Starting qr.refine on Sun May 19 17:41:23 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8jo4_36455.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8jo4_36455.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/8jo4_36455.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8jo4_36455.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8jo4_36455.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8jo4_36455.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 "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 257": "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: 11311 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5717 Classifications: {'peptide': 350} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain: "B" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5594 Inner-chain residues flagged as termini: ['pdbres="PRO B 40 "', 'pdbres="ASP B 53 "'] Classifications: {'peptide': 359} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Time building chain proxies: 1.31, per 1000 atoms: 0.12 Number of scatterers: 11311 At special positions: 0 Unit cell: (65.1, 82.77, 115.32, 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 27 16.00 O 1093 8.00 N 941 7.00 C 3596 6.00 H 5654 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: 2.21 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1348 Time building geometry restraints manager: 2.51 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: 5647 1.14 - 1.31: 974 1.31 - 1.48: 2221 1.48 - 1.64: 2533 1.64 - 1.81: 47 Bond restraints: 11422 Sorted by residual: bond pdb=" CB MET B 357 " pdb=" CG MET B 357 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.59e-01 bond pdb=" C ALA A 194 " pdb=" N ASN A 195 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.39e-01 bond pdb=" C VAL B 131 " pdb=" O VAL B 131 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.46e-01 bond pdb=" CB PRO A 212 " pdb=" CG PRO A 212 " ideal model delta sigma weight residual 1.492 1.527 -0.035 5.00e-02 4.00e+02 5.00e-01 bond pdb=" C VAL A 211 " pdb=" O VAL A 211 " ideal model delta sigma weight residual 1.231 1.244 -0.013 2.00e-02 2.50e+03 4.24e-01 ... (remaining 11417 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.70: 113 105.70 - 112.78: 13541 112.78 - 119.85: 2950 119.85 - 126.93: 4031 126.93 - 134.01: 57 Bond angle restraints: 20692 Sorted by residual: angle pdb=" CA CYS B 259 " pdb=" C CYS B 259 " pdb=" N PRO B 260 " ideal model delta sigma weight residual 116.90 121.13 -4.23 1.50e+00 4.44e-01 7.95e+00 angle pdb=" CA LEU B 173 " pdb=" C LEU B 173 " pdb=" N PRO B 174 " ideal model delta sigma weight residual 116.90 119.82 -2.92 1.50e+00 4.44e-01 3.80e+00 angle pdb=" CA TYR B 71 " pdb=" C TYR B 71 " pdb=" N PRO B 72 " ideal model delta sigma weight residual 116.90 119.74 -2.84 1.50e+00 4.44e-01 3.59e+00 angle pdb=" C SER A 241 " pdb=" CA SER A 241 " pdb=" CB SER A 241 " ideal model delta sigma weight residual 110.10 113.69 -3.59 1.90e+00 2.77e-01 3.58e+00 angle pdb=" N ASN A 98 " pdb=" CA ASN A 98 " pdb=" C ASN A 98 " ideal model delta sigma weight residual 111.00 105.89 5.11 2.80e+00 1.28e-01 3.33e+00 ... (remaining 20687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5011 17.93 - 35.86: 236 35.86 - 53.80: 99 53.80 - 71.73: 23 71.73 - 89.66: 4 Dihedral angle restraints: 5373 sinusoidal: 2943 harmonic: 2430 Sorted by residual: dihedral pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" N ALA A 240 " pdb=" CA ALA A 240 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" N ASP A 321 " pdb=" CA ASP A 321 " pdb=" CB ASP A 321 " pdb=" CG ASP A 321 " ideal model delta sinusoidal sigma weight residual -180.00 -120.45 -59.55 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN A 82 " pdb=" CA GLN