Starting qr.refine on Sun May 19 18:00:28 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6wik_21684.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6wik_21684.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/6wik_21684.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6wik_21684.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6wik_21684.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6wik_21684.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 "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 308": "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: 13230 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3225 Inner-chain residues flagged as termini: ['pdbres="ALA C 131 "', 'pdbres="ALA C 132 "', 'pdbres="GLY C 148 "'] Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "D" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3286 Inner-chain residues flagged as termini: ['pdbres="THR D 142 "', 'pdbres="ALA D 143 "'] Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 3} Link IDs: {'PTRANS': 14, 'TRANS': 204} Chain: "A" Number of atoms: 6719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6719 Inner-chain residues flagged as termini: ['pdbres="ALA A 237 "', 'pdbres="ALA A 289 "', 'pdbres="GLY A 395 "', 'pdbres="ILE A 453 "'] Classifications: {'peptide': 427} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 8, 'TRANS': 418} Chain breaks: 2 Time building chain proxies: 1.52, per 1000 atoms: 0.11 Number of scatterers: 13230 At special positions: 0 Unit cell: (129.47, 116.63, 85.6, 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 39 16.00 O 1247 8.00 N 1077 7.00 C 4253 6.00 H 6614 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 165 " - pdb=" SG CYS D 220 " distance=2.04 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: 2.42 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1582 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.24: 7507 1.24 - 1.51: 3191 1.51 - 1.78: 2617 1.78 - 2.05: 63 2.05 - 2.32: 2 Bond restraints: 13380 Sorted by residual: bond pdb=" CD1 TYR C 160 " pdb=" CE1 TYR C 160 " ideal model delta sigma weight residual 1.382 2.321 -0.939 3.00e-02 1.11e+03 9.80e+02 bond pdb=" CD2 TYR C 160 " pdb=" CE2 TYR C 160 " ideal model delta sigma weight residual 1.382 2.221 -0.839 3.00e-02 1.11e+03 7.81e+02 bond pdb=" CE1 TYR C 160 " pdb=" CZ TYR C 160 " ideal model delta sigma weight residual 1.378 1.964 -0.586 2.40e-02 1.74e+03 5.97e+02 bond pdb=" CE2 TYR C 160 " pdb=" CZ TYR C 160 " ideal model delta sigma weight residual 1.378 1.865 -0.487 2.40e-02 1.74e+03 4.12e+02 bond pdb=" CG TYR C 160 " pdb=" CD1 TYR C 160 " ideal model delta sigma weight residual 1.389 1.751 -0.362 2.10e-02 2.27e+03 2.96e+02 ... (remaining 13375 not shown) Histogram of bond angle deviations from ideal: 55.91 - 74.88: 1 74.88 - 93.84: 7 93.84 - 112.81: 15788 112.81 - 131.77: 8339 131.77 - 150.73: 23 Bond angle restraints: 24158 Sorted by residual: angle pdb=" CB ALA C 131 " pdb=" CA ALA C 131 " pdb=" HA ALA C 131 " ideal model delta sigma weight residual 109.00 55.91 53.09 3.00e+00 1.11e-01 3.13e+02 angle pdb=" C GLU C 130 " pdb=" N ALA C 131 " pdb=" CA ALA C 131 " ideal model delta sigma weight residual 121.70 150.73 -29.03 1.80e+00 3.09e-01 2.60e+02 angle pdb=" CG2 THR D 142 " pdb=" CB THR D 142 " pdb=" HB THR D 142 " ideal model delta sigma weight residual 108.00 75.17 32.83 3.00e+00 1.11e-01 1.20e+02 angle pdb=" N ALA C 131 " pdb=" CA ALA C 131 " pdb=" CB ALA C 131 " ideal model delta sigma weight residual 110.40 126.00 -15.60 1.50e+00 4.44e-01 1.08e+02 angle pdb=" H2 ALA C 131 " pdb=" N ALA C 131 " pdb=" H3 ALA