Starting qr.refine on Sun May 19 15:15:17 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7dnj_30785.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7dnj_30785.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/7dnj_30785.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7dnj_30785.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7dnj_30785.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7dnj_30785.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 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 107": "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: 5551 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3184 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "E" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1174 Classifications: {'peptide': 72} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "H" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1193 Classifications: {'peptide': 73} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 0.68, per 1000 atoms: 0.12 Number of scatterers: 5551 At special positions: 0 Unit cell: (67.925, 71.06, 110.77, 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 8 16.00 O 535 8.00 N 472 7.00 C 1736 6.00 H 2800 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: 1.04 Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Time building geometry restraints manager: 1.20 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: 2798 1.14 - 1.31: 487 1.31 - 1.47: 1016 1.47 - 1.64: 1275 1.64 - 1.80: 14 Bond restraints: 5590 Sorted by residual: bond pdb=" CB ARG A 149 " pdb=" CG ARG A 149 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.97e-01 bond pdb=" C VAL A 131 " pdb=" N ARG A 132 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 5.72e-01 bond pdb=" C MET A 95 " pdb=" N ASN A 96 " ideal model delta sigma weight residual 1.329 1.319 0.010 1.40e-02 5.10e+03 5.34e-01 bond pdb=" CD ARG A 149 " pdb=" HD3 ARG A 149 " ideal model delta sigma weight residual 1.090 1.077 0.013 2.00e-02 2.50e+03 4.35e-01 bond pdb=" C ASP A 8 " pdb=" N GLU A 9 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 4.35e-01 ... (remaining 5585 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.82: 85 106.82 - 113.59: 6828 113.59 - 120.36: 1789 120.36 - 127.13: 1425 127.13 - 133.90: 24 Bond angle restraints: 10151 Sorted by residual: angle pdb=" CA GLN A 122 " pdb=" C GLN A 122 " pdb=" N PRO A 123 " ideal model delta sigma weight residual 116.90 121.70 -4.80 1.50e+00 4.44e-01 1.02e+01 angle pdb=" CA GLU A 29 " pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 116.90 121.10 -4.20 1.50e+00 4.44e-01 7.85e+00 angle pdb=" CA ILE E 36 " pdb=" C ILE E 36 " pdb=" N PRO E 37 " ideal model delta sigma weight residual 116.90 119.74 -2.84 1.50e+00 4.44e-01 3.58e+00 angle pdb=" CA GLU E 34 " pdb=" C GLU E 34 " pdb=" N GLY E 35 " ideal model delta sigma weight residual 116.20 119.83 -3.63 2.00e+00 2.50e-01 3.29e+00 angle pdb=" CA ASN A 96 " pdb=" C ASN A 96 " pdb=" N PRO A 97 " ideal model delta sigma weight residual 116.90 119.60 -2.70 1.50e+00 4.44e-01 3.23e+00 ... (remaining 10146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 2317 15.91 - 31.81: 191 31.81 - 47.72: 41 47.72 - 63.62: 29 63.62 - 79.53: 6 Dihedral angle restraints: 2584 sinusoidal: 1470 harmonic: 1114 Sorted by residual: dihedral pdb=" CB LYS E 33 " pdb=" CG LYS E 33 " pdb=" CD LYS E 33 " pdb=" CE LYS E 33 " ideal model delta sinusoidal sigma weight residual -60.00 -116.56 56.56 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA GLN H 41 " pdb=" CB GLN H 41 " pdb=" CG GLN H 41 " pdb=" CD GLN H 41 " ideal model delta sinusoidal sigma weight residual 60.00 113.52 -53.52 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CA GLN H 41 " pdb=" C GLN H 41 " pdb=" N ARG H 42 " pdb=" CA ARG H 42 " ideal