A 82 " pdb=" CB GLN A 82 " pdb=" CG GLN A 82 " ideal model delta sinusoidal sigma weight residual -180.00 -121.03 -58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 555 0.029 - 0.057: 215 0.057 - 0.086: 55 0.086 - 0.114: 38 0.114 - 0.143: 14 Chirality restraints: 877 Sorted by residual: chirality pdb=" CA ILE B 167 " pdb=" N ILE B 167 " pdb=" C ILE B 167 " pdb=" CB ILE B 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE B 359 " pdb=" N ILE B 359 " pdb=" C ILE B 359 " pdb=" CB ILE B 359 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL A 236 " pdb=" N VAL A 236 " pdb=" C VAL A 236 " pdb=" CB VAL A 236 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 874 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 165 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO B 166 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 212 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 16 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.16e-01 pdb=" N PRO A 17 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 17 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 17 " 0.013 5.00e-02 4.00e+02 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1008 2.12 - 2.74: 19745 2.74 - 3.36: 34781 3.36 - 3.98: 47116 3.98 - 4.60: 69840 Nonbonded interactions: 172490 Sorted by model distance: nonbonded pdb=" HG SER A 175 " pdb=" OD2 ASP A 298 " model vdw 1.495 1.800 nonbonded pdb=" O ILE B 319 " pdb=" H ALA B 323 " model vdw 1.497 1.800 nonbonded pdb=" OE1 GLU A 343 " pdb=" HG1 THR B 353 " model vdw 1.513 1.800 nonbonded pdb="HH22 ARG B 118 " pdb=" O CYS B 376 " model vdw 1.524 1.800 nonbonded pdb=" O THR B 8 " pdb=" HD1 HIS B 103 " model vdw 1.534 1.800 ... (remaining 172485 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 27 15.96 2 O 1093 7.97 2 N 941 6.97 2 C 3596 5.97 2 H 5654 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 0.035 5768 Z= 0.183 ANGLE : 0.907 5.106 7805 Z= 0.438 CHIRALITY : 0.039 0.143 877 PLANARITY : 0.003 0.041 1004 DIHEDRAL : 11.622 89.662 2177 MIN NONBONDED DISTANCE : 2.067 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 2.39 RAMACHANDRAN PLOT: OUTLIERS : 0.14 % ALLOWED : 2.84 % FAVORED : 97.01 % ROTAMER: OUTLIERS : 2.09 % ALLOWED : 4.82 % FAVORED : 93.10 % 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: 0.24 (0.31), RESIDUES: 703 HELIX: 0.39 (0.26), RESIDUES: 379 SHEET: -0.52 (0.59), RESIDUES: 64 LOOP : 0.27 (0.40), RESIDUES: 260 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG B 337 TYR 0.007 0.001 TYR A 132 PHE 0.009 0.001 PHE A 125 TRP 0.009 0.001 TRP B 358 HIS 0.004 0.001 HIS A 300 Resolution of map is: 3.1942 Map-model correlation coefficient (CC) CC_mask : 0.7629 weight= None bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 Initial weight estimate from ratio of grad norms: 0.22961425275336939 cycle: 0 start: weight= 0.2296 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.2296 bond: 0.023 angle: 2.29 clash: 12.2 rota: 2.57 rama: f: 90.04 o: 0.28 Z: -5.19 cb: 0.59 shift=0.2926 cc_mask=0.7997 cycle: 1 start: weight= 0.1607 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.1607 bond: 0.018 angle: 2.00 clash: 6.2 rota: 1.77 rama: f: 94.03 o: 0.14 Z: -4.50 cb: 0.15 shift=0.2718 cc_mask=0.7936 cycle: 2 start: weight= 0.1125 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.1125 bond: 0.015 angle: 1.81 clash: 3.7 rota: 1.61 rama: f: 96.16 o: 0.00 Z: -3.75 cb: 0.15 shift=0.2501 cc_mask=0.7876 cycle: 3 start: weight= 0.0563 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.0563 bond: 0.012 angle: 1.60 clash: 1.2 rota: 1.61 rama: f: 97.58 o: 0.00 Z: -2.50 cb: 0.00 shift=0.2165 cc_mask=0.7772 cycle: 4 start: weight= 0.0394 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.0394 bond: 0.011 