Starting phenix.real_space_refine on Fri Aug 7 02:07:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mls_48379/08_2026/9mls_48379.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mls_48379/08_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_48379/08_2026/9mls_48379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mls_48379/08_2026/9mls_48379.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mls_48379/08_2026/9mls_48379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mls_48379/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 3.56, per 1000 atoms: 0.19 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: 1.49 Conformation dependent library (CDL) restraints added in 577.1 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: 3.46 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: 4.24 Time building geometry restraints manager: 2.18 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: 33179 1.98 - 3.96: 1351 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: 3.630 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.300 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- 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= 0.572 Angle : 0.985 9.889 15370 Z= 0.801 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 0.98524 / 0.80 (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 : 0.422 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: A 74 ILE cc_start: 0.9218 (mt) cc_final: 0.8961 (mt) REVERT: E 59 GLU cc_start: 0.7437 (pm20) cc_final: 0.6939 (pm20) outliers start: 1 outliers final: 1 residues processed: 230 average time/residue: 0.3071 time to fit residues: 90.6583 Evaluate side-chains 160 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 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: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.061789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047011 restraints weight = 122392.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048816 restraints weight = 48905.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050069 restraints weight = 29214.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050840 restraints weight = 21730.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051307 restraints weight = 18280.693| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10711 Z= 0.233 Angle : 0.739 7.571 15370 Z= 0.471 Chirality : 0.046 0.152 1755 Planarity : 0.006 0.049 1202 Dihedral : 28.767 103.371 3142 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.18 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: 0.90 (0.30), residues: 708 helix: 1.19 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.02 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 63 TYR 0.014 0.002 TYR C 39 PHE 0.007 0.001 PHE D 62 HIS 0.006 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.23 (10711) covalent geometry : angle 0.73913 / 0.47 (15370) hydrogen bonds : bond 0.06370 / 4.15 ( 648) hydrogen bonds : angle 3.98015 / 2.84 ( 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 170 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.432 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: B 63 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 92 GLU cc_start: 0.8579 (pm20) cc_final: 0.8183 (pm20) REVERT: D 73 GLU cc_start: 0.8794 (tp30) cc_final: 0.8336 (tp30) REVERT: D 110 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8452 (tm-30) REVERT: F 85 ASP cc_start: 0.8915 (m-30) cc_final: 0.8684 (m-30) REVERT: H 99 LEU cc_start: 0.9129 (mt) cc_final: 0.8896 (mp) outliers start: 12 outliers final: 9 residues processed: 165 average time/residue: 0.2822 time to fit residues: 61.1808 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 : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain D residue 70 ILE 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: 4.9990 chunk 59 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.061600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.046928 restraints weight = 123476.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048719 restraints weight = 49621.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049926 restraints weight = 29561.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050701 restraints weight = 21921.