Starting phenix.real_space_refine on Sat Jul 4 05:45:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mls_48379/07_2026/9mls_48379.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mls_48379/07_2026/9mls_48379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mls_48379/07_2026/9mls_48379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mls_48379/07_2026/9mls_48379.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mls_48379/07_2026/9mls_48379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mls_48379/07_2026/9mls_48379.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 214 5.49 5 S 14 5.16 5 C 5689 2.51 5 N 1890 2.21 5 O 2297 1.98 5 H 8421 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18525 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1585 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1517 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "D" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1460 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1495 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "F" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1691 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1436 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 3377 Classifications: {'DNA': 107} Link IDs: {'rna3p': 106} Chain: "J" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 3410 Classifications: {'DNA': 107} Link IDs: {'rna3p': 106} Time building chain proxies: 3.02, per 1000 atoms: 0.16 Number of scatterers: 18525 At special positions: 0 Unit cell: (79.98, 118.68, 116.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 214 15.00 O 2297 8.00 N 1890 7.00 C 5689 6.00 H 8421 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.32 Conformation dependent library (CDL) restraints added in 507.8 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1346 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 75.0% alpha, 2.5% beta 107 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.559A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.784A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.565A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.579A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.570A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.611A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.346A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.782A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 4.093A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.693A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.772A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.845A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.611A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.160A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.505A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.667A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.701A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.809A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.658A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.906A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.959A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.425A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 removed outlier: 4.034A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.246A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.108A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.005A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.648A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 373 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 275 hydrogen bonds 550 hydrogen bond angles 0 basepair planarities 107 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8417 1.03 - 1.22: 51 1.22 - 1.42: 4510 1.42 - 1.61: 6130 1.61 - 1.81: 24 Bond restraints: 19132 Sorted by residual: bond pdb=" C3' DC I 18 " pdb=" C2' DC I 18 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.07e+01 bond pdb=" C3' DG J -8 " pdb=" C2' DG J -8 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.00e+01 bond pdb=" C3' DC I 37 " pdb=" C2' DC I 37 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.91e+01 bond pdb=" C3' DT J 33 " pdb=" C2' DT J 33 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.83e+01 bond pdb=" C3' DA I -14 " pdb=" C2' DA I -14 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.77e+01 ... (remaining 19127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 33208 1.98 - 3.96: 1322 3.96 - 5.93: 136 5.93 - 7.91: 2 7.91 - 9.89: 1 Bond angle restraints: 34669 Sorted by residual: angle pdb=" O5' DT J -16 " pdb=" C5' DT J -16 " pdb=" C4' DT J -16 " ideal model delta sigma weight residual 109.40 114.95 -5.55 8.00e-01 1.56e+00 4.82e+01 angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 112.77 -4.77 7.00e-01 2.04e+00 4.65e+01 angle pdb=" O4' DC J -25 " pdb=" C1' DC J -25 " pdb=" N1 DC J -25 " ideal