Starting qr.refine on Sun May 19 20:25:55 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8r1f_18809.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8r1f_18809.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/8r1f_18809.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8r1f_18809.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8r1f_18809.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8r1f_18809.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 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 54": "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: 16668 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11116 Inner-chain residues flagged as termini: ['pdbres="PHE A 167 "', 'pdbres="VAL A 234 "'] Classifications: {'peptide': 681} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2394 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "C" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3158 Classifications: {'peptide': 202} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 186} Time building chain proxies: 1.82, per 1000 atoms: 0.11 Number of scatterers: 16668 At special positions: 0 Unit cell: (118.44, 110.88, 109.62, 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 57 16.00 O 1577 8.00 N 1431 7.00 C 5307 6.00 H 8296 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: 2.95 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 8267 1.15 - 1.31: 1437 1.31 - 1.48: 3387 1.48 - 1.65: 3669 1.65 - 1.81: 85 Bond restraints: 16845 Sorted by residual: bond pdb=" C HIS A 632 " pdb=" N PHE A 633 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.40e-02 5.10e+03 1.40e+00 bond pdb=" C ASN B 112 " pdb=" N CYS B 113 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 8.84e-01 bond pdb=" C GLU C 221 " pdb=" O GLU C 221 " ideal model delta sigma weight residual 1.231 1.249 -0.018 2.00e-02 2.50e+03 8.26e-01 bond pdb=" CG GLU B 121 " pdb=" HG2 GLU B 121 " ideal model delta sigma weight residual 1.090 1.072 0.018 2.00e-02 2.50e+03 8.17e-01 bond pdb=" C ARG A 814 " pdb=" N ALA A 815 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 8.13e-01 ... (remaining 16840 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.92: 202 105.92 - 112.92: 19472 112.92 - 119.93: 4806 119.93 - 126.93: 5855 126.93 - 133.94: 83 Bond angle restraints: 30418 Sorted by residual: angle pdb=" CA LEU B 19 " pdb=" C LEU B 19 " pdb=" N PRO B 20 " ideal model delta sigma weight residual 116.90 121.82 -4.92 1.50e+00 4.44e-01 1.08e+01 angle pdb=" CA SER A 147 " pdb=" C SER A 147 " pdb=" N PRO A 148 " ideal model delta sigma weight residual 116.90 121.55 -4.65 1.50e+00 4.44e-01 9.61e+00 angle pdb=" CA SER A 264 " pdb=" C SER A 264 " pdb=" N PRO A 265 " ideal model delta sigma weight residual 116.90 120.96 -4.06 1.50e+00 4.44e-01 7.34e+00 angle pdb=" C CYS B 113 " pdb=" N GLN B 114 " pdb=" CA GLN B 114 " ideal model delta sigma weight residual 121.70 126.01 -4.31 1.80e+00 3.09e-01 5.74e+00 angle pdb=" C PHE A 750 " pdb=" N ARG A 751 " pdb=" CA ARG A 751 " ideal model delta sigma weight residual 121.70 125.65 -3.95 1.80e+00 3.09e-01 4.83e+00 ... (remaining 30413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 7387 17.29 - 34.58: 379 34.58 - 51.87: 132 51.87 - 69.16: 33 69.16 - 86.45: 5 Dihedral angle restraints: 7936 sinusoidal: 4370 harmonic: 3566 Sorted by residual: dihedral pdb=" CA ARG C 209 " pdb=" CB ARG C 209 " pdb=" CG ARG C 209 " pdb=" CD ARG C 209 " ideal model delta sinusoidal sigma weight residual 60.00 117.00 -57.00 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " pdb=" CG ARG A 155 " pdb=" CD ARG A 155 " ideal model delta sinusoidal sigma weight residual -60.00 -114.03 54.03 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA ARG A 529 " pdb=" CB ARG A 529 " pdb=" CG ARG A 529 " pdb=" CD ARG A 529 " ideal model delta sinusoidal sigma