Starting qr.refine on Sun May 19 22:01:06 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvk_32142.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvk_32142.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/7vvk_32142.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvk_32142.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvk_32142.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvk_32142.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 TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 113": "OD1" <-> "OD2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib" Total number of atoms: 17880 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3835 Inner-chain residues flagged as termini: ['pdbres="ILE A 62 "', 'pdbres="GLY A 206 "'] Classifications: {'peptide': 230} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 5140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5140 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 864 Classifications: {'peptide': 55} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1912 Classifications: {'peptide': 128} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 580 Classifications: {'peptide': 34} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5549 Inner-chain residues flagged as termini: ['pdbres="GLU R 49 "', 'pdbres="GLU R 111 "', 'pdbres="TRP R 118 "', 'pdbres="VAL R 127 "', 'pdbres="VAL R 157 "', 'pdbres="THR R 163 "', 'pdbres="LEU R 174 "', 'pdbres="ARG R 179 "', 'pdbres="SER R 246 "', 'pdbres="TYR R 278 "', 'pdbres="THR R 392 "', 'pdbres="ASP R 398 "'] Classifications: {'peptide': 334} Modifications used: {'COO': 7, 'NH3': 7} Link IDs: {'PTRANS': 6, 'TRANS': 327} Chain breaks: 6 Time building chain proxies: 1.95, per 1000 atoms: 0.11 Number of scatterers: 17880 At special positions: 0 Unit cell: (129.48, 101.814, 129.48, 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 58 16.00 O 1655 8.00 N 1576 7.00 C 5720 6.00 H 8871 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.05 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 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: 3.36 Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 8848 1.16 - 1.34: 2954 1.34 - 1.52: 3213 1.52 - 1.70: 2978 1.70 - 1.88: 83 Bond restraints: 18076 Sorted by residual: bond pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " ideal model delta sigma weight residual 1.808 1.880 -0.072 3.30e-02 9.18e+02 4.79e+00 bond pdb=" CD GLU P 19 " pdb=" OE2 GLU P 19 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.28e+00 bond pdb=" CB LYS R 34 " pdb=" CG LYS R 34 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" CB ILE R 115 " pdb=" CG2 ILE R 115 " ideal model delta sigma weight residual 1.521 1.569 -0.048 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CG1 ILE R 135 " pdb=" CD1 ILE R 135 " ideal model delta sigma weight residual 1.513 1.567 -0.054 3.90e-02 6.57e+02 1.94e+00 ... (remaining 18071 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.66: 89 104.66 - 112.04: 19948 112.04 - 119.42: 4652 119.42 - 126.80: 7644 126.80 - 134.18: 143 Bond angle restraints: 32476 Sorted by residual: angle pdb=" C GLN R 47 " pdb=" N CYS R 48 " pdb=" CA CYS R 48 " ideal model delta sigma weight residual 121.70 113.85 7.85 1.80e+00 3.09e-01 1.90e+01 angle pdb=" C ASP R 113 " pdb=" N HIS R 114 " pdb=" CA HIS R 114 " ideal model delta sigma weight residual 121.70 128.38 -6.68 1.80e+00 3.09e-01 1.38e+01 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 121.70 127.28 -5.58 1.80e+00 3.09e-01 9.62e+00 angle pdb=" C GLU A 360 " pdb=" N ASN A 361 " pdb=" CA ASN A 361 " ideal model delta sigma weight residual 121.70 127.26 -5.56 1.80e+00 3.09e-01 9.56e+00 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 121.70 126.90 -5.20 1.80e+00 3.09e-01 8.34e+00 ... (remaining 32471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7800 17.61 - 35.23: 475 35.23 - 52.84: 173 52.84 - 70.46: 40 70.46 - 88.07: 8 Dihedral angle restraints: 8496 sinusoidal: 4516 harmonic: 3980 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 130.88 -37.88 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 117 " pdb=" CB CYS R 117 " ideal model delta sinusoidal sigma weight residual 93.00 60.68 32.32 