Starting qr.refine on Sun May 19 14:42:53 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ckz_16707.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ckz_16707.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/8ckz_16707.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ckz_16707.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ckz_16707.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ckz_16707.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 "B PHE 168": "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: 4513 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3342 Inner-chain residues flagged as termini: ['pdbres="VAL A 86 "', 'pdbres="MET A 96 "'] Classifications: {'peptide': 212} Modifications used: {'COO': 2, 'NH2': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Chain: "B" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1171 Classifications: {'peptide': 74} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 0.58, per 1000 atoms: 0.13 Number of scatterers: 4513 At special positions: 0 Unit cell: (70.68, 86.49, 99.51, 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 18 16.00 O 429 8.00 N 389 7.00 C 1416 6.00 H 2261 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: 0.89 Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Time building geometry restraints manager: 1.01 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: 2257 1.15 - 1.31: 393 1.31 - 1.48: 868 1.48 - 1.65: 1007 1.65 - 1.81: 32 Bond restraints: 4557 Sorted by residual: bond pdb=" N PRO A 125 " pdb=" CA PRO A 125 " ideal model delta sigma weight residual 1.466 1.478 -0.012 1.50e-02 4.44e+03 6.90e-01 bond pdb=" C PRO A 122 " pdb=" N PRO A 123 " ideal model delta sigma weight residual 1.341 1.329 0.012 1.60e-02 3.91e+03 5.87e-01 bond pdb=" CB PRO A 38 " pdb=" CG PRO A 38 " ideal model delta sigma weight residual 1.492 1.455 0.037 5.00e-02 4.00e+02 5.38e-01 bond pdb=" C ASN A 121 " pdb=" O ASN A 121 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.26e-01 bond pdb=" C MET A 118 " pdb=" N THR A 119 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.19e-01 ... (remaining 4552 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.19: 147 107.19 - 113.88: 5515 113.88 - 120.56: 1461 120.56 - 127.25: 1117 127.25 - 133.94: 35 Bond angle restraints: 8275 Sorted by residual: angle pdb=" CA ILE A 37 " pdb=" C ILE A 37 " pdb=" N PRO A 38 " ideal model delta sigma weight residual 116.90 119.75 -2.85 1.50e+00 4.44e-01 3.60e+00 angle pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N PRO A 122 " ideal model delta sigma weight residual 116.90 119.53 -2.63 1.50e+00 4.44e-01 3.07e+00 angle pdb=" CA LYS A 131 " pdb=" CB LYS A 131 " pdb=" CG LYS A 131 " ideal model delta sigma weight residual 114.10 117.59 -3.49 2.00e+00 2.50e-01 3.04e+00 angle pdb=" CA ILE A 124 " pdb=" C ILE A 124 " pdb=" N PRO A 125 " ideal model delta sigma weight residual 116.90 119.45 -2.55 1.50e+00 4.44e-01 2.88e+00 angle pdb=" CA ARG A 173 " pdb=" CB ARG A 173 " pdb=" CG ARG A 173 " ideal model delta sigma weight residual 114.10 117.27 -3.17 2.00e+00 2.50e-01 2.52e+00 ... (remaining 8270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 1981 17.34 - 34.68: 106 34.68 - 52.02: 42 52.02 - 69.36: 9 69.36 - 86.71: 1 Dihedral angle restraints: 2139 sinusoidal: 1209 harmonic: 930 Sorted by residual: dihedral pdb=" CB MET A 66 " pdb=" CG MET A 66 " pdb=" SD MET A 66 " pdb=" CE MET A 66 " ideal model delta sinusoidal sigma weight residual -60.00 -115.14 55.14 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" CA ALA A 47 " pdb=" C ALA A 47 " pdb=" N THR A 48 " pdb=" CA THR A 48 " ideal model delta harmonic sigma weight residual 180.00 165.05 14.95 0 5.00e+00 4.00e-02 8.94e+00 dihedral pdb=" CA PHE A 32 " pdb=" C PHE A 32 " pdb=" N SER A 33 " pdb=" CA SER