Starting qr.refine on Sun May 19 14:34:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7pcq_13325.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7pcq_13325.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/7pcq_13325.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7pcq_13325.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7pcq_13325.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7pcq_13325.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: 4381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2145 Classifications: {'peptide': 141} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2236 Classifications: {'peptide': 146} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Time building chain proxies: 0.57, per 1000 atoms: 0.13 Number of scatterers: 4381 At special positions: 0 Unit cell: (58.68, 61.288, 68.46, 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 6 16.00 O 395 8.00 N 382 7.00 C 1409 6.00 H 2189 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: 0.79 Adding C-beta torsion restraints... Number of C-beta restraints generated: 534 Time building geometry restraints manager: 0.91 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: 2186 1.14 - 1.31: 360 1.31 - 1.48: 910 1.48 - 1.65: 974 1.65 - 1.81: 9 Bond restraints: 4439 Sorted by residual: bond pdb=" C SER B 49 " pdb=" N THR B 50 " ideal model delta sigma weight residual 1.329 1.381 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N PRO B 125 " pdb=" CA PRO B 125 " ideal model delta sigma weight residual 1.466 1.481 -0.015 1.50e-02 4.44e+03 9.37e-01 bond pdb=" C PRO B 125 " pdb=" O PRO B 125 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.48e-01 bond pdb=" C TYR B 35 " pdb=" O TYR B 35 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 5.11e-01 bond pdb=" C VAL B 11 " pdb=" N THR B 12 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 4.86e-01 ... (remaining 4434 not shown) Histogram of bond angle deviations from ideal: 100.96 - 107.55: 246 107.55 - 114.14: 5234 114.14 - 120.73: 1488 120.73 - 127.32: 1044 127.32 - 133.91: 38 Bond angle restraints: 8050 Sorted by residual: angle pdb=" CA MET A 76 " pdb=" C MET A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 116.90 121.09 -4.19 1.50e+00 4.44e-01 7.79e+00 angle pdb=" CA PRO B 124 " pdb=" C PRO B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 116.90 119.33 -2.43 1.50e+00 4.44e-01 2.63e+00 angle pdb=" C GLY A 15 " pdb=" N LYS A 16 " pdb=" CA LYS A 16 " ideal model delta sigma weight residual 121.70 118.81 2.89 1.80e+00 3.09e-01 2.58e+00 angle pdb=" CA MET A 76 " pdb=" C MET A 76 " pdb=" O MET A 76 " ideal model delta sigma weight residual 120.80 118.22 2.58 1.70e+00 3.46e-01 2.31e+00 angle pdb=" CA ASN B 57 " pdb=" C ASN B 57 " pdb=" N PRO B 58 " ideal model delta sigma weight residual 116.90 119.18 -2.28 1.50e+00 4.44e-01 2.31e+00 ... (remaining 8045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 1932 15.73 - 31.47: 95 31.47 - 47.20: 40 47.20 - 62.94: 31 62.94 - 78.67: 1 Dihedral angle restraints: 2099 sinusoidal: 1097 harmonic: 1002 Sorted by residual: dihedral pdb=" CA ARG A 92 " pdb=" CB ARG A 92 " pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " ideal model delta sinusoidal sigma weight residual -60.00 -116.32 56.32 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CA ARG B 40 " pdb=" CB ARG B 40 " pdb=" CG ARG B 40 " pdb=" CD ARG B 40 " ideal model delta sinusoidal sigma weight residual -180.00 -126.84 -53.16 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" N PHE A 46 " pdb=" CA PHE A 46 " pdb=" CB PHE A 46 " pdb=" CG PHE A 46 " ideal model delta sinusoidal sigma weight residual -60.00 -102.13 42.13 3 1.50e+01 4.44e-03 7.55e+00 ... (remaining 2096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 222 0.022 - 0.044: 77 0.044 - 0.066: 19 0.066 - 0.088: 26 0.088 - 0.109: 6 Chirality restraints: 350 Sorted by residual: chirality pdb=" CA PRO B 36 " pdb=" N PRO B 36 " pdb=" C PRO B 36 " pdb=" CB PRO B 36 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.00e-01 chirality pdb=" CA VAL B 98 " pdb=" N VAL B 98 " pdb=" C VAL B 98 " pdb=" CB VAL B 98 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.56e-01 chirality pdb=" CA PRO A 77 " pdb=" N PRO A 77 " pdb=" C PRO A 77 " pdb=" CB PRO A 77 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.10e-01 ... (remaining 347 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO B 124 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 35 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.02e-01 pdb=" N PRO B 36 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 3 " -0.014 5.00e-02 4.00e+02 2.13e-02 7.27e-01 pdb=" N PRO A 4 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " -0.012 5.00e-02 4.00e+02 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 576 2.24 - 2.83: 9243 2.83 - 3.42: 12542 3.42 - 4.01: 16136 4.01 - 4.60: 24668 Nonbonded interactions: 63165 Sorted by model distance: nonbonded pdb=" O THR A 118 " pdb=" H HIS A 122 " model vdw 1.647 1.800 nonbonded pdb=" HE1 TRP A 14 " pdb=" OG1 THR A 67 " model vdw 1.651 1.800 nonbonded pdb=" O THR B 4 " pdb=" H LYS B 8 " model vdw 1.670 1.800 nonbonded pdb=" OE1 GLU A 27 " pdb=" HE2 HIS A 112 " model vdw 1.779 1.800 nonbonded pdb=" H THR A 137 " pdb=" HG1 THR A 137 " model vdw 1.787 2.000 ... (remaining 63160 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 6 15.96 2 O 395 7.97 2 N 382 6.97 2 C 1409 5.97 2 H 2189 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 0.052 2250 Z= 0.223 ANGLE : 0.851 4.460 3061 Z= 0.423 CHIRALITY : 0.032 0.109 350 PLANARITY : 0.003 0.028 391 DIHEDRAL : 10.870 78.670 784 MIN NONBONDED DISTANCE : 2.415 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.46 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.41 % FAVORED : 98.59 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 3.90 % FAVORED : 96.10 % 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: 2.20 (0.46), RESIDUES: 283 HELIX: 1.71 (0.32), RESIDUES: 220 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.79 (0.76), RESIDUES: 63 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.001 0.000 ARG B 30 TYR 0.003 0.001 TYR B 145 PHE 0.006 0.001 PHE A 46 TRP 0.004 0.001 TRP A 14 HIS 0.002 0.001 HIS B 97 Resolution of map is: 4.4964 Map-model correlation coefficient (CC) CC_mask : 0.8165 weight= None bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 Initial weight estimate from ratio of grad norms: 0.7282204875848322 cycle: 0 start: weight= 0.7282 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.7282 bond: 0.031 angle: 3.10 clash: 61.8 rota: 3.46 rama: f: 91.52 o: 0.00 Z: -6.30 cb: 1.50 shift=0.6375 cc_mask=0.8836 cycle: 1 start: weight= 0.3641 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.3641 bond: 0.020 angle: 2.17 clash: 20.1 rota: 0.43 rama: f: 96.47 o: 0.00 Z: -4.10 cb: 0.00 shift=0.4736 cc_mask=0.8697 cycle: 2 start: weight= 0.2549 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.2549 bond: 0.016 angle: 1.88 clash: 6.4 rota: 0.00 rama: f: 96.47 o: 0.00 Z: -3.20 cb: 0.00 shift=0.3882 cc_mask=0.8631 cycle: 3 start: weight= 0.1784 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.1784 bond: 0.014 angle: 1.69 clash: 1.6 rota: 0.00 rama: f: 97.53 o: 0.00 Z: -2.03 cb: 0.00 shift=0.3228 cc_mask=0.8561 cycle: 4 start: weight= 0.0892 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.0892 bond: 0.011 angle: 1.50 clash: 0.5 rota: 0.00 rama: f: 97.88 o: 0.00 Z: -0.81 cb: 0.00 shift=0.2425 cc_mask=0.8419 cycle: 5 start: weight= 0.0624 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.0624 bond: 0.011 angle: 1.45 clash: 0.2 rota: 0.00 rama: f: 97.53 o: 0.00 Z: -0.38 cb: 0.00 shift=0.2207 