model delta sigma weight residual 108.00 112.75 -4.75 7.00e-01 2.04e+00 4.60e+01 angle pdb=" O4' DT J -16 " pdb=" C1' DT J -16 " pdb=" N1 DT J -16 " ideal model delta sigma weight residual 108.00 112.59 -4.59 7.00e-01 2.04e+00 4.31e+01 angle pdb=" O4' DG I 48 " pdb=" C1' DG I 48 " pdb=" N9 DG I 48 " ideal model delta sigma weight residual 108.00 112.38 -4.38 7.00e-01 2.04e+00 3.92e+01 ... (remaining 34664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5880 17.95 - 35.90: 1009 35.90 - 53.85: 764 53.85 - 71.80: 373 71.80 - 89.75: 21 Dihedral angle restraints: 8047 sinusoidal: 5702 harmonic: 2345 Sorted by residual: dihedral pdb=" CA SER D 84 " pdb=" C SER D 84 " pdb=" N THR D 85 " pdb=" CA THR D 85 " ideal model delta harmonic sigma weight residual -180.00 -155.95 -24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA THR H 85 " pdb=" C THR H 85 " pdb=" N ILE H 86 " pdb=" CA ILE H 86 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASP H 48 " pdb=" C ASP H 48 " pdb=" N THR H 49 " pdb=" CA THR H 49 " ideal model delta harmonic sigma weight residual 180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 8044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 966 0.040 - 0.079: 468 0.079 - 0.119: 183 0.119 - 0.158: 112 0.158 - 0.198: 26 Chirality restraints: 1755 Sorted by residual: chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" C3' DA I 17 " pdb=" C4' DA I 17 " pdb=" O3' DA I 17 " pdb=" C2' DA I 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" C3' DA J 39 " pdb=" C4' DA J 39 " pdb=" O3' DA J 39 " pdb=" C2' DA J 39 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.70e-01 ... (remaining 1752 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 78 " 0.258 9.50e-02 1.11e+02 9.17e-02 3.03e+01 pdb=" NE ARG B 78 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 78 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 78 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 78 " -0.067 2.00e-02 2.50e+03 pdb="HH11 ARG B 78 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 78 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG B 78 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 78 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 83 " 0.329 9.50e-02 1.11e+02 1.13e-01 2.85e+01 pdb=" NE ARG H 83 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG H 83 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG H 83 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG H 83 " -0.044 2.00e-02 2.50e+03 pdb="HH11 ARG H 83 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG H 83 " 0.026 2.00e-02 2.50e+03 pdb="HH21 ARG H 83 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 83 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 83 " 0.280 9.50e-02 1.11e+02 9.64e-02 2.15e+01 pdb=" NE ARG E 83 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG E 83 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 83 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG E 83 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG E 83 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 83 " 0.009 2.00e-02 2.50e+03 pdb="HH21 ARG E 83 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 83 " 0.047 2.00e-02 2.50e+03 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 232 2.06 - 2.70: 24881 2.70 - 3.33: 48595 3.33 - 3.97: 64046 3.97 - 4.60: 101422 Nonbonded interactions: 239176 Sorted by model distance: nonbonded pdb=" OE1 GLU C 41 " pdb=" H GLU C 41 " model vdw 1.426 2.450 nonbonded pdb="HH22 ARG G 32 " pdb=" OE1 GLU H 32 " model vdw 1.530 2.450 nonbonded pdb=" OE1 GLU G 41 " pdb=" H GLU G 41 " model vdw 1.555 2.450 nonbonded pdb=" HG SER D 84 " pdb=" OP1 DG I -34 " model vdw 1.564 2.450 nonbonded pdb=" HZ2 LYS B 44 " pdb=" O LEU G 115 " model vdw 1.565 2.450 ... (remaining 239171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 45 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 13 through 108) } ncs_group { reference = (chain 'D' and resid 31 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.180 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10711 Z= 0.571 Angle : 0.977 9.889 15370 Z= 0.793 Chirality : 0.061 0.198 1755 Planarity : 0.012 0.120 1202 Dihedral : 26.247 89.753 4549 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.17 % Allowed : 12.06 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.28), residues: 708 helix: 0.02 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -0.62 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG G 20 TYR 0.022 0.004 TYR F 98 PHE 0.017 0.002 PHE A 78 HIS 0.007 0.003 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.57 (10711) covalent geometry : angle 0.97676 / 0.79 (15370) hydrogen bonds : bond 0.10281 / 6.98 ( 648) hydrogen bonds : angle 4.17976 / 2.92 ( 1648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9218 (mt) cc_final: 0.8966 (mt) REVERT: E 59 GLU cc_start: 0.7437 (pm20) cc_final: 0.6937 (pm20) outliers start: 1 outliers final: 1 residues processed: 230 average time/residue: 0.2515 time to fit residues: 73.9869 Evaluate side-chains 161 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 93 GLN B 93 GLN C 94 ASN D 64 ASN D 92 GLN E 68 GLN E 108 ASN F 25 ASN G 68 ASN G 89 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.062445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048087 restraints weight = 123544.