angle: 1.54 clash: 0.5 rota: 1.44 rama: f: 98.29 o: 0.00 Z: -2.09 cb: 0.00 shift=0.2064 cc_mask=0.7726 cycle: 5 start: weight= 0.0276 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.0276 bond: 0.010 angle: 1.51 clash: 0.5 rota: 1.44 rama: f: 98.44 o: 0.00 Z: -1.74 cb: 0.00 shift=0.2028 cc_mask=0.7685 cycle: 6 start: weight= 0.0138 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.0138 bond: 0.009 angle: 1.49 clash: 0.5 rota: 1.28 rama: f: 98.58 o: 0.00 Z: -1.39 cb: 0.00 shift=0.2043 cc_mask=0.7627 cycle: 7 start: weight= 0.0096 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.0096 bond: 0.009 angle: 1.49 clash: 0.4 rota: 1.28 rama: f: 98.72 o: 0.00 Z: -1.30 cb: 0.00 shift=0.2087 cc_mask=0.7604 cycle: 8 start: weight= 0.0068 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.0068 bond: 0.009 angle: 1.49 clash: 0.5 rota: 1.28 rama: f: 98.72 o: 0.00 Z: -1.25 cb: 0.00 shift=0.2068 cc_mask=0.7589 cycle: 9 start: weight= 0.0034 bond: 0.004 angle: 0.91 clash: 2.4 rota: 2.09 rama: f: 97.01 o: 0.14 Z: 0.24 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.0034 bond: 0.009 angle: 1.48 clash: 0.4 rota: 1.28 rama: f: 98.72 o: 0.00 Z: -1.21 cb: 0.00 shift=0.2123 cc_mask=0.7564 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0033767359027726445 start: weight= 0.0034 bond: 0.009 angle: 1.48 clash: 0.4 rota: 1.28 rama: f: 98.72 o: 0.00 Z: -1.21 cb: 0.00 shift=0.0000 cc_mask=0.7629 final: weight= 0.0034 bond: 0.009 angle: 1.48 clash: 0.4 rota: 1.28 rama: f: 98.72 o: 0.00 Z: -1.22 cb: 0.00 shift=0.2127 cc_mask=0.7564 start: weight= 0.0034 bond: 0.009 angle: 1.48 clash: 0.4 rota: 1.28 rama: f: 98.72 o: 0.00 Z: -1.22 cb: 0.00 shift=0.2127 cc_mask=0.7564 final: weight= 0.0034 bond: 0.009 angle: 1.46 clash: 0.5 rota: 0.96 rama: f: 99.00 o: 0.00 Z: -1.11 cb: 0.00 shift=0.2737 cc_mask=0.7521 start: weight= 0.0034 bond: 0.009 angle: 1.46 clash: 0.5 rota: 0.96 rama: f: 99.00 o: 0.00 Z: -1.11 cb: 0.00 shift=0.2737 cc_mask=0.7521 final: weight= 0.0034 bond: 0.009 angle: 1.48 clash: 0.3 rota: 0.96 rama: f: 98.86 o: 0.00 Z: -1.14 cb: 0.00 shift=0.3131 cc_mask=0.7487 start: weight= 0.0034 bond: 0.009 angle: 1.48 clash: 0.3 rota: 0.96 rama: f: 98.86 o: 0.00 Z: -1.14 cb: 0.00 shift=0.3131 cc_mask=0.7487 final: weight= 0.0034 bond: 0.009 angle: 1.47 clash: 0.4 rota: 1.12 rama: f: 98.72 o: 0.00 Z: -1.16 cb: 0.00 shift=0.3378 cc_mask=0.7462 start: weight= 0.0034 bond: 0.009 angle: 1.47 clash: 0.4 rota: 1.12 rama: f: 98.72 o: 0.00 Z: -1.16 cb: 0.00 shift=0.3378 cc_mask=0.7462 final: weight= 0.0034 bond: 0.009 angle: 1.48 clash: 0.4 rota: 1.12 rama: f: 98.86 o: 0.00 Z: -1.23 cb: 0.00 shift=0.3605 cc_mask=0.7441 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.032 5768 Z= 0.460 ANGLE : 1.476 9.257 7805 Z= 0.778 CHIRALITY : 0.112 0.346 877 PLANARITY : 0.018 0.239 1004 DIHEDRAL : 13.397 98.179 2177 MIN NONBONDED DISTANCE : 2.564 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.35 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.14 % FAVORED : 98.86 % ROTAMER: OUTLIERS : 1.12 % ALLOWED : 2.89 % FAVORED : 95.99 % 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: -1.23 (0.28), RESIDUES: 703 HELIX: -1.12 (0.20), RESIDUES: 382 SHEET: -1.70 (0.49), RESIDUES: 75 LOOP : 0.47 (0.42), RESIDUES: 246 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.020 0.005 ARG A 67 TYR 0.116 0.019 TYR A 256 PHE 0.045 0.010 PHE A 125 TRP 0.142 0.023 TRP B 342 HIS 0.007 0.002 HIS B 277 Resolution of map is: 3.1942 Map-model correlation coefficient (CC) CC_mask : 0.7441 =============================================================================== Job complete usr+sys time: 1730.35 seconds wall clock time: 19 minutes 2.78 seconds (1142.78 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)