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CA CYS R 131 " pdb=" C CYS R 131 " pdb=" N PRO R 132 " pdb=" CA PRO R 132 " ideal model delta harmonic sigma weight residual 180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1003 0.040 - 0.079: 270 0.079 - 0.119: 71 0.119 - 0.158: 21 0.158 - 0.197: 2 Chirality restraints: 1367 Sorted by residual: chirality pdb=" CB VAL P 31 " pdb=" CA VAL P 31 " pdb=" CG1 VAL P 31 " pdb=" CG2 VAL P 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ILE A 245 " pdb=" N ILE A 245 " pdb=" C ILE A 245 " pdb=" CB ILE A 245 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE N 51 " pdb=" N ILE N 51 " pdb=" C ILE N 51 " pdb=" CB ILE N 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1364 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 23 " 0.016 2.00e-02 2.50e+03 7.07e-03 2.00e+00 pdb=" CG TRP P 23 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP P 23 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP P 23 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP P 23 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP P 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 23 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 23 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP P 23 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP P 23 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP P 23 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP P 23 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 23 " 0.006 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 23 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP P 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 365 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 366 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 366 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 366 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 24 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LEU P 24 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU P 24 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG P 25 " 0.008 2.00e-02 2.50e+03 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1555 2.13 - 2.75: 31088 2.75 - 3.37: 51310 3.37 - 3.98: 70522 3.98 - 4.60: 103055 Nonbonded interactions: 257530 Sorted by model distance: nonbonded pdb=" OE1 GLN N 123 " pdb=" HG1 THR N 125 " model vdw 1.516 1.800 nonbonded pdb=" HH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 1.523 1.800 nonbonded pdb=" HE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 1.545 1.800 nonbonded pdb="HE22 GLN R 364 " pdb=" OH TYR R 429 " model vdw 1.560 1.800 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.564 1.800 ... (remaining 257525 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 58 15.96 2 O 1655 7.97 2 N 1576 6.97 2 C 5720 5.97 2 H 8871 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 0.072 9205 Z= 0.214 ANGLE : 0.958 7.848 12457 Z= 0.465 CHIRALITY : 0.041 0.197 1367 PLANARITY : 0.004 0.032 1591 DIHEDRAL : 12.814 88.074 3326 MIN NONBONDED DISTANCE : 1.892 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 4.99 RAMACHANDRAN PLOT: OUTLIERS : 0.46 % ALLOWED : 4.66 % FAVORED : 94.89 % ROTAMER: OUTLIERS : 1.03 % ALLOWED : 4.12 % FAVORED : 94.85 % 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: -1.70 (0.23), RESIDUES: 1095 HELIX: -1.21 (0.22), RESIDUES: 434 SHEET: -0.66 (0.35), RESIDUES: 216 LOOP : -1.06 (0.27), RESIDUES: 445 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.009 0.000 ARG R 146 TYR 0.010 0.001 TYR A 329 PHE 0.018 0.001 PHE R 335 TRP 0.015 0.001 TRP P 23 HIS 0.007 0.001 HIS P 14 Resolution of map is: 2.2246 Map-model correlation coefficient (CC) CC_mask : 0.6750 weight= None bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 Initial weight estimate from ratio of grad norms: 0.18587988274904846 cycle: 0 start: weight= 0.1859 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.1859 bond: 0.021 angle: 2.70 clash: 15.4 rota: 3.92 rama: f: 84.29 o: 2.01 Z: -5.26 cb: 3.98 shift=0.3734 cc_mask=0.6922 cycle: 1 start: weight= 0.1301 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.1301 bond: 0.017 angle: 2.29 clash: 8.7 rota: 2.06 rama: f: 89.50 o: 1.00 Z: -4.65 cb: 1.42 shift=0.3492 cc_mask=0.6891 cycle: 2 start: weight= 