A 33 " ideal model delta harmonic sigma weight residual 180.00 165.57 14.43 0 5.00e+00 4.00e-02 8.32e+00 ... (remaining 2136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 237 0.029 - 0.059: 68 0.059 - 0.088: 34 0.088 - 0.118: 11 0.118 - 0.147: 1 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE A 153 " pdb=" N ILE A 153 " pdb=" C ILE A 153 " pdb=" CB ILE A 153 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA ILE B 153 " pdb=" N ILE B 153 " pdb=" C ILE B 153 " pdb=" CB ILE B 153 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.84e-01 ... (remaining 348 not shown) Planarity restraints: 671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 121 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 122 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 37 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 38 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 48 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.15e-01 pdb=" N PRO A 49 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.013 5.00e-02 4.00e+02 ... (remaining 668 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 461 2.21 - 2.81: 9076 2.81 - 3.40: 12831 3.40 - 4.00: 16130 4.00 - 4.60: 24029 Nonbonded interactions: 62527 Sorted by model distance: nonbonded pdb=" O HIS A 62 " pdb=" H MET A 66 " model vdw 1.612 1.800 nonbonded pdb=" H ILE A 150 " pdb=" OE2 GLU A 175 " model vdw 1.631 1.800 nonbonded pdb="HE21 GLN B 155 " pdb=" O GLU B 159 " model vdw 1.639 1.800 nonbonded pdb=" H SER B 149 " pdb=" OD2 ASP B 152 " model vdw 1.664 1.800 nonbonded pdb=" OD1 ASN A 195 " pdb=" H CYS A 198 " model vdw 1.665 1.800 ... (remaining 62522 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 18 15.96 2 O 429 7.97 2 N 389 6.97 2 C 1416 5.97 2 H 2261 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 0.037 2296 Z= 0.199 ANGLE : 0.933 5.293 3115 Z= 0.451 CHIRALITY : 0.037 0.147 351 PLANARITY : 0.004 0.034 406 DIHEDRAL : 11.205 86.706 877 MIN NONBONDED DISTANCE : 2.418 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 2.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.79 % FAVORED : 98.21 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.81 % FAVORED : 99.19 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 5.56 % 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: -0.95 (0.45), RESIDUES: 280 HELIX: -0.83 (0.34), RESIDUES: 187 SHEET: -1.70 (1.32), RESIDUES: 9 LOOP : 0.53 (0.61), RESIDUES: 84 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.001 ARG A 162 TYR 0.006 0.001 TYR B 169 PHE 0.002 0.001 PHE B 161 TRP 0.005 0.001 TRP A 117 HIS 0.001 0.001 HIS A 120 Resolution of map is: 3.1607 Map-model correlation coefficient (CC) CC_mask : 0.7659 weight= None bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 Initial weight estimate from ratio of grad norms: 0.3110292016642071 cycle: 0 start: weight= 0.3110 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.3110 bond: 0.023 angle: 2.22 clash: 5.5 rota: 0.81 rama: f: 94.64 o: 0.36 Z: -5.55 cb: 1.12 shift=0.3061 cc_mask=0.8002 cycle: 1 start: weight= 0.2177 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.2177 bond: 0.019 angle: 1.93 clash: 2.2 rota: 0.40 rama: f: 96.79 o: 0.36 Z: -4.55 cb: 0.37 shift=0.2693 cc_mask=0.7952 cycle: 2 start: weight= 0.1524 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.1524 bond: 0.015 angle: 1.75 clash: 0.4 rota: 0.81 rama: f: 97.86 o: 0.00 Z: -3.63 cb: 0.37 shift=0.2414 cc_mask=0.7901 cycle: 3 start: weight= 0.0762 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.0762 bond: 0.012 angle: 1.55 clash: 0.2 rota: 0.40 rama: f: 98.57 o: 0.00 Z: -2.29 cb: 0.37 shift=0.1941 cc_mask=0.7820 cycle: 4 start: weight= 0.0533 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.0533 bond: 0.011 angle: 1.50 clash: 0.0 rota: 0.40 rama: f: 98.93 o: 