model delta harmonic sigma weight residual 180.00 165.24 14.76 0 5.00e+00 4.00e-02 8.71e+00 ... (remaining 2581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 272 0.028 - 0.056: 110 0.056 - 0.084: 36 0.084 - 0.112: 15 0.112 - 0.140: 8 Chirality restraints: 441 Sorted by residual: chirality pdb=" CA ILE E 44 " pdb=" N ILE E 44 " pdb=" C ILE E 44 " pdb=" CB ILE E 44 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE H 36 " pdb=" N ILE H 36 " pdb=" C ILE H 36 " pdb=" CB ILE H 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE E 13 " pdb=" N ILE E 13 " pdb=" C ILE E 13 " pdb=" CB ILE E 13 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 438 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 30 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 122 " 0.015 5.00e-02 4.00e+02 2.22e-02 7.86e-01 pdb=" N PRO A 123 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 37 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.51e-01 pdb=" N PRO E 38 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.011 5.00e-02 4.00e+02 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 551 2.14 - 2.76: 10407 2.76 - 3.37: 16123 3.37 - 3.99: 21523 3.99 - 4.60: 31807 Nonbonded interactions: 80411 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 23 " pdb=" OE1 GLU A 60 " model vdw 1.530 1.800 nonbonded pdb=" H3 MET H 1 " pdb=" O VAL H 17 " model vdw 1.543 1.800 nonbonded pdb=" O ASP E 21 " pdb=" HG1 THR E 55 " model vdw 1.549 1.800 nonbonded pdb=" O ILE H 36 " pdb="HE22 GLN H 41 " model vdw 1.609 1.800 nonbonded pdb=" O THR E 14 " pdb=" HZ1 LYS E 33 " model vdw 1.616 1.800 ... (remaining 80406 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 8 15.96 2 O 535 7.97 2 N 472 6.97 2 C 1736 5.97 2 H 2800 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 0.025 2790 Z= 0.196 ANGLE : 0.947 4.800 3774 Z= 0.460 CHIRALITY : 0.039 0.140 441 PLANARITY : 0.004 0.029 490 DIHEDRAL : 13.883 79.531 1076 MIN NONBONDED DISTANCE : 2.023 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 4.87 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.46 % FAVORED : 95.54 % ROTAMER: OUTLIERS : 0.65 % ALLOWED : 2.27 % FAVORED : 97.09 % 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: -2.12 (0.43), RESIDUES: 336 HELIX: -1.92 (0.34), RESIDUES: 172 SHEET: -0.85 (0.77), RESIDUES: 51 LOOP : -0.35 (0.58), RESIDUES: 113 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.001 ARG H 42 TYR 0.006 0.001 TYR A 13 PHE 0.011 0.001 PHE A 107 TRP 0.004 0.001 TRP A 75 HIS 0.004 0.001 HIS A 111 Resolution of map is: 3.5028 Map-model correlation coefficient (CC) CC_mask : 0.8183 weight= None bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 Initial weight estimate from ratio of grad norms: 0.46583995135341943 cycle: 0 start: weight= 0.4658 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.4658 bond: 0.028 angle: 2.59 clash: 21.1 rota: 2.27 rama: f: 93.75 o: 0.00 Z: -4.62 cb: 1.23 shift=0.3148 cc_mask=0.8478 cycle: 1 start: weight= 0.3261 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.3261 bond: 0.022 angle: 2.28 clash: 13.0 rota: 2.59 rama: f: 96.13 o: 0.00 Z: -3.96 cb: 0.92 shift=0.2956 cc_mask=0.8429 cycle: 2 start: weight= 0.2283 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.2283 bond: 0.018 angle: 2.04 clash: 6.1 rota: 2.59 rama: f: 97.32 o: 0.00 Z: -3.36 cb: 0.62 shift=0.2687 cc_mask=0.8383 cycle: 3 start: weight= 0.1141 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.1141 bond: 0.013 angle: 1.78 clash: 2.5 rota: 1.29 rama: f: 97.92 o: 0.00 Z: -2.75 cb: 0.62 shift=0.2386 cc_mask=0.8303 cycle: 4 start: weight= 0.0799 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.0799 bond: 0.012 angle: 1.72 clash: 2.0 rota: 1.29 rama: f: 97.92 o: 0.00 Z: -2.37 cb: 0.31 shift=0.2313 cc_mask=0.8273 cycle: 5 start: weight= 0.0559 