C 131 " ideal model delta sigma weight residual 109.47 79.24 30.23 3.00e+00 1.11e-01 1.02e+02 ... (remaining 24153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 5699 16.87 - 33.75: 385 33.75 - 50.62: 167 50.62 - 67.49: 70 67.49 - 84.37: 10 Dihedral angle restraints: 6331 sinusoidal: 3376 harmonic: 2955 Sorted by residual: dihedral pdb=" N ALA C 131 " pdb=" C ALA C 131 " pdb=" CA ALA C 131 " pdb=" CB ALA C 131 " ideal model delta harmonic sigma weight residual 122.90 143.55 -20.65 0 2.50e+00 1.60e-01 6.82e+01 dihedral pdb=" CB CYS D 165 " pdb=" SG CYS D 165 " pdb=" SG CYS D 220 " pdb=" CB CYS D 220 " ideal model delta sinusoidal sigma weight residual -86.00 -134.77 48.77 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA TRP D 213 " pdb=" C TRP D 213 " pdb=" N PRO D 214 " pdb=" CA PRO D 214 " ideal model delta harmonic sigma weight residual 180.00 -152.32 -27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 6328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 1071 0.234 - 0.468: 2 0.468 - 0.702: 0 0.702 - 0.936: 0 0.936 - 1.170: 1 Chirality restraints: 1074 Sorted by residual: chirality pdb=" CB THR D 142 " pdb=" CA THR D 142 " pdb=" OG1 THR D 142 " pdb=" CG2 THR D 142 " both_signs ideal model delta sigma weight residual False 2.55 1.38 1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" CA ALA C 131 " pdb=" N ALA C 131 " pdb=" C ALA C 131 " pdb=" CB ALA C 131 " both_signs ideal model delta sigma weight residual False 2.54 2.08 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CA PRO D 144 " pdb=" N PRO D 144 " pdb=" C PRO D 144 " pdb=" CB PRO D 144 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1071 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 171 " 0.118 5.00e-02 4.00e+02 1.82e-01 5.33e+01 pdb=" N PRO D 172 " -0.316 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " 0.105 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " 0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 143 " 0.106 5.00e-02 4.00e+02 1.60e-01 4.08e+01 pdb=" N PRO D 144 " -0.276 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 147 " 0.085 5.00e-02 4.00e+02 1.30e-01 2.68e+01 pdb=" N PRO D 148 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO D 148 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO D 148 " 0.067 5.00e-02 4.00e+02 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 375 1.92 - 2.59: 13871 2.59 - 3.26: 41024 3.26 - 3.93: 51891 3.93 - 4.60: 77652 Nonbonded interactions: 184813 Sorted by model distance: nonbonded pdb=" HA ALA C 131 " pdb=" HB3 ALA C 131 " model vdw 1.253 1.872 nonbonded pdb=" O THR D 142 " pdb=" H2 ALA D 143 " model vdw 1.342 1.920 nonbonded pdb=" O TRP D 213 " pdb=" H SER D 215 " model vdw 1.352 1.800 nonbonded pdb=" O GLU C 130 " pdb=" H2 ALA C 131 " model vdw 1.398 1.920 nonbonded pdb=" HZ3 LYS D 140 " pdb=" O SER D 197 " model vdw 1.418 1.800 ... (remaining 184808 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 39 15.96 2 O 1247 7.97 2 N 1077 6.97 2 C 4253 5.97 2 H 6614 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 : 0.020 0.939 6766 Z= 0.933 ANGLE : 1.162 29.033 9214 Z= 0.565 CHIRALITY : 0.059 1.170 1074 PLANARITY : 0.011 0.182 1145 DIHEDRAL : 13.250 84.365 2375 MIN NONBONDED DISTANCE : 1.940 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 14.98 RAMACHANDRAN PLOT: OUTLIERS : 2.71 % ALLOWED : 8.83 % FAVORED : 88.46 % ROTAMER: OUTLIERS : 2.60 % ALLOWED : 8.88 % FAVORED : 88.52 % CBETA DEVIATIONS : 0.13 % PEPTIDE PLANE: CIS-PROLINE : 3.23 % 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: -3.34 (0.25), RESIDUES: 849 HELIX: -1.30 (0.24), RESIDUES: 359 SHEET: -1.75 (0.34), RESIDUES: 