Starting qr.refine on Sun May 19 13:44:57 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6j6j_0689.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6j6j_0689.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/6j6j_0689.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6j6j_0689.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6j6j_0689.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6j6j_0689.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: 1731 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1731 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Time building chain proxies: 0.30, per 1000 atoms: 0.17 Number of scatterers: 1731 At special positions: 0 Unit cell: (47.385, 58.968, 57.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 180 8.00 N 155 7.00 C 557 6.00 H 839 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: 0.29 Adding C-beta torsion restraints... Number of C-beta restraints generated: 206 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.09: 822 1.09 - 1.21: 17 1.21 - 1.32: 146 1.32 - 1.43: 288 1.43 - 1.55: 480 Bond restraints: 1753 Sorted by residual: bond pdb=" C GLU A 51 " pdb=" N SER A 52 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 5.94e-01 bond pdb=" CA GLY A 99 " pdb=" C GLY A 99 " ideal model delta sigma weight residual 1.516 1.503 0.013 1.80e-02 3.09e+03 5.23e-01 bond pdb=" C ALA A 50 " pdb=" N GLU A 51 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 4.47e-01 bond pdb=" CA GLY A 94 " pdb=" C GLY A 94 " ideal model delta sigma weight residual 1.516 1.504 0.012 1.80e-02 3.09e+03 4.35e-01 bond pdb=" N GLY A 94 " pdb=" CA GLY A 94 " ideal model delta sigma weight residual 1.451 1.441 0.010 1.60e-02 3.91e+03 3.55e-01 ... (remaining 1748 not shown) Histogram of bond angle deviations from ideal: 102.78 - 109.02: 831 109.02 - 115.27: 1283 115.27 - 121.51: 582 121.51 - 127.75: 413 127.75 - 134.00: 14 Bond angle restraints: 3123 Sorted by residual: angle pdb=" N PRO A 64 " pdb=" CA PRO A 64 " pdb=" C PRO A 64 " ideal model delta sigma weight residual 112.10 116.28 -4.18 2.50e+00 1.60e-01 2.79e+00 angle pdb=" C SER A 62 " pdb=" N ALA A 63 " pdb=" CA ALA A 63 " ideal model delta sigma weight residual 121.70 124.62 -2.92 1.80e+00 3.09e-01 2.62e+00 angle pdb=" N ALA A 63 " pdb=" CA ALA A 63 " pdb=" C ALA A 63 " ideal model delta sigma weight residual 111.00 106.73 4.27 2.80e+00 1.28e-01 2.33e+00 angle pdb=" N VAL A 97 " pdb=" CA VAL A 97 " pdb=" C VAL A 97 " ideal model delta sigma weight residual 111.00 106.83 4.17 2.80e+00 1.28e-01 2.22e+00 angle pdb=" C TRP A 108 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " ideal model delta sigma weight residual 121.70 124.25 -2.55 1.80e+00 3.09e-01 2.01e+00 ... (remaining 3118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 759 17.44 - 34.87: 54 34.87 - 52.31: 14 52.31 - 69.75: 4 69.75 - 87.19: 1 Dihedral angle restraints: 832 sinusoidal: 426 harmonic: 406 Sorted by residual: dihedral pdb=" CA ALA A 63 " pdb=" C ALA A 63 " pdb=" N PRO A 64 " pdb=" CA PRO A 64 " ideal model delta harmonic sigma weight residual 180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ILE A 17 " pdb=" CB ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sinusoidal sigma weight residual 60.00 104.31 -44.31 3 1.50e+01 4.44e-03 7.97e+00 dihedral pdb=" CA GLN A 107 " pdb=" C GLN A 107 " pdb=" N TRP A 108 " pdb=" CA TRP A 108 " ideal model delta harmonic sigma weight residual -180.00 -166.68 -13.32 0 5.00e+00 4.00e-02 7.10e+00 ... (remaining 829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 76 0.027 - 0.054: 40 0.054 - 0.082: 14 0.082 - 0.109: 4 0.109 - 0.136: 5 Chirality restraints: 139 Sorted by residual: 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 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL A 97 " pdb=" N VAL A 97 " pdb=" C VAL A 97 " pdb=" CB VAL A 97 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 