Starting qr.refine on Sun May 19 13:53:40 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6xmx_22265.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6xmx_22265.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/6xmx_22265.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6xmx_22265.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6xmx_22265.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6xmx_22265.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 None 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: 1976 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1976 Classifications: {'peptide': 122} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 119} Time building chain proxies: 0.31, per 1000 atoms: 0.16 Number of scatterers: 1976 At special positions: 0 Unit cell: (58.575, 56.1, 56.1, 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 11 16.00 O 177 8.00 N 170 7.00 C 618 6.00 H 1000 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: 0.34 Adding C-beta torsion restraints... Number of C-beta restraints generated: 238 Time building geometry restraints manager: 0.39 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: 995 1.15 - 1.31: 163 1.31 - 1.48: 385 1.48 - 1.65: 430 1.65 - 1.81: 17 Bond restraints: 1990 Sorted by residual: bond pdb=" CA THR A 32 " pdb=" CB THR A 32 " ideal model delta sigma weight residual 1.540 1.524 0.016 2.70e-02 1.37e+03 3.48e-01 bond pdb=" C CYS A 121 " pdb=" O CYS A 121 " ideal model delta sigma weight residual 1.231 1.242 -0.011 2.00e-02 2.50e+03 2.88e-01 bond pdb=" C SER A 54 " pdb=" N GLY A 55 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.40e-02 5.10e+03 2.70e-01 bond pdb=" CA THR A 120 " pdb=" CB THR A 120 " ideal model delta sigma weight residual 1.540 1.526 0.014 2.70e-02 1.37e+03 2.64e-01 bond pdb=" C LEU A 87 " pdb=" O LEU A 87 " ideal model delta sigma weight residual 1.231 1.241 -0.010 2.00e-02 2.50e+03 2.63e-01 ... (remaining 1985 not shown) Histogram of bond angle deviations from ideal: 100.64 - 106.76: 20 106.76 - 112.88: 2339 112.88 - 119.00: 393 119.00 - 125.11: 796 125.11 - 131.23: 42 Bond angle restraints: 3590 Sorted by residual: angle pdb=" C THR A 92 " pdb=" N SER A 93 " pdb=" CA SER A 93 " ideal model delta sigma weight residual 121.70 125.82 -4.12 1.80e+00 3.09e-01 5.23e+00 angle pdb=" CA THR A 92 " pdb=" C THR A 92 " pdb=" N SER A 93 " ideal model delta sigma weight residual 116.20 119.45 -3.25 2.00e+00 2.50e-01 2.65e+00 angle pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N VAL A 34 " ideal model delta sigma weight residual 116.20 119.35 -3.15 2.00e+00 2.50e-01 2.48e+00 angle pdb=" N MET A 114 " pdb=" CA MET A 114 " pdb=" C MET A 114 " ideal model delta sigma weight residual 111.00 106.60 4.40 2.80e+00 1.28e-01 2.47e+00 angle pdb=" C ILE A 125 " pdb=" CA ILE A 125 " pdb=" CB ILE A 125 " ideal model delta sigma weight residual 111.60 108.64 2.96 2.00e+00 2.50e-01 2.19e+00 ... (remaining 3585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 852 15.72 - 31.43: 51 31.43 - 47.15: 18 47.15 - 62.86: 6 62.86 - 78.58: 2 Dihedral angle restraints: 929 sinusoidal: 510 harmonic: 419 Sorted by residual: dihedral pdb=" N GLU A 81 " pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" CG GLU A 81 " ideal model delta sinusoidal sigma weight residual 180.00 126.47 53.53 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CA ARG A 26 " pdb=" CB ARG A 26 " pdb=" CG ARG A 26 " pdb=" CD ARG A 26 " ideal model delta sinusoidal sigma weight residual -60.00 -104.56 44.56 3 1.50e+01 4.44e-03 8.01e+00 dihedral pdb=" CA