weight residual -180.00 -128.92 -51.08 3 1.50e+01 4.44e-03 8.97e+00 ... (remaining 7933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 834 0.031 - 0.061: 302 0.061 - 0.092: 70 0.092 - 0.122: 45 0.122 - 0.153: 9 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ILE B 34 " pdb=" N ILE B 34 " pdb=" C ILE B 34 " pdb=" CB ILE B 34 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE A 444 " pdb=" N ILE A 444 " pdb=" C ILE A 444 " pdb=" CB ILE A 444 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL C 157 " pdb=" N VAL C 157 " pdb=" C VAL C 157 " pdb=" CB VAL C 157 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1257 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 306 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 307 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 734 " -0.131 9.50e-02 1.11e+02 4.38e-02 2.10e+00 pdb=" NE ARG A 734 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 734 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 734 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 734 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 734 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 141 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO C 142 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " 0.017 5.00e-02 4.00e+02 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 875 2.06 - 2.70: 23987 2.70 - 3.33: 50031 3.33 - 3.97: 64113 3.97 - 4.60: 95622 Nonbonded interactions: 234628 Sorted by model distance: nonbonded pdb="HE21 GLN A 410 " pdb=" O GLU A 415 " model vdw 1.429 1.800 nonbonded pdb=" H SER B 118 " pdb=" OE1 GLU B 121 " model vdw 1.480 1.800 nonbonded pdb=" O LEU A 770 " pdb=" HG1 THR A 774 " model vdw 1.523 1.800 nonbonded pdb=" O GLY A 154 " pdb=" HG SER A 158 " model vdw 1.563 1.800 nonbonded pdb=" OE1 GLU A 860 " pdb=" HE ARG A 861 " model vdw 1.571 1.800 ... (remaining 234623 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 57 15.96 2 O 1577 7.97 2 N 1431 6.97 2 C 5307 5.97 2 H 8296 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 0.019 8549 Z= 0.189 ANGLE : 0.933 4.925 11554 Z= 0.454 CHIRALITY : 0.038 0.153 1260 PLANARITY : 0.005 0.057 1505 DIHEDRAL : 10.847 77.471 3280 MIN NONBONDED DISTANCE : 2.300 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.54 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.75 % FAVORED : 97.25 % ROTAMER: OUTLIERS : 0.32 % ALLOWED : 2.34 % FAVORED : 97.35 % 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: -0.54 (0.25), RESIDUES: 1017 HELIX: -0.35 (0.21), RESIDUES: 483 SHEET: -0.55 (0.47), RESIDUES: 117 LOOP : -0.04 (0.32), RESIDUES: 417 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.005 0.001 ARG C 267 TYR 0.016 0.001 TYR A 494 PHE 0.018 0.002 PHE A 730 TRP 0.011 0.002 TRP A 791 HIS 0.004 0.001 HIS C 168 Resolution of map is: 3.8623 Map-model correlation coefficient (CC) CC_mask : 0.5466 weight= None bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 Initial weight estimate from ratio of grad norms: 0.26694017966396427 cycle: 0 start: weight= 0.2669 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.2669 bond: 0.023 angle: 2.80 clash: 29.1 rota: 3.29 rama: f: 84.27 o: 2.65 Z: -5.02 cb: 4.92 shift=0.4858 cc_mask=0.5888 cycle: 1 start: weight= 0.1869 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.1869 bond: 0.019 angle: 2.36 clash: 15.1 rota: 1.91 rama: f: 88.69 o: 0.98 Z: -4.31 cb: 1.64 shift=0.4339 cc_mask=0.5829 cycle: 2 start: weight= 0.1308 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.1308 bond: 0.015 angle: 2.04 clash: 6.8 rota: 0.74 rama: f: 93.22 o: 0.39 Z: -3.62 cb: 0.51 shift=0.3704 cc_mask=0.5764 cycle: 3 start: weight= 0.0654 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.0654 bond: 0.012 angle: 1.68 clash: 1.7 rota: 0.53 rama: f: 96.46 o: 0.20 Z: -2.43 cb: 0.00 shift=0.2685 cc_mask=0.5649 cycle: 4 