136 not shown) Planarity restraints: 275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 63 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.71e-01 pdb=" N PRO A 64 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 29 " -0.008 2.00e-02 2.50e+03 4.17e-03 5.21e-01 pdb=" CG PHE A 29 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 29 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 29 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 29 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 29 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 29 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 29 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 29 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 63 " 0.003 2.00e-02 2.50e+03 6.34e-03 4.03e-01 pdb=" C ALA A 63 " -0.011 2.00e-02 2.50e+03 pdb=" O ALA A 63 " 0.004 2.00e-02 2.50e+03 pdb=" N PRO A 64 " 0.004 2.00e-02 2.50e+03 ... (remaining 272 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.16: 142 2.16 - 2.75: 2780 2.75 - 3.33: 4030 3.33 - 3.92: 5651 3.92 - 4.50: 7663 Nonbonded interactions: 20266 Sorted by model distance: nonbonded pdb=" OE1 GLN A 24 " pdb=" H GLN A 24 " model vdw 1.578 1.800 nonbonded pdb=" H3 GLY A 16 " pdb=" H ILE A 17 " model vdw 1.629 2.000 nonbonded pdb=" OD1 ASN A 23 " pdb=" HG SER A 27 " model vdw 1.645 1.800 nonbonded pdb=" HG1 THR A 18 " pdb=" O VAL A 31 " model vdw 1.700 1.800 nonbonded pdb=" HG1 THR A 114 " pdb=" O ASN A 118 " model vdw 1.710 1.800 ... (remaining 20261 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: 4 Type Number sf(0) Gaussians O 180 7.97 2 N 155 6.97 2 C 557 5.97 2 H 839 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 0.018 914 Z= 0.181 ANGLE : 0.921 4.271 1251 Z= 0.427 CHIRALITY : 0.043 0.136 139 PLANARITY : 0.003 0.023 158 DIHEDRAL : 11.854 62.010 294 MIN NONBONDED DISTANCE : 2.298 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.74 RAMACHANDRAN PLOT: OUTLIERS : 1.71 % ALLOWED : 7.69 % FAVORED : 90.60 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 7.95 % FAVORED : 92.05 % 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: -3.04 (0.65), RESIDUES: 117 HELIX: NONE (NONE), RESIDUES: 0 SHEET: -0.99 (0.61), RESIDUES: 57 LOOP : -3.17 (0.60), RESIDUES: 60 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.001 0.000 ARG A 84 TYR 0.005 0.001 TYR A 60 PHE 0.011 0.002 PHE A 29 TRP 0.007 0.001 TRP A 92 HIS 0.001 0.001 HIS A 87 Resolution of map is: 3.2675 Map-model correlation coefficient (CC) CC_mask : 0.6498 weight= None bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 Initial weight estimate from ratio of grad norms: 0.31725866907862027 cycle: 0 start: weight= 0.3173 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.3173 bond: 0.021 angle: 2.40 clash: 6.9 rota: 4.55 rama: f: 88.89 o: 2.56 Z: -5.36 cb: 0.97 shift=0.4496 cc_mask=0.6991 cycle: 1 start: weight= 0.2221 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.2221 bond: 0.017 angle: 2.06 clash: 4.6 rota: 3.41 rama: f: 89.74 o: 1.71 Z: -4.37 cb: 0.97 shift=0.4158 cc_mask=0.6935 cycle: 2 start: weight= 0.1555 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.1555 bond: 0.015 angle: 1.86 clash: 1.7 rota: 2.27 rama: f: 92.31 o: 1.71 Z: -3.85 cb: 0.00 shift=0.3904 cc_mask=0.6885 cycle: 3 start: weight= 0.0777 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0777 bond: 0.012 angle: 1.66 clash: 0.6 rota: 2.27 rama: f: 94.02 o: 0.85 Z: -2.77 cb: 0.00 shift=0.3210 cc_mask=0.6782 cycle: 4 start: weight= 0.0544 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0544 bond: 0.011 angle: 1.62 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.85 Z: -2.26 cb: 0.00 shift=0.2860 cc_mask=0.6734 cycle: 5 start: weight= 0.0381 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0381 bond: 0.010 angle: 1.60 clash: 0.0 rota: 1.14 rama: f: 94.87 o: 0.85 Z: -1.98 cb: 0.00 shift=0.2586 