0.2248 cc_mask=0.7568 cycle: 8 start: weight= 0.0094 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.0094 bond: 0.009 angle: 1.55 clash: 0.4 rota: 0.80 rama: f: 98.31 o: 0.00 Z: -2.37 cb: 0.00 shift=0.2253 cc_mask=0.7548 cycle: 9 start: weight= 0.0047 bond: 0.004 angle: 0.96 clash: 3.4 rota: 0.00 rama: f: 95.95 o: 0.00 Z: -1.84 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.0047 bond: 0.009 angle: 1.55 clash: 0.0 rota: 0.80 rama: f: 97.97 o: 0.00 Z: -2.34 cb: 0.00 shift=0.2282 cc_mask=0.7520 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.004688597451613425 start: weight= 0.0047 bond: 0.009 angle: 1.55 clash: 0.0 rota: 0.80 rama: f: 97.97 o: 0.00 Z: -2.34 cb: 0.00 shift=0.0000 cc_mask=0.7545 final: weight= 0.0047 bond: 0.009 angle: 1.55 clash: 0.0 rota: 0.80 rama: f: 97.64 o: 0.00 Z: -2.33 cb: 0.00 shift=0.2291 cc_mask=0.7520 start: weight= 0.0047 bond: 0.009 angle: 1.55 clash: 0.0 rota: 0.80 rama: f: 97.64 o: 0.00 Z: -2.33 cb: 0.00 shift=0.2291 cc_mask=0.7520 final: weight= 0.0047 bond: 0.009 angle: 1.52 clash: 0.2 rota: 0.40 rama: f: 97.64 o: 0.00 Z: -2.25 cb: 0.00 shift=0.3032 cc_mask=0.7506 start: weight= 0.0047 bond: 0.009 angle: 1.52 clash: 0.2 rota: 0.40 rama: f: 97.64 o: 0.00 Z: -2.25 cb: 0.00 shift=0.3032 cc_mask=0.7506 final: weight= 0.0047 bond: 0.009 angle: 1.53 clash: 0.6 rota: 0.40 rama: f: 97.97 o: 0.00 Z: -2.06 cb: 0.00 shift=0.3557 cc_mask=0.7485 start: weight= 0.0047 bond: 0.009 angle: 1.53 clash: 0.6 rota: 0.40 rama: f: 97.97 o: 0.00 Z: -2.06 cb: 0.00 shift=0.3557 cc_mask=0.7485 final: weight= 0.0047 bond: 0.009 angle: 1.52 clash: 1.3 rota: 0.40 rama: f: 97.97 o: 0.00 Z: -2.05 cb: 0.00 shift=0.3910 cc_mask=0.7465 start: weight= 0.0047 bond: 0.009 angle: 1.52 clash: 1.3 rota: 0.40 rama: f: 97.97 o: 0.00 Z: -2.05 cb: 0.00 shift=0.3910 cc_mask=0.7465 final: weight= 0.0047 bond: 0.009 angle: 1.53 clash: 0.8 rota: 0.40 rama: f: 97.64 o: 0.00 Z: -2.15 cb: 0.00 shift=0.4225 cc_mask=0.7446 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.034 2446 Z= 0.480 ANGLE : 1.532 8.850 3320 Z= 0.821 CHIRALITY : 0.110 0.378 358 PLANARITY : 0.025 0.169 435 DIHEDRAL : 13.422 85.911 909 MIN NONBONDED DISTANCE : 2.626 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.84 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.36 % FAVORED : 97.64 % ROTAMER: OUTLIERS : 0.40 % ALLOWED : 3.19 % FAVORED : 96.41 % 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: -2.15 (0.42), RESIDUES: 296 HELIX: -0.96 (0.41), RESIDUES: 113 SHEET: -3.73 (0.75), RESIDUES: 31 LOOP : -1.17 (0.45), RESIDUES: 152 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.022 0.004 ARG A 118 TYR 0.113 0.024 TYR A 80 PHE 0.030 0.011 PHE A 195 TRP 0.107 0.019 TRP A 34 HIS 0.012 0.002 HIS A 69 Resolution of map is: 3.5299 Map-model correlation coefficient (CC) CC_mask : 0.7446 =============================================================================== Job complete usr+sys time: 476.18 seconds wall clock time: 8 minutes 37.74 seconds (517.74 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)