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049947 restraints weight = 48877.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.051259 restraints weight = 29007.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052045 restraints weight = 21421.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.052526 restraints weight = 18007.186| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10711 Z= 0.222 Angle : 0.723 7.228 15370 Z= 0.464 Chirality : 0.046 0.165 1755 Planarity : 0.006 0.057 1202 Dihedral : 28.725 104.355 3142 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.01 % Allowed : 18.09 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.30), residues: 708 helix: 1.23 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -0.95 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 30 TYR 0.014 0.002 TYR C 39 PHE 0.008 0.001 PHE A 78 HIS 0.006 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.22 (10711) covalent geometry : angle 0.72337 / 0.46 (15370) hydrogen bonds : bond 0.06316 / 4.12 ( 648) hydrogen bonds : angle 3.88002 / 2.76 ( 1648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7733 (mt-10) REVERT: C 92 GLU cc_start: 0.8569 (pm20) cc_final: 0.8183 (pm20) REVERT: D 73 GLU cc_start: 0.8753 (tp30) cc_final: 0.8345 (tp30) REVERT: D 110 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8422 (tm-30) REVERT: F 85 ASP cc_start: 0.8890 (m-30) cc_final: 0.8663 (m-30) REVERT: H 99 LEU cc_start: 0.9107 (mt) cc_final: 0.8866 (mp) outliers start: 12 outliers final: 9 residues processed: 166 average time/residue: 0.2486 time to fit residues: 53.9767 Evaluate side-chains 158 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 106 HIS H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.062006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047502 restraints weight = 123338.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.049300 restraints weight = 49412.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.050524 restraints weight = 29418.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.051306 restraints weight = 21891.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.051757 restraints weight = 18464.591| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10711 Z= 0.174 Angle : 0.640 6.643 15370 Z= 0.427 Chirality : 0.042 0.149 1755 Planarity : 0.005 0.040 1202 Dihedral : 28.961 103.831 3138 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.68 % Allowed : 19.10 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.30), residues: 708 helix: 1.67 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 39 TYR 0.010 0.001 TYR F 98 PHE 0.007 0.001 PHE A 84 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (10711) covalent geometry : angle 0.64009 / 0.43 (15370) hydrogen bonds : bond 0.05625 / 3.68 ( 648) hydrogen bonds : angle 3.64135 / 2.60 ( 1648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7779 (mt-10) REVERT: D 54 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8619 (mmmm) REVERT: D 73 GLU cc_start: 0.8682 (tp30) cc_final: 0.8328 (tp30) REVERT: D 110 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8355 (tm-30) REVERT: E 81 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8539 (p0) outliers start: 16 outliers final: 12 residues processed: 168 average time/residue: 0.2360 time to fit residues: 52.7513 Evaluate side-chains 165 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.062182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047934 restraints weight = 123617.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049825 restraints weight = 49125.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051126 restraints weight = 28879.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051956 restraints weight = 21113.