ARG A 44 " pdb=" CB ARG A 44 " pdb=" CG ARG A 44 " pdb=" CD ARG A 44 " ideal model delta sinusoidal sigma weight residual -180.00 -136.67 -43.33 3 1.50e+01 4.44e-03 7.79e+00 ... (remaining 926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 99 0.026 - 0.052: 33 0.052 - 0.078: 17 0.078 - 0.103: 3 0.103 - 0.129: 8 Chirality restraints: 160 Sorted by residual: chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 157 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 81 " 0.003 2.00e-02 2.50e+03 5.88e-03 3.46e-01 pdb=" C GLU A 81 " -0.010 2.00e-02 2.50e+03 pdb=" O GLU A 81 " 0.004 2.00e-02 2.50e+03 pdb=" N GLY A 82 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 81 " 0.003 2.00e-02 2.50e+03 5.27e-03 2.78e-01 pdb=" N GLY A 82 " -0.009 2.00e-02 2.50e+03 pdb=" CA GLY A 82 " 0.002 2.00e-02 2.50e+03 pdb=" H GLY A 82 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 79 " 0.008 5.00e-02 4.00e+02 1.28e-02 2.62e-01 pdb=" N PRO A 80 " -0.022 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " 0.006 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " 0.007 5.00e-02 4.00e+02 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 143 2.14 - 2.75: 3496 2.75 - 3.37: 5504 3.37 - 3.98: 7155 3.98 - 4.60: 10363 Nonbonded interactions: 26661 Sorted by model distance: nonbonded pdb=" O TYR A 58 " pdb=" HG1 THR A 62 " model vdw 1.521 1.800 nonbonded pdb=" O PHE A 89 " pdb=" H SER A 93 " model vdw 1.525 1.800 nonbonded pdb=" HZ3 LYS A 47 " pdb=" O CYS A 67 " model vdw 1.596 1.800 nonbonded pdb=" O THR A 92 " pdb=" HG SER A 93 " model vdw 1.604 1.800 nonbonded pdb=" O ASP A 88 " pdb=" HG1 THR A 92 " model vdw 1.622 1.800 ... (remaining 26656 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 11 15.96 2 O 177 7.97 2 N 170 6.97 2 C 618 5.97 2 H 1000 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 0.016 990 Z= 0.181 ANGLE : 0.911 4.399 1336 Z= 0.445 CHIRALITY : 0.040 0.129 160 PLANARITY : 0.002 0.013 169 DIHEDRAL : 13.694 78.578 370 MIN NONBONDED DISTANCE : 2.290 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.52 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 3.33 % FAVORED : 96.67 % ROTAMER: OUTLIERS : 0.89 % ALLOWED : 0.00 % FAVORED : 99.11 % 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: 0.14 (0.70), RESIDUES: 120 HELIX: 0.52 (0.54), RESIDUES: 73 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -0.42 (0.90), RESIDUES: 47 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG A 28 TYR 0.002 0.001 TYR A 58 PHE 0.004 0.001 PHE A 43 HIS 0.001 0.001 HIS A 14 Resolution of map is: 3.5863 Map-model correlation coefficient (CC) CC_mask : 0.5258 weight= None bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 Initial weight estimate from ratio of grad norms: 0.3897298640953954 cycle: 0 start: weight= 0.3897 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.3897 bond: 0.021 angle: 2.91 clash: 34.5 rota: 7.14 rama: f: 79.17 o: 4.17 Z: -6.38 cb: 3.36 shift=0.8077 cc_mask=0.6771 cycle: 1 start: weight= 0.2728 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.2728 bond: 0.017 angle: 2.42 clash: 21.3 rota: 1.79 rama: f: 87.50 o: 1.67 Z: -5.62 cb: 0.00 shift=0.6588 cc_mask=0.6551 cycle: 2 start: weight= 0.1910 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.1910 bond: 0.014 angle: 2.11 clash: 11.2 rota: 0.89 rama: f: 87.50 o: 0.83 Z: -4.98 cb: 0.00 shift=0.5678 cc_mask=0.6388 cycle: 3 start: weight= 0.0955 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.0955 bond: 0.011 angle: 1.75 clash: 3.0 rota: 0.00 rama: f: 95.83 o: 0.00 Z: -3.55 cb: 0.00 shift=0.3791 cc_mask=0.5977 