cc_mask=0.8357 cycle: 6 start: weight= 0.0437 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.0437 bond: 0.010 angle: 1.43 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: -0.12 cb: 0.00 shift=0.2072 cc_mask=0.8315 cycle: 7 start: weight= 0.0219 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.0219 bond: 0.010 angle: 1.40 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.12 cb: 0.00 shift=0.1977 cc_mask=0.8257 cycle: 8 start: weight= 0.0153 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.0153 bond: 0.009 angle: 1.40 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.19 cb: 0.00 shift=0.1928 cc_mask=0.8239 cycle: 9 start: weight= 0.0107 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.0107 bond: 0.009 angle: 1.40 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.20 cb: 0.00 shift=0.1921 cc_mask=0.8227 cycle: 10 start: weight= 0.0054 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.0054 bond: 0.009 angle: 1.40 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.22 cb: 0.00 shift=0.1918 cc_mask=0.8211 cycle: 11 start: weight= 0.0037 bond: 0.004 angle: 0.85 clash: 0.5 rota: 0.00 rama: f: 98.59 o: 0.00 Z: 2.20 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.0037 bond: 0.009 angle: 1.40 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.24 cb: 0.00 shift=0.1903 cc_mask=0.8206 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.003748255531294222 start: weight= 0.0037 bond: 0.009 angle: 1.40 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.8165 final: weight= 0.0037 bond: 0.009 angle: 1.40 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.24 cb: 0.00 shift=0.1908 cc_mask=0.8206 start: weight= 0.0037 bond: 0.009 angle: 1.40 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.24 cb: 0.00 shift=0.1908 cc_mask=0.8206 final: weight= 0.0037 bond: 0.009 angle: 1.37 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.02 cb: 0.00 shift=0.2538 cc_mask=0.8191 start: weight= 0.0037 bond: 0.009 angle: 1.37 clash: 0.0 rota: 0.00 rama: f: 97.53 o: 0.00 Z: 0.02 cb: 0.00 shift=0.2538 cc_mask=0.8191 final: weight= 0.0037 bond: 0.009 angle: 1.38 clash: 0.2 rota: 0.00 rama: f: 97.53 o: 0.00 Z: -0.27 cb: 0.00 shift=0.3075 cc_mask=0.8163 start: weight= 0.0037 bond: 0.009 angle: 1.38 clash: 0.2 rota: 0.00 rama: f: 97.53 o: 0.00 Z: -0.27 cb: 0.00 shift=0.3075 cc_mask=0.8163 final: weight= 0.0037 bond: 0.009 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 97.88 o: 0.00 Z: -0.39 cb: 0.00 shift=0.3422 cc_mask=0.8137 start: weight= 0.0037 bond: 0.009 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 97.88 o: 0.00 Z: -0.39 cb: 0.00 shift=0.3422 cc_mask=0.8137 final: weight= 0.0037 bond: 0.009 angle: 1.39 clash: 0.0 rota: 0.00 rama: f: 97.88 o: 0.00 Z: -0.48 cb: 0.00 shift=0.3719 cc_mask=0.8116 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.094 2250 Z= 0.501 ANGLE : 1.388 9.203 3061 Z= 0.802 CHIRALITY : 0.106 0.363 350 PLANARITY : 0.014 0.152 391 DIHEDRAL : 10.904 114.010 784 MIN NONBONDED DISTANCE : 2.558 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.12 % FAVORED : 97.88 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.00 % FAVORED : 100.00 % 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: -0.48 (0.45), RESIDUES: 283 HELIX: -0.75 (0.28), RESIDUES: 215 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 1.98 (0.83), RESIDUES: 68 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.017 0.005 ARG B 104 TYR 0.076 0.020 TYR B 145 PHE 0.032 0.008 PHE B 85 TRP 0.090 0.023 TRP B 15 HIS 0.008 0.002 HIS B 146 Resolution of map is: 4.4964 Map-model correlation coefficient (CC) CC_mask : 0.8116 =============================================================================== Job complete usr+sys time: 447.51 seconds wall clock time: 8 minutes 17.23 seconds (497.23 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)