Starting qr.refine on Sun May 19 15:46:23 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8cl2_16710.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8cl2_16710.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 { real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8cl2_16710.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8cl2_16710.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8cl2_16710.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8cl2_16710.pdb" } 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 None 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: 5440 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1053 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "C" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1029 Classifications: {'peptide': 65} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3358 Inner-chain residues flagged as termini: ['pdbres="HIS A 87 "', 'pdbres="MET A 96 "'] Classifications: {'peptide': 213} Modifications used: {'COO': 2, 'NH2': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Time building chain proxies: 0.67, per 1000 atoms: 0.12 Number of scatterers: 5440 At special positions: 0 Unit cell: (87.42, 74.4, 97.65, 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 23 16.00 O 519 8.00 N 469 7.00 C 1710 6.00 H 2719 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: 0.98 Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Time building geometry restraints manager: 1.13 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: 2713 1.15 - 1.31: 478 1.31 - 1.48: 1048 1.48 - 1.65: 1215 1.65 - 1.81: 40 Bond restraints: 5494 Sorted by residual: bond pdb=" N PRO A 125 " pdb=" CA PRO A 125 " ideal model delta sigma weight residual 1.466 1.481 -0.015 1.50e-02 4.44e+03 1.03e+00 bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.72e-01 bond pdb=" C LEU C 189 " pdb=" N LEU C 190 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.41e-01 bond pdb=" C ASN A 5 " pdb=" N LEU A 6 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.21e-01 bond pdb=" C ASN A 121 " pdb=" O ASN A 121 " ideal model delta sigma weight residual 1.231 1.247 -0.016 2.00e-02 2.50e+03 6.16e-01 ... (remaining 5489 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.27: 116 106.27 - 113.19: 6567 113.19 - 120.12: 1655 120.12 - 127.04: 1592 127.04 - 133.96: 42 Bond angle restraints: 9972 Sorted by residual: angle pdb=" C ARG A 97 " pdb=" N GLU A 98 " pdb=" CA GLU A 98 " ideal model delta sigma weight residual 121.70 117.97 3.73 1.80e+00 3.09e-01 4.30e+00 angle pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N PRO A 122 " ideal model delta sigma weight residual 116.90 119.73 -2.83 1.50e+00 4.44e-01 3.56e+00 angle pdb=" CA ILE A 37 " pdb=" C ILE A 37 " pdb=" N PRO A 38 " ideal model delta sigma weight residual 116.90 119.70 -2.80 1.50e+00 4.44e-01 3.50e+00 angle pdb=" N ILE A 124 " pdb=" CA ILE A 124 " pdb=" C ILE A 124 " ideal model delta sigma weight residual 111.00 106.25 4.75 2.80e+00 1.28e-01 2.88e+00 angle pdb=" C LEU A 189 " pdb=" N LEU A 190 " pdb=" CA LEU A 190 " ideal model delta sigma weight residual 121.70 118.66 3.04 1.80e+00 3.09e-01 2.85e+00 ... (remaining 9967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 2384 15.67 - 31.33: 130 31.33 - 47.00: 46 47.00 - 62.67: 22 62.67 - 78.34: 1 Dihedral angle restraints: 2583 sinusoidal: 1455 harmonic: 1128 Sorted by residual: dihedral pdb=" CA GLU C 175 " pdb=" C GLU C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta harmonic sigma weight residual -180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS A 62 " pdb=" C HIS A 62 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA GLY A 61 " pdb=" C GLY A 61 " pdb=" N HIS A 62 " pdb=" CA HIS A 62 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 296 0.031 - 0.062: 81 0.062 - 0.093: 31 0.093 - 0.124: 10 