Starting phenix.real_space_refine on Fri Sep 11 03:04:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12er_76384/09_2026/12er_76384.cif Found real_map, /net/cci-nas-00/data/ceres_data/12er_76384/09_2026/12er_76384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12er_76384/09_2026/12er_76384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12er_76384/09_2026/12er_76384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12er_76384/09_2026/12er_76384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12er_76384/09_2026/12er_76384.map" } resolution = 2.99 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= 0.000 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4286 2.51 5 N 1139 2.21 5 O 1389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6845 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1633 Classifications: {'peptide': 216} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 204} Chain: "C" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 313 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "D" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1649 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 207} Chain: "E" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1594 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 196} Time building chain proxies: 1.72, per 1000 atoms: 0.25 Number of scatterers: 6845 At special positions: 0 Unit cell: (67.959, 84.739, 146.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1389 8.00 N 1139 7.00 C 4286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 21 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 41 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS E 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 195 " distance=2.03 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: 0.50 Conformation dependent library (CDL) restraints added in 397.8 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 23 sheets defined 10.4% alpha, 51.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.813A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.672A pdb=" N ASP B 82 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.952A pdb=" N SER C 29 " --> pdb=" O GLN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 46 removed outlier: 4.416A pdb=" N ARG C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.747A pdb=" N LYS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER D 67 " --> pdb=" O SER D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 67' Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.910A pdb=" N THR D 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.777A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 183 through 189 Processing helix chain 'E' and resid 209 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.527A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.572A pdb=" N ALA A 92 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET A 34 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 127 removed outlier: 3.742A pdb=" N GLY A 142 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR A 178 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 127 removed outlier: 3.742A pdb=" N GLY A 142 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR A 178 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 157 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.537A pdb=" N SER B 72 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.668A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.979A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118 removed outlier: 6.289A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 155 removed outlier: 4.123A pdb=" N TRP B 148 " --> pdb=" O ARG B 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.819A pdb=" N ALA C 20 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.167A pdb=" N TRP D 36 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 52 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP D 38 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.550A pdb=" N TYR D 110 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP D 101 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE D 108 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 128 through 132 removed outlier: 5.279A pdb=" N ALA D 145 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL D 192 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLY D 147 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL D 190 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU D 149 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER D 188 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 128 through 132 removed outlier: 5.279A pdb=" N ALA D 145 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL D 192 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLY D 147 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL D 190 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU D 149 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER D 188 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 162 removed outlier: 4.739A pdb=" N TYR D 202 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP E 91 " --> pdb=" O HIS E 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 17 through 23 removed outlier: 3.529A pdb=" N SER E 66 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 116 through 120 removed outlier: 6.226A pdb=" N TYR E 174 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 116 through 120 removed outlier: 6.226A pdb=" N TYR E 174 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 156 through 157 removed outlier: 3.941A pdb=" N TRP E 150 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR E 147 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS E 206 " --> pdb=" O CYS E 195 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2196 1.35 - 1.47: 1778 1.47 - 1.58: 3000 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 7010 Sorted by residual: bond pdb=" CB GLU B 79 " pdb=" CG GLU B 79 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" CA ASN D 212 " pdb=" CB ASN D 212 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.67e-01 bond pdb=" CB ASP D 216 " pdb=" CG ASP D 216 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.61e-01 bond pdb=" CB GLN A 108 " pdb=" CG