cc_mask=0.6676 cycle: 6 start: weight= 0.0190 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0190 bond: 0.010 angle: 1.60 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.62 cb: 0.00 shift=0.2367 cc_mask=0.6594 cycle: 7 start: weight= 0.0133 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0133 bond: 0.010 angle: 1.59 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.59 cb: 0.00 shift=0.2247 cc_mask=0.6556 cycle: 8 start: weight= 0.0093 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0093 bond: 0.009 angle: 1.59 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.52 cb: 0.00 shift=0.2202 cc_mask=0.6524 cycle: 9 start: weight= 0.0047 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0047 bond: 0.009 angle: 1.60 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.51 cb: 0.00 shift=0.2259 cc_mask=0.6483 cycle: 10 start: weight= 0.0033 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0033 bond: 0.009 angle: 1.59 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.51 cb: 0.00 shift=0.2218 cc_mask=0.6474 cycle: 11 start: weight= 0.0023 bond: 0.004 angle: 0.92 clash: 1.7 rota: 0.00 rama: f: 90.60 o: 1.71 Z: -3.04 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0023 bond: 0.009 angle: 1.59 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.49 cb: 0.00 shift=0.2203 cc_mask=0.6468 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.002286166365953874 start: weight= 0.0023 bond: 0.009 angle: 1.59 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.49 cb: 0.00 shift=0.0000 cc_mask=0.6498 final: weight= 0.0023 bond: 0.009 angle: 1.60 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.49 cb: 0.00 shift=0.2247 cc_mask=0.6467 start: weight= 0.0023 bond: 0.009 angle: 1.60 clash: 0.0 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.49 cb: 0.00 shift=0.2247 cc_mask=0.6467 final: weight= 0.0023 bond: 0.009 angle: 1.59 clash: 0.0 rota: 1.14 rama: f: 96.58 o: 0.85 Z: -0.94 cb: 0.00 shift=0.3237 cc_mask=0.6421 start: weight= 0.0023 bond: 0.009 angle: 1.59 clash: 0.0 rota: 1.14 rama: f: 96.58 o: 0.85 Z: -0.94 cb: 0.00 shift=0.3237 cc_mask=0.6421 final: weight= 0.0023 bond: 0.009 angle: 1.59 clash: 0.6 rota: 1.14 rama: f: 95.73 o: 0.85 Z: -1.00 cb: 0.00 shift=0.3801 cc_mask=0.6363 start: weight= 0.0023 bond: 0.009 angle: 1.59 clash: 0.6 rota: 1.14 rama: f: 95.73 o: 0.85 Z: -1.00 cb: 0.00 shift=0.3801 cc_mask=0.6363 final: weight= 0.0023 bond: 0.009 angle: 1.60 clash: 0.6 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.10 cb: 0.00 shift=0.4276 cc_mask=0.6320 start: weight= 0.0023 bond: 0.009 angle: 1.60 clash: 0.6 rota: 1.14 rama: f: 95.73 o: 0.00 Z: -1.10 cb: 0.00 shift=0.4276 cc_mask=0.6320 final: weight= 0.0023 bond: 0.009 angle: 1.62 clash: 0.6 rota: 1.14 rama: f: 94.87 o: 0.00 Z: -1.95 cb: 0.00 shift=0.4728 cc_mask=0.6294 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.028 914 Z= 0.493 ANGLE : 1.618 8.895 1251 Z= 0.869 CHIRALITY : 0.106 0.299 139 PLANARITY : 0.021 0.236 158 DIHEDRAL : 14.005 110.846 294 MIN NONBONDED DISTANCE : 2.608 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.58 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 5.13 % FAVORED : 94.87 % ROTAMER: OUTLIERS : 1.14 % ALLOWED : 2.27 % FAVORED : 96.59 % 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: -1.95 (0.72), RESIDUES: 117 HELIX: -4.86 (0.25), RESIDUES: 6 SHEET: -1.07 (0.51), RESIDUES: 69 LOOP : -0.76 (1.07), RESIDUES: 42 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.006 0.002 ARG A 59 TYR 0.081 0.016 TYR A 43 PHE 0.017 0.006 PHE A 29 TRP 0.074 0.014 TRP A 92 HIS 0.003 0.001 HIS A 87 Resolution of map is: 3.2675 Map-model correlation coefficient (CC) CC_mask : 0.6294 =============================================================================== Job complete usr+sys time: 238.48 seconds wall clock time: 4 minutes 37.32 seconds (277.32 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)