0.00 Z: -1.87 cb: 0.37 shift=0.1797 cc_mask=0.7784 cycle: 5 start: weight= 0.0373 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.0373 bond: 0.010 angle: 1.47 clash: 0.0 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.68 cb: 0.00 shift=0.1710 cc_mask=0.7755 cycle: 6 start: weight= 0.0187 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.0187 bond: 0.009 angle: 1.44 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.55 cb: 0.00 shift=0.1636 cc_mask=0.7708 cycle: 7 start: weight= 0.0131 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.0131 bond: 0.009 angle: 1.43 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.51 cb: 0.00 shift=0.1636 cc_mask=0.7692 cycle: 8 start: weight= 0.0091 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.0091 bond: 0.009 angle: 1.42 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.48 cb: 0.00 shift=0.1633 cc_mask=0.7679 cycle: 9 start: weight= 0.0046 bond: 0.004 angle: 0.93 clash: 2.0 rota: 0.00 rama: f: 98.21 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.0046 bond: 0.009 angle: 1.42 clash: 0.4 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.47 cb: 0.00 shift=0.1639 cc_mask=0.7664 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.004574034318324038 start: weight= 0.0046 bond: 0.009 angle: 1.42 clash: 0.4 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7659 final: weight= 0.0046 bond: 0.009 angle: 1.42 clash: 0.4 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.49 cb: 0.00 shift=0.1661 cc_mask=0.7664 start: weight= 0.0046 bond: 0.009 angle: 1.42 clash: 0.4 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.49 cb: 0.00 shift=0.1661 cc_mask=0.7664 final: weight= 0.0046 bond: 0.009 angle: 1.41 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.72 cb: 0.00 shift=0.2177 cc_mask=0.7636 start: weight= 0.0046 bond: 0.009 angle: 1.41 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.72 cb: 0.00 shift=0.2177 cc_mask=0.7636 final: weight= 0.0046 bond: 0.009 angle: 1.42 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.68 cb: 0.00 shift=0.2586 cc_mask=0.7609 start: weight= 0.0046 bond: 0.009 angle: 1.42 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.68 cb: 0.00 shift=0.2586 cc_mask=0.7609 final: weight= 0.0046 bond: 0.009 angle: 1.42 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.77 cb: 0.00 shift=0.2875 cc_mask=0.7586 start: weight= 0.0046 bond: 0.009 angle: 1.42 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.77 cb: 0.00 shift=0.2875 cc_mask=0.7586 final: weight= 0.0046 bond: 0.009 angle: 1.43 clash: 0.2 rota: 0.00 rama: f: 99.29 o: 0.00 Z: -1.77 cb: 0.00 shift=0.3050 cc_mask=0.7571 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.031 2296 Z= 0.456 ANGLE : 1.427 8.860 3115 Z= 0.743 CHIRALITY : 0.110 0.404 351 PLANARITY : 0.018 0.154 406 DIHEDRAL : 12.668 82.352 877 MIN NONBONDED DISTANCE : 2.624 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.22 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 0.71 % FAVORED : 99.29 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 1.62 % FAVORED : 98.38 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 5.56 % 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: -1.77 (0.42), RESIDUES: 280 HELIX: -1.32 (0.29), RESIDUES: 190 SHEET: -2.26 (1.75), RESIDUES: 9 LOOP : -0.06 (0.64), RESIDUES: 81 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.018 0.004 ARG B 167 TYR 0.088 0.018 TYR A 164 PHE 0.014 0.006 PHE B 161 TRP 0.048 0.016 TRP B 184 HIS 0.003 0.001 HIS A 120 Resolution of map is: 3.1607 Map-model correlation coefficient (CC) CC_mask : 0.7571 =============================================================================== Job complete usr+sys time: 415.06 seconds wall clock time: 7 minutes 37.46 seconds (457.46 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)