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052420 restraints weight = 17620.083| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10711 Z= 0.166 Angle : 0.627 7.506 15370 Z= 0.411 Chirality : 0.041 0.153 1755 Planarity : 0.004 0.040 1202 Dihedral : 29.058 105.125 3138 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.68 % Allowed : 19.93 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.30), residues: 708 helix: 2.00 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.29 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.015 0.002 TYR H 80 PHE 0.008 0.001 PHE D 67 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.17 (10711) covalent geometry : angle 0.62697 / 0.41 (15370) hydrogen bonds : bond 0.05149 / 3.37 ( 648) hydrogen bonds : angle 3.48822 / 2.49 ( 1648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 VAL cc_start: 0.9223 (t) cc_final: 0.8894 (p) REVERT: B 63 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 84 MET cc_start: 0.7887 (mpp) cc_final: 0.7673 (mmt) REVERT: D 54 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8584 (mmmm) REVERT: D 65 ASP cc_start: 0.9305 (t0) cc_final: 0.8937 (t0) REVERT: D 73 GLU cc_start: 0.8703 (tp30) cc_final: 0.8402 (tp30) REVERT: D 110 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8347 (tm-30) REVERT: H 90 GLU cc_start: 0.8631 (mp0) cc_final: 0.8144 (mp0) outliers start: 16 outliers final: 12 residues processed: 177 average time/residue: 0.2206 time to fit residues: 52.2569 Evaluate side-chains 170 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 10.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.060197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045816 restraints weight = 126220.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.047581 restraints weight = 50790.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048788 restraints weight = 30363.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049556 restraints weight = 22644.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050005 restraints weight = 19176.710| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10711 Z= 0.227 Angle : 0.646 6.668 15370 Z= 0.422 Chirality : 0.041 0.156 1755 Planarity : 0.005 0.040 1202 Dihedral : 29.159 103.290 3138 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.35 % Allowed : 21.61 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.30), residues: 708 helix: 1.87 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.44 (0.39), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.025 0.002 TYR H 80 PHE 0.008 0.001 PHE A 84 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.23 (10711) covalent geometry : angle 0.64617 / 0.42 (15370) hydrogen bonds : bond 0.05966 / 3.93 ( 648) hydrogen bonds : angle 3.81152 / 2.73 ( 1648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 VAL cc_start: 0.9410 (t) cc_final: 0.9131 (p) REVERT: B 63 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 84 MET cc_start: 0.7988 (mpp) cc_final: 0.7692 (mmt) REVERT: D 40 LYS cc_start: 0.9239 (mttp) cc_final: 0.8986 (mttm) REVERT: D 54 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8615 (mmmm) REVERT: D 73 GLU cc_start: 0.8756 (tp30) cc_final: 0.8457 (tp30) REVERT: D 110 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8423 (tm-30) REVERT: F 44 LYS cc_start: 0.8509 (tppt) cc_final: 0.8290 (tppt) REVERT: H 90 GLU cc_start: 0.8787 (mp0) cc_final: 0.8140 (mp0) outliers start: 14 outliers final: 13 residues processed: 158 average time/residue: 0.2453 time to fit residues: 51.2147 Evaluate side-chains 157 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 35 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.060517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.046129 restraints weight = 122531.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047933 restraints weight = 48849.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049170 restraints weight = 28906.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049951 restraints weight = 21359.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050417 restraints weight = 17993.836| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10711 Z= 0.170 Angle : 0.612 7.265 15370 Z= 0.403 Chirality : 0.041 0.190 1755 Planarity : 0.004 0.038 1202 Dihedral : 29.257 104.029 3138 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.18 % Allowed : 22.61 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.31), residues: 708 helix: 2.20 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 20 TYR 0.013 0.001 TYR D 80 PHE 0.008 0.001 PHE D 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.17 (10711) covalent geometry : angle 0.61205 / 0.40 (15370) hydrogen bonds : bond 0.05324 / 3.50 ( 648) hydrogen bonds : angle 3.55577 / 2.54 ( 1648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8310 (tp30) cc_final: 0.8043 (tp30) REVERT: B 43 VAL cc_start: 0.9407 (t) cc_final: 0.9147 (p) REVERT: B 63 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 84 MET cc_start: 0.7932 (mpp) cc_final: 0.7602 (mmt) REVERT: D 65 ASP cc_start: 0.9305 (t0) cc_final: 0.8980 (t0) REVERT: D 73 GLU cc_start: 0.8762 (tp30) cc_final: 0.8489 (tp30) REVERT: D 96 ARG cc_start: 0.8813 (mtm110) cc_final: 0.8608 (ttm110) REVERT: D 110 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8459 (tm-30) REVERT: F 44 LYS cc_start: 0.8543 (tppt) cc_final: 0.8299 (tppt) REVERT: H 90 GLU cc_start: 0.8893 (mp0) cc_final: 0.8298 (mp0) outliers start: 13 outliers final: 10 residues processed: 162 average time/residue: 0.2619 time to fit residues: 55.8459 Evaluate side-chains 155 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 0.0170 chunk 6 optimal weight: 2.