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.051171 restraints weight = 18494.694| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10711 Z= 0.182 Angle : 0.646 6.685 15370 Z= 0.430 Chirality : 0.042 0.139 1755 Planarity : 0.005 0.040 1202 Dihedral : 28.961 102.551 3138 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.18 % Allowed : 19.60 % 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: 1.33 (0.30), residues: 708 helix: 1.62 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.25 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 39 TYR 0.008 0.001 TYR F 98 PHE 0.007 0.001 PHE H 62 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.18 (10711) covalent geometry : angle 0.64630 / 0.43 (15370) hydrogen bonds : bond 0.05739 / 3.75 ( 648) hydrogen bonds : angle 3.69834 / 2.64 ( 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 172 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.488 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: B 63 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7793 (mt-10) REVERT: D 54 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8598 (mmmm) REVERT: D 73 GLU cc_start: 0.8698 (tp30) cc_final: 0.8356 (tp30) REVERT: D 110 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8387 (tm-30) REVERT: E 81 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8551 (p0) REVERT: H 31 LYS cc_start: 0.8159 (mptt) cc_final: 0.7804 (mmmm) REVERT: H 99 LEU cc_start: 0.9092 (mt) cc_final: 0.8872 (mp) outliers start: 13 outliers final: 10 residues processed: 167 average time/residue: 0.2627 time to fit residues: 58.5593 Evaluate side-chains 165 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 4.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.061434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047287 restraints weight = 125191.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049114 restraints weight = 49324.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.050362 restraints weight = 29002.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.051170 restraints weight = 21209.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.051628 restraints weight = 17686.172| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3225 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= 0.175 Angle : 0.633 7.278 15370 Z= 0.416 Chirality : 0.041 0.154 1755 Planarity : 0.005 0.048 1202 Dihedral : 29.064 103.322 3138 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.85 % Allowed : 19.60 % Favored : 77.55 % 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: 1.64 (0.30), residues: 708 helix: 1.92 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 77 TYR 0.016 0.001 TYR D 80 PHE 0.008 0.001 PHE D 67 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.18 (10711) covalent geometry : angle 0.63349 / 0.42 (15370) hydrogen bonds : bond 0.05360 / 3.51 ( 648) hydrogen bonds : angle 3.59489 / 2.57 ( 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 178 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.435 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: 0.9275 (t) cc_final: 0.8956 (p) REVERT: B 63 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 84 MET cc_start: 0.7920 (mpp) cc_final: 0.7662 (mmt) REVERT: D 54 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8588 (mmmm) REVERT: D 73 GLU cc_start: 0.8692 (tp30) cc_final: 0.8366 (tp30) REVERT: D 110 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8370 (tm-30) REVERT: F 44 LYS cc_start: 0.8429 (tppt) cc_final: 0.8215 (tppt) REVERT: H 31 LYS cc_start: 0.8069 (mptt) cc_final: 0.7765 (mmmm) REVERT: H 90 GLU cc_start: 0.8638 (mp0) cc_final: 0.8169 (mp0) outliers start: 17 outliers final: 12 residues processed: 173 average time/residue: 0.2515 time to fit residues: 58.1483 Evaluate side-chains 163 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain G residue 101 THR 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: 10.0000 chunk 83 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.059658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.045188 restraints weight = 126424.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.046933 restraints weight = 50810.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048107 restraints weight = 30342.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048875 restraints weight = 22630.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049339 restraints weight = 19133.870| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10711 Z= 0.228 Angle : 0.656 7.201 15370 Z= 0.425 Chirality : 0.041 0.152 1755 Planarity : 0.005 0.040 1202 Dihedral : 29.183 101.779 3138 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.68 % Allowed : 20.44 % Favored : 76.88 % 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: 1.51 (0.30), residues: 708 helix: 1.84 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.53 (0.39), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.009 0.002 TYR D 80 PHE 0.006 0.001 PHE H 62 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.23 (10711) covalent geometry : angle 0.65597 / 0.43 (15370) hydrogen bonds : bond 0.06135 / 4.04 ( 648) hydrogen bonds : angle 3.86551 / 2.78 ( 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 162 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.406 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: 0.9429 (t) cc_final: 0.9167 (p) REVERT: B 63 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 84 MET cc_start: 0.7996 (mpp) cc_final: 0.7716 (mmt) REVERT: D 40 LYS cc_start: 0.9235 (mttp) cc_final: 0.8994 (mttm) REVERT: D 54 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8591 (mmmm) REVERT: D 73 GLU cc_start: 0.8756 (tp30) cc_final: 0.8435 (tp30) REVERT: D 110 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8480 (tm-30) REVERT: F 44 LYS cc_start: 0.8558 (tppt) cc_final: 0.8332 (tppt) REVERT: H 31 LYS cc_start: 0.8201 (mptt) cc_final: 0.7856 (mmmm) REVERT: H 90 GLU cc_start: 0.8814 (mp0) cc_final: 0.8147 (mp0) outliers start: 16 outliers final: 13 residues processed: 157 average time/residue: 0.2272 time to fit residues: 47.2644 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 30 THR 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 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: 1.9990 chunk 4 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.060481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.045970 restraints weight = 122574.