190 LOOP : -3.55 (0.31), RESIDUES: 300 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.004 0.001 ARG D 59 TYR 0.043 0.002 TYR C 160 PHE 0.026 0.002 PHE D 171 TRP 0.022 0.002 TRP D 179 HIS 0.019 0.003 HIS D 224 Resolution of map is: 4.2232 Map-model correlation coefficient (CC) CC_mask : 0.7073 weight= None bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 Initial weight estimate from ratio of grad norms: 0.40215642679182884 cycle: 0 start: weight= 0.4022 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.4022 bond: 0.040 angle: 2.28 clash: 14.2 rota: 1.91 rama: f: 88.28 o: 2.84 Z: -3.61 cb: 0.63 shift=0.0517 cc_mask=0.7222 cycle: 1 start: weight= 0.2011 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.2011 bond: 0.033 angle: 1.96 clash: 12.0 rota: 1.91 rama: f: 88.28 o: 2.60 Z: -3.52 cb: 0.51 shift=0.0388 cc_mask=0.7155 cycle: 2 start: weight= 0.1005 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.1005 bond: 0.031 angle: 1.79 clash: 12.6 rota: 2.19 rama: f: 88.08 o: 2.48 Z: -3.48 cb: 0.63 shift=0.0263 cc_mask=0.7105 cycle: 3 start: weight= 0.0503 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0503 bond: 0.037 angle: 2.16 clash: 13.3 rota: 2.46 rama: f: 88.17 o: 2.49 Z: -3.48 cb: 0.51 shift=0.0238 cc_mask=0.7089 cycle: 4 start: weight= 0.0251 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0251 bond: 0.041 angle: 2.30 clash: 12.3 rota: 2.05 rama: f: 88.06 o: 2.36 Z: -3.47 cb: 0.88 shift=0.0292 cc_mask=0.7082 cycle: 5 start: weight= 0.0126 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0126 bond: 0.035 angle: 2.01 clash: 13.5 rota: 2.32 rama: f: 87.72 o: 2.72 Z: -3.44 cb: 0.88 shift=0.0210 cc_mask=0.7076 cycle: 6 start: weight= 0.0063 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0063 bond: 0.028 angle: 1.75 clash: 12.4 rota: 2.19 rama: f: 88.08 o: 2.48 Z: -3.50 cb: 0.51 shift=0.0244 cc_mask=0.7076 cycle: 7 start: weight= 0.0044 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0044 bond: 0.030 angle: 1.90 clash: 13.2 rota: 2.32 rama: f: 87.72 o: 2.72 Z: -3.40 cb: 0.63 shift=0.0212 cc_mask=0.7075 cycle: 8 start: weight= 0.0022 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0022 bond: 0.030 angle: 1.86 clash: 13.8 rota: 2.19 rama: f: 87.96 o: 2.72 Z: -3.44 cb: 0.76 shift=0.0211 cc_mask=0.7074 cycle: 9 start: weight= 0.0011 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0011 bond: 0.037 angle: 1.90 clash: 11.5 rota: 2.19 rama: f: 88.48 o: 2.26 Z: -3.49 cb: 0.63 shift=0.0320 cc_mask=0.7078 cycle: 10 start: weight= 0.0005 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0005 bond: 0.029 angle: 1.77 clash: 13.5 rota: 2.19 rama: f: 87.96 o: 2.60 Z: -3.41 cb: 0.51 shift=0.0208 cc_mask=0.7074 cycle: 11 start: weight= 0.0004 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0004 bond: 0.037 angle: 2.08 clash: 13.2 rota: 2.32 rama: f: 87.72 o: 2.72 Z: -3.44 cb: 1.01 shift=0.0233 cc_mask=0.7074 cycle: 12 start: weight= 0.0002 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0002 bond: 0.036 angle: 1.91 clash: 12.7 rota: 2.19 rama: f: 88.48 o: 2.26 Z: -3.51 cb: 0.63 shift=0.0288 cc_mask=0.7075 cycle: 13 start: weight= 0.0001 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0001 bond: 0.030 angle: 1.69 clash: 13.1 rota: 2.19 rama: f: 88.31 o: 2.48 Z: -3.49 cb: 0.38 shift=0.0229 cc_mask=0.7075 cycle: 14 start: weight= 0.0000 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0000 bond: 0.027 angle: 1.73 clash: 13.2 rota: 2.19 rama: f: 87.96 o: 2.83 Z: -3.43 cb: 0.51 shift=0.0185 cc_mask=0.7074 cycle: 15 start: weight= 0.0000 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0000 bond: 