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.060726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046325 restraints weight = 125315.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048133 restraints weight = 49970.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049355 restraints weight = 29569.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.050119 restraints weight = 21995.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050475 restraints weight = 18618.815| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10711 Z= 0.152 Angle : 0.607 7.333 15370 Z= 0.398 Chirality : 0.040 0.147 1755 Planarity : 0.004 0.039 1202 Dihedral : 29.278 104.664 3138 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.18 % Allowed : 22.28 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.31), residues: 708 helix: 2.41 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 20 TYR 0.017 0.001 TYR C 39 PHE 0.009 0.001 PHE A 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (10711) covalent geometry : angle 0.60739 / 0.40 (15370) hydrogen bonds : bond 0.04903 / 3.25 ( 648) hydrogen bonds : angle 3.32611 / 2.37 ( 1648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8308 (tp30) cc_final: 0.8028 (tp30) REVERT: A 68 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8629 (tm130) REVERT: B 43 VAL cc_start: 0.9372 (t) cc_final: 0.9168 (p) REVERT: B 63 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7797 (mt-10) REVERT: B 84 MET cc_start: 0.7896 (mpp) cc_final: 0.7594 (mmt) REVERT: C 90 ASP cc_start: 0.8801 (t70) cc_final: 0.8321 (t0) REVERT: D 73 GLU cc_start: 0.8757 (tp30) cc_final: 0.8534 (tp30) REVERT: E 59 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7682 (pm20) REVERT: E 110 CYS cc_start: 0.9161 (m) cc_final: 0.8956 (m) REVERT: F 44 LYS cc_start: 0.8555 (tppt) cc_final: 0.8323 (tppt) REVERT: H 51 ILE cc_start: 0.9270 (tp) cc_final: 0.9047 (tp) REVERT: H 75 SER cc_start: 0.9502 (t) cc_final: 0.9218 (p) REVERT: H 90 GLU cc_start: 0.8915 (mp0) cc_final: 0.8309 (mp0) outliers start: 13 outliers final: 10 residues processed: 167 average time/residue: 0.2554 time to fit residues: 56.5478 Evaluate side-chains 161 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.059877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.045437 restraints weight = 126056.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047201 restraints weight = 50510.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048400 restraints weight = 30111.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049162 restraints weight = 22397.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049618 restraints weight = 18919.055| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10711 Z= 0.184 Angle : 0.613 7.235 15370 Z= 0.400 Chirality : 0.039 0.152 1755 Planarity : 0.004 0.038 1202 Dihedral : 29.322 104.417 3138 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.51 % Allowed : 22.78 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.31), residues: 708 helix: 2.36 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.56 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 83 TYR 0.014 0.001 TYR G 39 PHE 0.009 0.001 PHE D 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.18 (10711) covalent geometry : angle 0.61310 / 0.40 (15370) hydrogen bonds : bond 0.05328 / 3.52 ( 648) hydrogen bonds : angle 3.49766 / 2.50 ( 1648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8296 (tp30) cc_final: 0.8011 (tp30) REVERT: A 68 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.8652 (tm130) REVERT: A 79 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8545 (ttpp) REVERT: B 63 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 84 MET cc_start: 0.7950 (mpp) cc_final: 0.7632 (mmt) REVERT: C 92 GLU cc_start: 0.8896 (mp0) cc_final: 0.8581 (mp0) REVERT: D 73 GLU cc_start: 0.8819 (tp30) cc_final: 0.8567 (tp30) REVERT: E 59 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: F 44 LYS cc_start: 0.8612 (tppt) cc_final: 0.8369 (tppt) REVERT: H 75 SER cc_start: 0.9511 (t) cc_final: 0.9253 (p) REVERT: H 90 GLU cc_start: 0.8979 (mp0) cc_final: 0.8402 (mp0) outliers start: 15 outliers final: 10 residues processed: 158 average time/residue: 0.2566 time to fit residues: 53.9533 Evaluate side-chains 156 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.060459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.045840 restraints weight = 124833.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.047659 restraints weight = 49944.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048902 restraints weight = 29675.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049683 restraints weight = 22024.