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.0559 bond: 0.011 angle: 1.68 clash: 1.6 rota: 0.97 rama: f: 98.21 o: 0.00 Z: -2.06 cb: 0.31 shift=0.2317 cc_mask=0.8245 cycle: 6 start: weight= 0.0280 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.0280 bond: 0.010 angle: 1.65 clash: 1.1 rota: 1.29 rama: f: 98.21 o: 0.00 Z: -1.61 cb: 0.00 shift=0.2345 cc_mask=0.8201 cycle: 7 start: weight= 0.0196 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.0196 bond: 0.009 angle: 1.64 clash: 1.1 rota: 1.29 rama: f: 98.21 o: 0.00 Z: -1.43 cb: 0.00 shift=0.2380 cc_mask=0.8186 cycle: 8 start: weight= 0.0137 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.0137 bond: 0.009 angle: 1.64 clash: 1.1 rota: 1.29 rama: f: 98.21 o: 0.00 Z: -1.42 cb: 0.00 shift=0.2399 cc_mask=0.8172 cycle: 9 start: weight= 0.0069 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.0069 bond: 0.009 angle: 1.63 clash: 1.1 rota: 1.29 rama: f: 98.21 o: 0.00 Z: -1.40 cb: 0.00 shift=0.2426 cc_mask=0.8159 cycle: 10 start: weight= 0.0048 bond: 0.004 angle: 0.95 clash: 4.9 rota: 0.65 rama: f: 95.54 o: 0.00 Z: -2.12 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.0048 bond: 0.009 angle: 1.64 clash: 0.9 rota: 1.29 rama: f: 98.21 o: 0.00 Z: -1.43 cb: 0.00 shift=0.2433 cc_mask=0.8154 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.004795490388218115 start: weight= 0.0048 bond: 0.009 angle: 1.64 clash: 0.9 rota: 1.29 rama: f: 98.21 o: 0.00 Z: -1.43 cb: 0.00 shift=0.0000 cc_mask=0.8183 final: weight= 0.0048 bond: 0.009 angle: 1.64 clash: 1.1 rota: 1.29 rama: f: 98.21 o: 0.00 Z: -1.43 cb: 0.00 shift=0.2446 cc_mask=0.8154 start: weight= 0.0048 bond: 0.009 angle: 1.64 clash: 1.1 rota: 1.29 rama: f: 98.21 o: 0.00 Z: -1.43 cb: 0.00 shift=0.2446 cc_mask=0.8154 final: weight= 0.0048 bond: 0.009 angle: 1.59 clash: 0.5 rota: 2.27 rama: f: 98.81 o: 0.00 Z: -1.41 cb: 0.00 shift=0.3315 cc_mask=0.8105 start: weight= 0.0048 bond: 0.009 angle: 1.59 clash: 0.5 rota: 2.27 rama: f: 98.81 o: 0.00 Z: -1.41 cb: 0.00 shift=0.3315 cc_mask=0.8105 final: weight= 0.0048 bond: 0.009 angle: 1.58 clash: 0.7 rota: 2.59 rama: f: 98.51 o: 0.00 Z: -1.35 cb: 0.00 shift=0.3817 cc_mask=0.8074 start: weight= 0.0048 bond: 0.009 angle: 1.58 clash: 0.7 rota: 2.59 rama: f: 98.51 o: 0.00 Z: -1.35 cb: 0.00 shift=0.3817 cc_mask=0.8074 final: weight= 0.0048 bond: 0.009 angle: 1.58 clash: 0.5 rota: 2.27 rama: f: 97.92 o: 0.00 Z: -1.33 cb: 0.00 shift=0.4224 cc_mask=0.8045 start: weight= 0.0048 bond: 0.009 angle: 1.58 clash: 0.5 rota: 2.27 rama: f: 97.92 o: 0.00 Z: -1.33 cb: 0.00 shift=0.4224 cc_mask=0.8045 final: weight= 0.0048 bond: 0.009 angle: 1.58 clash: 0.9 rota: 2.27 rama: f: 97.62 o: 0.00 Z: -1.33 cb: 0.00 shift=0.4563 cc_mask=0.8020 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.030 2790 Z= 0.459 ANGLE : 1.585 9.019 3774 Z= 0.834 CHIRALITY : 0.124 0.377 441 PLANARITY : 0.019 0.199 490 DIHEDRAL : 14.410 100.877 1076 MIN NONBONDED DISTANCE : 2.592 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.90 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.38 % FAVORED : 97.62 % ROTAMER: OUTLIERS : 2.27 % ALLOWED : 4.53 % FAVORED : 93.20 % 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: -1.33 (0.43), RESIDUES: 336 HELIX: -1.90 (0.29), RESIDUES: 171 SHEET: -1.22 (0.76), RESIDUES: 47 LOOP : 1.47 (0.62), RESIDUES: 118 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.019 0.003 ARG A 12 TYR 0.059 0.016 TYR A 5 PHE 0.022 0.006 PHE A 37 TRP 0.070 0.027 TRP A 177 HIS 0.003 0.001 HIS E 68 Resolution of map is: 3.5028 Map-model correlation coefficient (CC) CC_mask : 0.8020 =============================================================================== Job complete usr+sys time: 511.35 seconds wall clock time: 9 minutes 21.28 seconds (561.28 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)