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047778 restraints weight = 48702.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.048998 restraints weight = 28703.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049780 restraints weight = 21224.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.050239 restraints weight = 17832.336| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10711 Z= 0.154 Angle : 0.612 6.944 15370 Z= 0.402 Chirality : 0.041 0.186 1755 Planarity : 0.004 0.038 1202 Dihedral : 29.249 102.970 3138 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.01 % Allowed : 22.45 % 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: 2.01 (0.31), residues: 708 helix: 2.27 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.52 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 20 TYR 0.007 0.001 TYR E 99 PHE 0.010 0.001 PHE D 67 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (10711) covalent geometry : angle 0.61231 / 0.40 (15370) hydrogen bonds : bond 0.05254 / 3.46 ( 648) hydrogen bonds : angle 3.44773 / 2.47 ( 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 167 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.414 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: A 59 GLU cc_start: 0.8276 (tp30) cc_final: 0.8006 (tp30) REVERT: A 68 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8609 (tm130) REVERT: B 63 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 84 MET cc_start: 0.7928 (mpp) cc_final: 0.7659 (mmt) REVERT: C 90 ASP cc_start: 0.8831 (t70) cc_final: 0.8396 (t0) REVERT: D 48 ASP cc_start: 0.9048 (m-30) cc_final: 0.8578 (p0) REVERT: D 54 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8546 (mmmm) REVERT: D 65 ASP cc_start: 0.9303 (t0) cc_final: 0.9088 (t70) REVERT: D 73 GLU cc_start: 0.8720 (tp30) cc_final: 0.8407 (tp30) REVERT: D 96 ARG cc_start: 0.8803 (mtm110) cc_final: 0.8600 (ttm110) REVERT: E 59 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: F 44 LYS cc_start: 0.8549 (tppt) cc_final: 0.8303 (tppt) REVERT: H 31 LYS cc_start: 0.8179 (mptt) cc_final: 0.7846 (mmmm) REVERT: H 90 GLU cc_start: 0.8870 (mp0) cc_final: 0.8312 (mp0) outliers start: 12 outliers final: 9 residues processed: 166 average time/residue: 0.2444 time to fit residues: 53.7923 Evaluate side-chains 161 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN 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 85 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 79 ILE 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: 0.6980 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.060363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.045956 restraints weight = 123748.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047737 restraints weight = 49207.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048963 restraints weight = 29018.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.049743 restraints weight = 21397.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.050140 restraints weight = 17983.272| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10711 Z= 0.164 Angle : 0.612 6.818 15370 Z= 0.399 Chirality : 0.040 0.153 1755 Planarity : 0.004 0.038 1202 Dihedral : 29.266 103.068 3138 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.18 % Allowed : 22.45 % Favored : 75.38 % 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: 2.15 (0.31), residues: 708 helix: 2.38 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.50 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 20 TYR 0.016 0.001 TYR C 39 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 0.00272 / 0.16 (10711) covalent geometry : angle 0.61230 / 0.40 (15370) hydrogen bonds : bond 0.05130 / 3.39 ( 648) hydrogen bonds : angle 3.41775 / 2.45 ( 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 163 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.408 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: A 59 GLU cc_start: 0.8308 (tp30) cc_final: 0.8022 (tp30) REVERT: A 68 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8648 (tm130) REVERT: B 43 VAL cc_start: 0.9445 (t) cc_final: 0.9230 (p) REVERT: B 63 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7828 (mt-10) REVERT: B 84 MET cc_start: 0.7940 (mpp) cc_final: 0.7661 (mmt) REVERT: C 92 GLU cc_start: 0.8905 (mp0) cc_final: 0.8570 (mp0) REVERT: D 54 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8490 (mmmm) REVERT: D 73 GLU cc_start: 0.8778 (tp30) cc_final: 0.8524 (tp30) REVERT: E 59 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: F 44 LYS cc_start: 0.8583 (tppt) cc_final: 0.8343 (tppt) REVERT: H 31 LYS cc_start: 0.8199 (mptt) cc_final: 0.7843 (mmmm) REVERT: H 90 GLU cc_start: 0.8927 (mp0) cc_final: 0.8386 (mp0) outliers start: 13 outliers final: 8 residues processed: 162 average time/residue: 0.2347 time to fit residues: 50.4087 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 : 0.392 ------------------------------------------------------------------------------- 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 E residue 59 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: 9.9990 chunk 78 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 23 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 = 0.3364 r_free = 0.3364 target = 0.059954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.045520 restraints weight = 123261.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.047295 restraints weight = 49410.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048518 restraints weight = 29206.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049293 restraints weight = 21578.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.049736 restraints weight = 18114.468| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4200 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= 0.173 Angle : 0.619 7.562 15370 Z= 0.400 Chirality : 0.039 0.153 1755 Planarity : 0.004 0.038 1202 Dihedral : 29.315 103.009 3138 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 2.11 (0.31), residues: 708 helix: 2.38 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.60 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 83 TYR 0.013 0.001 TYR G 39 PHE 0.011 0.001 PHE A 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (10711) covalent geometry : angle 0.61930 / 0.40 (15370) hydrogen bonds : bond 0.05239 / 3.46 ( 648) hydrogen bonds : angle 3.46226 / 2.49 ( 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 162 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.401 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: A 59 GLU cc_start: 0.8319 (tp30) cc_final: 0.8027 (tp30) REVERT: A 68 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8663 (tm130) REVERT: B 63 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7845 (mt-10) REVERT: B 84 MET cc_start: 0.7957 (mpp) cc_final: 0.7672 (mmt) REVERT: C 92 GLU cc_start: 0.8919 (mp0) cc_final: 0.8550 (mp0) REVERT: D 54 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8487 (mmmm) REVERT: D 73 GLU cc_start: 0.8805 (tp30) cc_final: 0.8563 (tp30) REVERT: D 96 ARG cc_start: 0.8798 (mtm110) cc_final: 0.8583 (ttm110) REVERT: E 59 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: F 44 LYS cc_start: 0.8637 (tppt) cc_final: 0.8385 (tppt) REVERT: H 31 LYS cc_start: 0.8266 (mptt) cc_final: 0.7891 (mmmm) REVERT: H 90 GLU cc_start: 0.8968 (mp0) cc_final: 0.8425 (mp0) outliers start: 14 outliers final: 10 residues processed: 161 average time/residue: 0.2435 time to fit residues: 52.4000 Evaluate side-chains 153 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 85 THR Chi-restraints excluded: chain E residue 59 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=1.50 ------------------------------------------------------------------------------- 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: 0.7980 chunk 87 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.060333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.045673 restraints weight = 125512.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.047450 restraints weight = 50436.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048660 restraints weight = 30071.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.049431 restraints weight = 22399.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.049885 restraints weight = 18896.995| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4372 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= 0.156 Angle : 0.609 8.106 15370 Z= 0.395 Chirality : 0.039 0.140 1755 Planarity : 0.004 0.038 1202 Dihedral : 29.333 103.291 3138 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.35 % Allowed : 23.95 % 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: 2.29 (0.31), residues: 708 helix: 2.50 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.50 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 39 TYR 0.013 0.001 TYR H 80 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 0.00259 / 0.16 (10711) covalent geometry : angle 0.60945 / 0.39 (15370) hydrogen bonds : bond 0.04953 / 3.27 ( 648) hydrogen bonds : angle 3.32097 / 2.39 ( 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 165 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 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: A 59 GLU cc_start: 0.8301 (tp30) cc_final: 0.8013 (tp30) REVERT: A 68 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.8650 (tm130) REVERT: B 63 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 84 MET cc_start: 0.7948 (mpp) cc_final: 0.7688 (mmt) REVERT: C 92 GLU cc_start: 0.8913 (mp0) cc_final: 0.8526 (mp0) REVERT: D 96 ARG cc_start: 0.8801 (mtm110) cc_final: 0.8534 (ttm110) REVERT: E 59 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7796 (pm20) REVERT: F 44 LYS cc_start: 0.8650 (tppt) cc_final: 0.8428 (tptt) REVERT: H 31 LYS cc_start: 0.8261 (mptt) cc_final: 0.7881 (mmmm) REVERT: H 75 SER cc_start: 0.9516 (t) cc_final: 0.9250 (p) REVERT: H 90 GLU cc_start: 0.8961 (mp0) cc_final: 0.8406 (mp0) outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.2307 time to fit residues: 50.3624 Evaluate side-chains 156 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 85 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 95 VAL 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: 7.9990 chunk 84 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.059411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.044815 restraints weight = 125481.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046572 restraints weight = 50828.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047769 restraints weight = 30452.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048519 restraints weight = 22696.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048970 restraints weight = 19151.780| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10711 Z= 0.193 Angle : 0.632 7.727 15370 Z= 0.403 Chirality : 0.039 0.151 1755 Planarity : 0.004 0.038 1202 Dihedral : 29.373 102.513 3138 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.01 % Allowed : 24.62 % Favored : 73.37 % 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: 2.13 (0.31), residues: 708 helix: 2.41 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.63 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.016 0.001 TYR H 80 PHE 0.013 0.001 PHE D 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.19 (10711) covalent geometry : angle 0.63180 / 0.40 (15370) hydrogen bonds : bond 0.05405 / 3.57 ( 648) hydrogen bonds : angle 3.53564 / 2.55 ( 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 159 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.381 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: 0.8327 (tp30) cc_final: 0.8034 (tp30) REVERT: A 68 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.8670 (tm130) REVERT: A 79 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8572 (ttpp) REVERT: B 63 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 84 MET cc_start: 0.7979 (mpp) cc_final: 0.7722 (mmt) REVERT: C 92 GLU cc_start: 0.8921 (mp0) cc_final: 0.8531 (mp0) REVERT: D 54 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8470 (mmmm) REVERT: D 96 ARG cc_start: 0.8821 (mtm110) cc_final: 0.8530 (ttm110) REVERT: E 59 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: F 44 LYS cc_start: 0.8691 (tppt) cc_final: 0.8418 (tptt) REVERT: H 75 SER cc_start: 0.9532 (t) cc_final: 0.9270 (p) REVERT: H 90 GLU cc_start: 0.8994 (mp0) cc_final: 0.8472 (mp0) outliers start: 12 outliers final: 8 residues processed: 158 average time/residue: 0.2448 time to fit residues: 51.0924 Evaluate side-chains 153 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 E residue 59 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 Chi-restraints excluded: chain H residue 95 VAL 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: 0.7980 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.060125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045529 restraints weight = 125107.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047302 restraints weight = 50389.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048509 restraints weight = 30103.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049270 restraints weight = 22402.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049706 restraints weight = 18929.124| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4668 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= 0.152 Angle : 0.612 7.735 15370 Z= 0.392 Chirality : 0.039 0.137 1755 Planarity : 0.004 0.040 1202 Dihedral : 29.416 103.091 3138 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.68 % Allowed : 24.96 % Favored : 73.37 % 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: 2.38 (0.32), residues: 708 helix: 2.59 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.56 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 71 TYR 0.011 0.001 TYR H 80 PHE 0.010 0.001 PHE D 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (10711) covalent geometry : angle 0.61186 / 0.39 (15370) hydrogen bonds : bond 0.04928 / 3.25 ( 648) hydrogen bonds : angle 3.27710 / 2.36 ( 1648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2941.48 seconds wall clock time: 50 minutes 46.65 seconds (3046.65 seconds total)