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.050095 restraints weight = 18609.814| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10711 Z= 0.153 Angle : 0.601 7.526 15370 Z= 0.392 Chirality : 0.039 0.142 1755 Planarity : 0.004 0.040 1202 Dihedral : 29.344 104.995 3138 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.35 % Allowed : 23.45 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.31), residues: 708 helix: 2.54 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.55 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.013 0.001 TYR H 80 PHE 0.008 0.001 PHE A 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (10711) covalent geometry : angle 0.60147 / 0.39 (15370) hydrogen bonds : bond 0.04917 / 3.25 ( 648) hydrogen bonds : angle 3.29545 / 2.36 ( 1648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8281 (tp30) cc_final: 0.7997 (tp30) REVERT: A 68 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8651 (tm130) REVERT: B 63 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7821 (mt-10) REVERT: B 84 MET cc_start: 0.7952 (mpp) cc_final: 0.7667 (mmt) REVERT: C 92 GLU cc_start: 0.8907 (mp0) cc_final: 0.8573 (mp0) REVERT: D 73 GLU cc_start: 0.8786 (tp30) cc_final: 0.8579 (tp30) REVERT: D 96 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8568 (ttm110) REVERT: E 59 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: F 44 LYS cc_start: 0.8602 (tppt) cc_final: 0.8380 (tptt) REVERT: H 75 SER cc_start: 0.9487 (t) cc_final: 0.9225 (p) REVERT: H 90 GLU cc_start: 0.8975 (mp0) cc_final: 0.8393 (mp0) outliers start: 14 outliers final: 12 residues processed: 162 average time/residue: 0.2355 time to fit residues: 50.6746 Evaluate side-chains 159 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.059441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.045244 restraints weight = 125360.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047009 restraints weight = 50433.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048218 restraints weight = 29926.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048970 restraints weight = 22098.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.049407 restraints weight = 18631.815| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10711 Z= 0.208 Angle : 0.631 7.243 15370 Z= 0.404 Chirality : 0.039 0.156 1755 Planarity : 0.004 0.038 1202 Dihedral : 29.366 103.972 3138 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.18 % Allowed : 23.62 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.31), residues: 708 helix: 2.30 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 76 TYR 0.015 0.002 TYR H 80 PHE 0.012 0.001 PHE A 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.21 (10711) covalent geometry : angle 0.63064 / 0.40 (15370) hydrogen bonds : bond 0.05491 / 3.62 ( 648) hydrogen bonds : angle 3.61737 / 2.60 ( 1648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8324 (tp30) cc_final: 0.8040 (tp30) REVERT: A 68 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.8674 (tm130) REVERT: B 63 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7866 (mt-10) REVERT: B 84 MET cc_start: 0.7986 (mpp) cc_final: 0.7685 (mmt) REVERT: C 92 GLU cc_start: 0.8915 (mp0) cc_final: 0.8559 (mp0) REVERT: D 73 GLU cc_start: 0.8813 (tp30) cc_final: 0.8562 (tp30) REVERT: D 96 ARG cc_start: 0.8817 (mtm110) cc_final: 0.8545 (ttm110) REVERT: E 59 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: F 44 LYS cc_start: 0.8666 (tppt) cc_final: 0.8437 (tptt) REVERT: H 75 SER cc_start: 0.9497 (t) cc_final: 0.9243 (p) REVERT: H 90 GLU cc_start: 0.9016 (mp0) cc_final: 0.8317 (mp0) outliers start: 13 outliers final: 11 residues processed: 155 average time/residue: 0.2361 time to fit residues: 48.5223 Evaluate side-chains 154 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.060106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045596 restraints weight = 125205.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.047382 restraints weight = 50301.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.048599 restraints weight = 29970.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049373 restraints weight = 22237.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049811 restraints weight = 18772.748| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10711 Z= 0.152 Angle : 0.599 7.215 15370 Z= 0.389 Chirality : 0.039 0.139 1755 Planarity : 0.004 0.040 1202 Dihedral : 29.416 104.811 3138 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.84 % Allowed : 24.46 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.31), residues: 708 helix: 2.50 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.56 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 71 TYR 0.011 0.001 TYR D 118 PHE 0.010 0.001 PHE A 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (10711) covalent geometry : angle 0.59936 / 0.39 (15370) hydrogen bonds : bond 0.04985 / 3.28 ( 648) hydrogen bonds : angle 3.32859 / 2.38 ( 1648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2947.41 seconds wall clock time: 50 minutes 54.48 seconds (3054.48 seconds total)