0.124 - 0.155: 2 Chirality restraints: 420 Sorted by residual: chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 153 " pdb=" N ILE A 153 " pdb=" C ILE A 153 " pdb=" CB ILE A 153 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 417 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 186 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C THR C 186 " -0.031 2.00e-02 2.50e+03 pdb=" O THR C 186 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU C 187 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 186 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C THR A 186 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 186 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 187 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 195 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO B 196 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " 0.015 5.00e-02 4.00e+02 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 302 2.06 - 2.70: 7838 2.70 - 3.33: 16576 3.33 - 3.97: 19832 3.97 - 4.60: 29850 Nonbonded interactions: 74398 Sorted by model distance: nonbonded pdb=" O ASN B 195 " pdb=" H LYS B 199 " model vdw 1.431 1.800 nonbonded pdb=" O ASN A 195 " pdb=" H LYS A 199 " model vdw 1.527 1.800 nonbonded pdb=" O ASN C 195 " pdb=" H LYS C 199 " model vdw 1.540 1.800 nonbonded pdb=" HG SER B 178 " pdb=" OE2 GLU A 180 " model vdw 1.593 1.800 nonbonded pdb=" O ILE A 153 " pdb="HD22 ASN A 193 " model vdw 1.606 1.800 ... (remaining 74393 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 23 15.96 2 O 519 7.97 2 N 469 6.97 2 C 1710 5.97 2 H 2719 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 0.044 2775 Z= 0.198 ANGLE : 0.924 5.224 3762 Z= 0.450 CHIRALITY : 0.037 0.155 420 PLANARITY : 0.004 0.027 491 DIHEDRAL : 10.485 78.336 1060 MIN NONBONDED DISTANCE : 2.385 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.10 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.08 % FAVORED : 97.92 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.00 % FAVORED : 100.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 4.76 % 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: -0.63 (0.41), RESIDUES: 337 HELIX: -0.52 (0.30), RESIDUES: 229 SHEET: -1.96 (0.86), RESIDUES: 9 LOOP : 0.53 (0.59), RESIDUES: 99 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.001 ARG A 100 TYR 0.008 0.001 TYR B 169 PHE 0.002 0.001 PHE B 161 TRP 0.006 0.001 TRP A 184 HIS 0.002 0.001 HIS A 87 Resolution of map is: 3.5842 Map-model correlation coefficient (CC) CC_mask : 0.7717 weight= None bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 Initial weight estimate from ratio of grad norms: 0.3535639170116757 cycle: 0 start: weight= 0.3536 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.3536 bond: 0.026 angle: 2.45 clash: 11.6 rota: 1.35 rama: f: 96.74 o: 0.00 Z: -4.46 cb: 1.23 shift=0.3622 cc_mask=0.8087 cycle: 1 start: weight= 0.2475 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.2475 bond: 0.021 angle: 2.10 clash: 5.9 rota: 0.67 rama: f: 98.52 o: 0.00 Z: -3.56 cb: 0.92 shift=0.3069 cc_mask=0.8029 cycle: 2 start: weight= 0.1732 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.1732 bond: 0.017 angle: 1.86 clash: 2.0 rota: 0.00 rama: f: 99.41 o: 0.00 Z: -2.86 cb: 0.62 shift=0.2593 cc_mask=0.7973 cycle: 3 start: weight= 0.0866 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.0866 bond: 0.012 angle: 1.61 clash: 0.0 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -1.85 cb: 0.31 shift=0.2021 cc_mask=0.7881 cycle: 4 start: weight= 0.0606 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.0606 bond: 0.011 angle: 1.54 clash: 0.0 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -1.53 cb: 0.31 shift=0.1850 cc_mask=0.7844 cycle: 5 start: weight= 0.0424 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.0424 bond: 0.010 angle: 1.50 clash: 0.0 