start: weight= 0.0458 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.0458 bond: 0.010 angle: 1.58 clash: 0.8 rota: 0.53 rama: f: 97.54 o: 0.00 Z: -1.97 cb: 0.00 shift=0.2302 cc_mask=0.5601 cycle: 5 start: weight= 0.0320 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.0320 bond: 0.010 angle: 1.52 clash: 0.5 rota: 0.42 rama: f: 98.03 o: 0.00 Z: -1.60 cb: 0.00 shift=0.2028 cc_mask=0.5559 cycle: 6 start: weight= 0.0160 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.0160 bond: 0.009 angle: 1.47 clash: 0.3 rota: 0.42 rama: f: 98.53 o: 0.00 Z: -1.23 cb: 0.00 shift=0.1812 cc_mask=0.5498 cycle: 7 start: weight= 0.0112 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.0112 bond: 0.009 angle: 1.46 clash: 0.2 rota: 0.42 rama: f: 98.53 o: 0.00 Z: -1.10 cb: 0.00 shift=0.1748 cc_mask=0.5476 cycle: 8 start: weight= 0.0079 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.0079 bond: 0.009 angle: 1.46 clash: 0.2 rota: 0.42 rama: f: 98.53 o: 0.00 Z: -1.03 cb: 0.00 shift=0.1742 cc_mask=0.5461 cycle: 9 start: weight= 0.0039 bond: 0.004 angle: 0.93 clash: 0.5 rota: 0.32 rama: f: 97.25 o: 0.00 Z: -0.54 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.0039 bond: 0.009 angle: 1.45 clash: 0.1 rota: 0.42 rama: f: 98.53 o: 0.00 Z: -0.95 cb: 0.00 shift=0.1720 cc_mask=0.5442 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.003925655649660718 start: weight= 0.0039 bond: 0.009 angle: 1.45 clash: 0.1 rota: 0.42 rama: f: 98.53 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.5466 final: weight= 0.0039 bond: 0.009 angle: 1.45 clash: 0.1 rota: 0.42 rama: f: 98.53 o: 0.00 Z: -0.95 cb: 0.00 shift=0.1723 cc_mask=0.5442 start: weight= 0.0039 bond: 0.009 angle: 1.45 clash: 0.1 rota: 0.42 rama: f: 98.53 o: 0.00 Z: -0.95 cb: 0.00 shift=0.1723 cc_mask=0.5442 final: weight= 0.0039 bond: 0.009 angle: 1.43 clash: 0.2 rota: 0.32 rama: f: 98.43 o: 0.00 Z: -1.04 cb: 0.00 shift=0.2429 cc_mask=0.5395 start: weight= 0.0039 bond: 0.009 angle: 1.43 clash: 0.2 rota: 0.32 rama: f: 98.43 o: 0.00 Z: -1.04 cb: 0.00 shift=0.2429 cc_mask=0.5395 final: weight= 0.0039 bond: 0.009 angle: 1.45 clash: 0.2 rota: 0.21 rama: f: 98.33 o: 0.00 Z: -1.26 cb: 0.00 shift=0.2937 cc_mask=0.5359 start: weight= 0.0039 bond: 0.009 angle: 1.45 clash: 0.2 rota: 0.21 rama: f: 98.33 o: 0.00 Z: -1.26 cb: 0.00 shift=0.2937 cc_mask=0.5359 final: weight= 0.0039 bond: 0.009 angle: 1.44 clash: 0.1 rota: 0.11 rama: f: 98.43 o: 0.00 Z: -1.36 cb: 0.00 shift=0.3289 cc_mask=0.5328 start: weight= 0.0039 bond: 0.009 angle: 1.44 clash: 0.1 rota: 0.11 rama: f: 98.43 o: 0.00 Z: -1.36 cb: 0.00 shift=0.3289 cc_mask=0.5328 final: weight= 0.0039 bond: 0.009 angle: 1.45 clash: 0.1 rota: 0.11 rama: f: 98.53 o: 0.00 Z: -1.37 cb: 0.00 shift=0.3640 cc_mask=0.5302 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.030 8549 Z= 0.463 ANGLE : 1.452 9.379 11554 Z= 0.771 CHIRALITY : 0.106 0.363 1260 PLANARITY : 0.020 0.226 1505 DIHEDRAL : 11.754 89.861 3280 MIN NONBONDED DISTANCE : 2.603 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.12 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.47 % FAVORED : 98.53 % ROTAMER: OUTLIERS : 0.11 % ALLOWED : 0.96 % FAVORED : 98.94 % 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: -1.37 (0.23), RESIDUES: 1017 HELIX: -1.47 (0.18), RESIDUES: 480 SHEET: -2.02 (0.41), RESIDUES: 118 LOOP : 0.53 (0.30), RESIDUES: 419 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.020 0.004 ARG A 506 TYR 0.100 0.016 TYR A 776 PHE 0.075 0.012 PHE A 730 TRP 0.079 0.018 TRP A 600 HIS 0.011 0.002 HIS C 214 Resolution of map is: 3.8623 Map-model correlation coefficient (CC) CC_mask : 0.5302 =============================================================================== Job complete usr+sys time: 2377.86 seconds wall clock time: 30 minutes 3.48 seconds (1803.48 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)