0.026 angle: 1.62 clash: 13.5 rota: 2.19 rama: f: 88.19 o: 2.83 Z: -3.43 cb: 0.51 shift=0.0181 cc_mask=0.7074 cycle: 16 start: weight= 0.0000 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0000 bond: 0.029 angle: 1.76 clash: 13.6 rota: 2.32 rama: f: 88.19 o: 2.48 Z: -3.46 cb: 0.25 shift=0.0220 cc_mask=0.7075 cycle: 17 start: weight= 0.0000 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0000 bond: 0.032 angle: 1.90 clash: 13.0 rota: 2.19 rama: f: 87.84 o: 2.72 Z: -3.45 cb: 0.76 shift=0.0222 cc_mask=0.7074 cycle: 18 start: weight= 0.0000 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0000 bond: 0.032 angle: 1.81 clash: 11.1 rota: 2.05 rama: f: 88.72 o: 2.38 Z: -3.51 cb: 0.76 shift=0.0359 cc_mask=0.7079 cycle: 19 start: weight= 0.0000 bond: 0.020 angle: 1.16 clash: 15.0 rota: 2.60 rama: f: 88.46 o: 2.71 Z: -3.34 cb: 0.13 shift=0.0000 cc_mask=0.7073 final: weight= 0.0000 bond: 0.037 angle: 2.08 clash: 13.3 rota: 2.05 rama: f: 87.72 o: 2.72 Z: -3.46 cb: 1.01 shift=0.0262 cc_mask=0.7074 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 2.946708925559024e-06 start: weight= 0.0000 bond: 0.037 angle: 2.08 clash: 13.3 rota: 2.05 rama: f: 87.72 o: 2.72 Z: -3.46 cb: 1.01 shift=0.0000 cc_mask=0.7073 final: weight= 0.0000 bond: 0.035 angle: 1.94 clash: 13.4 rota: 2.46 rama: f: 88.19 o: 2.60 Z: -3.45 cb: 0.51 shift=0.0214 cc_mask=0.7075 start: weight= 0.0000 bond: 0.035 angle: 1.94 clash: 13.4 rota: 2.46 rama: f: 88.19 o: 2.60 Z: -3.45 cb: 0.51 shift=0.0214 cc_mask=0.7075 final: weight= 0.0000 bond: 0.040 angle: 1.86 clash: 10.7 rota: 2.05 rama: f: 89.55 o: 2.38 Z: -3.40 cb: 0.76 shift=0.0541 cc_mask=0.7082 start: weight= 0.0000 bond: 0.040 angle: 1.86 clash: 10.7 rota: 2.05 rama: f: 89.55 o: 2.38 Z: -3.40 cb: 0.76 shift=0.0541 cc_mask=0.7082 final: weight= 0.0000 bond: 0.040 angle: 2.04 clash: 10.1 rota: 2.05 rama: f: 89.79 o: 2.38 Z: -3.34 cb: 0.88 shift=0.0551 cc_mask=0.7081 start: weight= 0.0000 bond: 0.040 angle: 2.04 clash: 10.1 rota: 2.05 rama: f: 89.79 o: 2.38 Z: -3.34 cb: 0.88 shift=0.0551 cc_mask=0.7081 final: weight= 0.0000 bond: 0.041 angle: 2.04 clash: 9.7 rota: 2.05 rama: f: 90.02 o: 2.38 Z: -3.30 cb: 0.76 shift=0.0560 cc_mask=0.7081 start: weight= 0.0000 bond: 0.041 angle: 2.04 clash: 9.7 rota: 2.05 rama: f: 90.02 o: 2.38 Z: -3.30 cb: 0.76 shift=0.0560 cc_mask=0.7081 final: weight= 0.0000 bond: 0.039 angle: 2.05 clash: 9.4 rota: 1.91 rama: f: 90.27 o: 2.37 Z: -3.20 cb: 0.63 shift=0.0617 cc_mask=0.7081 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.039 1.461 6766 Z= 1.922 ANGLE : 2.045 47.359 9214 Z= 1.097 CHIRALITY : 0.215 4.793 1074 PLANARITY : 0.023 0.413 1145 DIHEDRAL : 13.298 87.794 2375 MIN NONBONDED DISTANCE : 1.633 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 9.39 RAMACHANDRAN PLOT: OUTLIERS : 2.37 % ALLOWED : 7.35 % FAVORED : 90.27 % ROTAMER: OUTLIERS : 1.91 % ALLOWED : 7.24 % FAVORED : 90.85 % CBETA DEVIATIONS : 0.63 % PEPTIDE PLANE: CIS-PROLINE : 3.23 % 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: -3.20 (0.25), RESIDUES: 843 HELIX: -1.46 (0.22), RESIDUES: 372 SHEET: -1.74 (0.34), RESIDUES: 194 LOOP : -3.09 (0.34), RESIDUES: 277 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.020 0.003 ARG D 59 TYR 0.486 0.017 TYR C 160 PHE 0.055 0.008 PHE C 138 TRP 0.082 0.015 TRP D 213 HIS 0.010 0.003 HIS C 218 Resolution of map is: 4.2232 Map-model correlation coefficient (CC) CC_mask : 0.7081 =============================================================================== Job complete usr+sys time: 3773.08 seconds wall clock time: 39 minutes 30.74 seconds (2370.74 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)