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -1.18 cb: 0.31 shift=0.1731 cc_mask=0.7811 cycle: 6 start: weight= 0.0212 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.0212 bond: 0.010 angle: 1.47 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -0.94 cb: 0.31 shift=0.1662 cc_mask=0.7765 cycle: 7 start: weight= 0.0149 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.0149 bond: 0.009 angle: 1.47 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -0.92 cb: 0.31 shift=0.1667 cc_mask=0.7746 cycle: 8 start: weight= 0.0104 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.0104 bond: 0.009 angle: 1.46 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -0.92 cb: 0.31 shift=0.1669 cc_mask=0.7734 cycle: 9 start: weight= 0.0052 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.0052 bond: 0.009 angle: 1.46 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -0.96 cb: 0.31 shift=0.1701 cc_mask=0.7717 cycle: 10 start: weight= 0.0036 bond: 0.004 angle: 0.92 clash: 1.1 rota: 0.00 rama: f: 97.92 o: 0.00 Z: -0.63 cb: 0.00 shift=0.0000 cc_mask=0.7717 final: weight= 0.0036 bond: 0.009 angle: 1.46 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -0.96 cb: 0.31 shift=0.1698 cc_mask=0.7713 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0036396886113443314 start: weight= 0.0036 bond: 0.009 angle: 1.46 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -0.96 cb: 0.31 shift=0.0000 cc_mask=0.7717 final: weight= 0.0036 bond: 0.009 angle: 1.46 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -0.96 cb: 0.31 shift=0.1700 cc_mask=0.7712 start: weight= 0.0036 bond: 0.009 angle: 1.46 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -0.96 cb: 0.31 shift=0.1700 cc_mask=0.7712 final: weight= 0.0036 bond: 0.009 angle: 1.44 clash: 0.2 rota: 0.34 rama: f: 99.70 o: 0.00 Z: -1.24 cb: 0.31 shift=0.2179 cc_mask=0.7684 start: weight= 0.0036 bond: 0.009 angle: 1.44 clash: 0.2 rota: 0.34 rama: f: 99.70 o: 0.00 Z: -1.24 cb: 0.31 shift=0.2179 cc_mask=0.7684 final: weight= 0.0036 bond: 0.009 angle: 1.45 clash: 0.2 rota: 0.34 rama: f: 99.70 o: 0.00 Z: -1.42 cb: 0.31 shift=0.2610 cc_mask=0.7660 start: weight= 0.0036 bond: 0.009 angle: 1.45 clash: 0.2 rota: 0.34 rama: f: 99.70 o: 0.00 Z: -1.42 cb: 0.31 shift=0.2610 cc_mask=0.7660 final: weight= 0.0036 bond: 0.009 angle: 1.44 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -1.63 cb: 0.31 shift=0.2955 cc_mask=0.7641 start: weight= 0.0036 bond: 0.009 angle: 1.44 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -1.63 cb: 0.31 shift=0.2955 cc_mask=0.7641 final: weight= 0.0036 bond: 0.009 angle: 1.45 clash: 0.2 rota: 0.00 rama: f: 99.70 o: 0.00 Z: -1.67 cb: 0.31 shift=0.3098 cc_mask=0.7634 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.051 2775 Z= 0.468 ANGLE : 1.449 9.446 3762 Z= 0.741 CHIRALITY : 0.114 0.359 420 PLANARITY : 0.019 0.192 491 DIHEDRAL : 12.135 97.010 1060 MIN NONBONDED DISTANCE : 2.598 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.18 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 0.30 % FAVORED : 99.70 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 1.35 % FAVORED : 98.65 % CBETA DEVIATIONS : 0.31 % PEPTIDE PLANE: CIS-PROLINE : 4.76 % 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: -1.67 (0.38), RESIDUES: 337 HELIX: -1.27 (0.27), RESIDUES: 229 SHEET: -3.83 (0.87), RESIDUES: 9 LOOP : 0.17 (0.55), RESIDUES: 99 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.016 0.005 ARG A 162 TYR 0.125 0.016 TYR C 164 PHE 0.023 0.008 PHE A 161 TRP 0.096 0.018 TRP B 184 HIS 0.003 0.001 HIS A 12 Resolution of map is: 3.5842 Map-model correlation coefficient (CC) CC_mask : 0.7634 =============================================================================== Job complete usr+sys time: 536.02 seconds wall clock time: 9 minutes 45.86 seconds (585.86 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)