0.0911 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.0911 bond: 0.014 angle: 2.02 clash: 5.3 rota: 1.55 rama: f: 92.05 o: 0.73 Z: -3.91 cb: 0.38 shift=0.3234 cc_mask=0.6863 cycle: 3 start: weight= 0.0455 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.0455 bond: 0.011 angle: 1.74 clash: 2.1 rota: 1.03 rama: f: 94.79 o: 0.46 Z: -2.79 cb: 0.09 shift=0.2875 cc_mask=0.6812 cycle: 4 start: weight= 0.0319 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.0319 bond: 0.011 angle: 1.68 clash: 1.1 rota: 0.82 rama: f: 95.43 o: 0.37 Z: -2.30 cb: 0.00 shift=0.2690 cc_mask=0.6790 cycle: 5 start: weight= 0.0223 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.0223 bond: 0.010 angle: 1.63 clash: 0.9 rota: 0.72 rama: f: 95.89 o: 0.27 Z: -1.94 cb: 0.00 shift=0.2506 cc_mask=0.6769 cycle: 6 start: weight= 0.0112 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.0112 bond: 0.009 angle: 1.59 clash: 0.8 rota: 0.62 rama: f: 96.53 o: 0.18 Z: -1.62 cb: 0.00 shift=0.2368 cc_mask=0.6735 cycle: 7 start: weight= 0.0078 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.0078 bond: 0.009 angle: 1.58 clash: 0.7 rota: 0.62 rama: f: 96.53 o: 0.18 Z: -1.55 cb: 0.00 shift=0.2365 cc_mask=0.6722 cycle: 8 start: weight= 0.0055 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.0055 bond: 0.009 angle: 1.57 clash: 0.7 rota: 0.62 rama: f: 96.53 o: 0.18 Z: -1.52 cb: 0.00 shift=0.2351 cc_mask=0.6713 cycle: 9 start: weight= 0.0027 bond: 0.004 angle: 0.96 clash: 5.0 rota: 1.03 rama: f: 94.89 o: 0.46 Z: -1.70 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.0027 bond: 0.009 angle: 1.57 clash: 0.7 rota: 0.62 rama: f: 96.44 o: 0.27 Z: -1.51 cb: 0.00 shift=0.2358 cc_mask=0.6699 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0027335727906928503 start: weight= 0.0027 bond: 0.009 angle: 1.57 clash: 0.7 rota: 0.62 rama: f: 96.44 o: 0.27 Z: -1.51 cb: 0.00 shift=0.0000 cc_mask=0.6750 final: weight= 0.0027 bond: 0.009 angle: 1.57 clash: 0.7 rota: 0.62 rama: f: 96.44 o: 0.27 Z: -1.51 cb: 0.00 shift=0.2362 cc_mask=0.6699 start: weight= 0.0027 bond: 0.009 angle: 1.57 clash: 0.7 rota: 0.62 rama: f: 96.44 o: 0.27 Z: -1.51 cb: 0.00 shift=0.2362 cc_mask=0.6699 final: weight= 0.0027 bond: 0.009 angle: 1.53 clash: 0.7 rota: 0.72 rama: f: 97.08 o: 0.27 Z: -1.74 cb: 0.00 shift=0.3147 cc_mask=0.6659 start: weight= 0.0027 bond: 0.009 angle: 1.53 clash: 0.7 rota: 0.72 rama: f: 97.08 o: 0.27 Z: -1.74 cb: 0.00 shift=0.3147 cc_mask=0.6659 final: weight= 0.0027 bond: 0.009 angle: 1.56 clash: 0.6 rota: 0.72 rama: f: 96.80 o: 0.18 Z: -1.82 cb: 0.09 shift=0.3578 cc_mask=0.6638 start: weight= 0.0027 bond: 0.009 angle: 1.56 clash: 0.6 rota: 0.72 rama: f: 96.80 o: 0.18 Z: -1.82 cb: 0.09 shift=0.3578 cc_mask=0.6638 final: weight= 0.0027 bond: 0.009 angle: 1.55 clash: 0.6 rota: 0.72 rama: f: 96.80 o: 0.09 Z: -1.80 cb: 0.19 shift=0.3896 cc_mask=0.6620 start: weight= 0.0027 bond: 0.009 angle: 1.55 clash: 0.6 rota: 0.72 rama: f: 96.80 o: 0.09 Z: -1.80 cb: 0.19 shift=0.3896 cc_mask=0.6620 final: weight= 0.0027 bond: 0.009 angle: 1.56 clash: 0.5 rota: 0.72 rama: f: 96.71 o: 0.18 Z: -1.86 cb: 0.09 shift=0.4150 cc_mask=0.6601 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.159 9205 Z= 0.474 ANGLE : 1.555 9.220 12457 Z= 0.833 CHIRALITY : 0.117 0.439 1367 PLANARITY : 0.019 0.249 1591 DIHEDRAL : 12.883 123.780 3326 MIN NONBONDED DISTANCE : 2.565 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.50 RAMACHANDRAN PLOT: OUTLIERS : 0.18 % ALLOWED : 3.11 % FAVORED : 96.71 % ROTAMER: OUTLIERS : 0.72 % ALLOWED : 4.33 % FAVORED : 94.95 % CBETA DEVIATIONS : 0.09 % 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: -1.86 (0.22), RESIDUES: 1095 HELIX: -1.26 (0.20), RESIDUES: 445 SHEET: -1.62 (0.31), RESIDUES: 206 LOOP : -0.71 (0.28), RESIDUES: 444 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.023 0.005 ARG R 146 TYR 0.077 0.017 TYR A 381 PHE 0.064 0.011 PHE G 61 TRP 0.125 0.021 TRP R 298 HIS 0.009 0.002 HIS B 54 Resolution of map is: 2.2246 Map-model correlation coefficient (CC) CC_mask : 0.6601 =============================================================================== Job complete usr+sys time: 2568.74 seconds wall clock time: 33 minutes 31.81 seconds (2011.81 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)