cycle: 4 start: weight= 0.0668 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.0668 bond: 0.010 angle: 1.62 clash: 2.5 rota: 0.00 rama: f: 96.67 o: 0.00 Z: -2.69 cb: 0.00 shift=0.2944 cc_mask=0.5785 cycle: 5 start: weight= 0.0468 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.0468 bond: 0.009 angle: 1.55 clash: 0.5 rota: 0.00 rama: f: 96.67 o: 0.00 Z: -2.18 cb: 0.00 shift=0.2507 cc_mask=0.5636 cycle: 6 start: weight= 0.0234 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.0234 bond: 0.009 angle: 1.47 clash: 0.5 rota: 0.00 rama: f: 97.50 o: 0.00 Z: -1.17 cb: 0.00 shift=0.2005 cc_mask=0.5425 cycle: 7 start: weight= 0.0164 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.0164 bond: 0.009 angle: 1.45 clash: 0.0 rota: 0.89 rama: f: 97.50 o: 0.00 Z: -0.86 cb: 0.00 shift=0.1892 cc_mask=0.5356 cycle: 8 start: weight= 0.0115 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.89 rama: f: 96.67 o: 0.00 Z: 0.14 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.0115 bond: 0.009 angle: 1.44 clash: 0.0 rota: 0.89 rama: f: 97.50 o: 0.00 Z: -0.76 cb: 0.00 shift=0.1859 cc_mask=0.5306 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.011462832195239792 start: weight= 0.0115 bond: 0.009 angle: 1.44 clash: 0.0 rota: 0.89 rama: f: 97.50 o: 0.00 Z: -0.76 cb: 0.00 shift=0.0000 cc_mask=0.5258 final: weight= 0.0115 bond: 0.009 angle: 1.44 clash: 0.0 rota: 0.89 rama: f: 97.50 o: 0.00 Z: -0.72 cb: 0.00 shift=0.1837 cc_mask=0.5306 start: weight= 0.0115 bond: 0.009 angle: 1.44 clash: 0.0 rota: 0.89 rama: f: 97.50 o: 0.00 Z: -0.72 cb: 0.00 shift=0.1837 cc_mask=0.5306 final: weight= 0.0115 bond: 0.008 angle: 1.45 clash: 0.5 rota: 0.00 rama: f: 96.67 o: 0.00 Z: -0.98 cb: 0.00 shift=0.2562 cc_mask=0.5336 start: weight= 0.0115 bond: 0.008 angle: 1.45 clash: 0.5 rota: 0.00 rama: f: 96.67 o: 0.00 Z: -0.98 cb: 0.00 shift=0.2562 cc_mask=0.5336 final: weight= 0.0115 bond: 0.009 angle: 1.45 clash: 0.0 rota: 0.00 rama: f: 96.67 o: 0.00 Z: -1.07 cb: 0.00 shift=0.3295 cc_mask=0.5381 start: weight= 0.0115 bond: 0.009 angle: 1.45 clash: 0.0 rota: 0.00 rama: f: 96.67 o: 0.00 Z: -1.07 cb: 0.00 shift=0.3295 cc_mask=0.5381 final: weight= 0.0115 bond: 0.009 angle: 1.46 clash: 0.0 rota: 0.00 rama: f: 96.67 o: 0.00 Z: -1.31 cb: 0.00 shift=0.3611 cc_mask=0.5403 start: weight= 0.0115 bond: 0.009 angle: 1.46 clash: 0.0 rota: 0.00 rama: f: 96.67 o: 0.00 Z: -1.31 cb: 0.00 shift=0.3611 cc_mask=0.5403 final: weight= 0.0115 bond: 0.009 angle: 1.46 clash: 0.0 rota: 0.89 rama: f: 96.67 o: 0.00 Z: -1.22 cb: 0.00 shift=0.4008 cc_mask=0.5415 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.027 990 Z= 0.455 ANGLE : 1.463 9.289 1336 Z= 0.773 CHIRALITY : 0.117 0.342 160 PLANARITY : 0.015 0.109 169 DIHEDRAL : 13.255 134.746 370 MIN NONBONDED DISTANCE : 2.643 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 3.33 % FAVORED : 96.67 % ROTAMER: OUTLIERS : 0.89 % ALLOWED : 1.79 % FAVORED : 97.32 % 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: -1.22 (0.68), RESIDUES: 120 HELIX: -1.27 (0.47), RESIDUES: 75 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.44 (0.95), RESIDUES: 45 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.020 0.004 ARG A 26 TYR 0.036 0.008 TYR A 91 PHE 0.041 0.010 PHE A 43 HIS 0.002 0.001 HIS A 116 Resolution of map is: 3.5863 Map-model correlation coefficient (CC) CC_mask : 0.5415 =============================================================================== Job complete usr+sys time: 219.60 seconds wall clock time: 4 minutes 11.79 seconds (251.79 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)