GLN A 108 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.45e-01 bond pdb=" C ARG E 53 " pdb=" O ARG E 53 " ideal model delta sigma weight residual 1.238 1.249 -0.011 1.28e-02 6.10e+03 7.35e-01 ... (remaining 7005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 9409 1.56 - 3.13: 130 3.13 - 4.69: 21 4.69 - 6.25: 2 6.25 - 7.81: 1 Bond angle restraints: 9563 Sorted by residual: angle pdb=" C GLY E 152 " pdb=" N ASP E 153 " pdb=" CA ASP E 153 " ideal model delta sigma weight residual 121.54 126.58 -5.04 1.91e+00 2.74e-01 6.97e+00 angle pdb=" CB GLU B 79 " pdb=" CG GLU B 79 " pdb=" CD GLU B 79 " ideal model delta sigma weight residual 112.60 116.84 -4.24 1.70e+00 3.46e-01 6.21e+00 angle pdb=" CA LEU D 186 " pdb=" CB LEU D 186 " pdb=" CG LEU D 186 " ideal model delta sigma weight residual 116.30 124.11 -7.81 3.50e+00 8.16e-02 4.98e+00 angle pdb=" CA GLU B 79 " pdb=" CB GLU B 79 " pdb=" CG GLU B 79 " ideal model delta sigma weight residual 114.10 118.38 -4.28 2.00e+00 2.50e-01 4.59e+00 angle pdb=" CA GLN A 108 " pdb=" CB GLN A 108 " pdb=" CG GLN A 108 " ideal model delta sigma weight residual 114.10 118.20 -4.10 2.00e+00 2.50e-01 4.21e+00 ... (remaining 9558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3792 17.31 - 34.63: 290 34.63 - 51.94: 97 51.94 - 69.26: 18 69.26 - 86.57: 7 Dihedral angle restraints: 4204 sinusoidal: 1583 harmonic: 2621 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 87 " pdb=" CB CYS E 87 " ideal model delta sinusoidal sigma weight residual 93.00 139.42 -46.42 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual 93.00 52.22 40.78 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.49 33.51 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 4201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 617 0.025 - 0.051: 302 0.051 - 0.076: 67 0.076 - 0.101: 58 0.101 - 0.127: 43 Chirality restraints: 1087 Sorted by residual: chirality pdb=" CA ASP B 170 " pdb=" N ASP B 170 " pdb=" C ASP B 170 " pdb=" CB ASP B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE E 138 " pdb=" N ILE E 138 " pdb=" C ILE E 138 " pdb=" CB ILE E 138 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE B 144 " pdb=" N ILE B 144 " pdb=" C ILE B 144 " pdb=" CB ILE B 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 1084 not shown) Planarity restraints: 1223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 156 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO D 157 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 157 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 157 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 151 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 152 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 212 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C ASN D 212 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN D 212 " -0.011 2.00e-02 2.50e+03 pdb=" N THR D 213 " -0.010 2.00e-02 2.50e+03 ... (remaining 1220 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.94: 2890 2.94 - 3.43: 6037 3.43 - 3.92: 11434 3.92 - 4.41: 12717 4.41 - 4.90: 21912 Nonbonded interactions: 54990 Sorted by model distance: nonbonded pdb=" O ASN D 212 " pdb=" OD1 ASN D 212 " model vdw 2.445 3.040 nonbonded pdb=" N ASP A 104 " pdb=" OD1 ASP A 104 " model vdw 2.544 3.120 nonbonded pdb=" N ASN D 212 " pdb=" N THR D 213 " model vdw 2.613 2.560 nonbonded pdb=" C SER D 72 " pdb=" OG SER D 72 " model vdw 2.621 2.616 nonbonded pdb=" O THR A 91 " pdb=" OG1 THR A 91 " model vdw 2.634 3.040 ... (remaining 54985 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.240 Find NCS groups from input model: 0.050 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.002 0.036 7023 Z= 0.090 Angle : 0.484 7.813 9589 Z= 0.254 Chirality : 0.041 0.127 1087 Planarity : 0.004 0.042 1223 Dihedral : 14.397 86.572 2489 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.12 % Favored : 97.66 % Rotamer: Outliers : 1.79 % Allowed : 19.18 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.29), residues: 896 helix: -0.24 (0.68), residues: 58 sheet: 0.91 (0.25), residues: 431 loop : 0.65 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 216 TYR 0.007 0.001 TYR E 86 PHE 0.013 0.001 PHE A 149 TRP 0.007 0.001 TRP B 163 HIS 0.008 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 ( 7010) covalent geometry : angle 0.48334 / 0.25 ( 9563) SS BOND : bond 0.00163 / 0.10 ( 13) SS BOND : angle 0.64476 / 0.40 ( 26) hydrogen bonds : bond 0.22171 / 14.80 ( 273) hydrogen bonds : angle 8.85776 / 6.26 ( 810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7929 (t70) cc_final: 0.7688 (t70) REVERT: A 82 GLU cc_start: 0.7208 (tt0) cc_final: 0.6787 (mt-10) REVERT: B 45 LYS cc_start: 0.7872 (tttt) cc_final: 0.7601 (tttp) REVERT: B 56 SER cc_start: 0.8482 (t) cc_final: 0.8271 (m) REVERT: B 81 GLU cc_start: 0.8108 (pt0) cc_final: 0.7864 (pt0) REVERT: B 143 ASP cc_start: 0.7497 (m-30) cc_final: 0.7227 (m-30) REVERT: D 48 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: D 142 SER cc_start: 0.8412 (p) cc_final: 0.8033 (m) REVERT: D 209 LYS cc_start: 0.8258 (mmpt) cc_final: 0.8041 (mmtm) REVERT: E 52 ASP cc_start: 0.7239 (m-30) cc_final: 0.6577 (t0) REVERT: E 53 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7242 (ttm110) REVERT: E 62 SER cc_start: 0.7626 (OUTLIER) cc_final: 0.7335 (p) outliers start: 14 outliers final: 12 residues processed: 121 average time/residue: 0.4941 time to fit residues: 63.4841 Evaluate side-chains 122 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN D 41 GLN D 172 HIS D 179 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.177902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122161 restraints weight = 8004.699| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.75 r_work: 0.3281 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7023 Z= 0.233 Angle : 0.657 9.734 9589 Z= 0.344 Chirality : 0.047 0.160 1087 Planarity : 0.005 0.050 1223 Dihedral : 5.742 51.174 1000 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.68 % Favored : 97.10 % Rotamer: Outliers : 4.86 % Allowed : 15.73 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.91 (0.29), residues: 896 helix: 0.02 (0.70), residues: 52 sheet: 0.81 (0.25), residues: 413 loop : 0.64 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 46 TYR 0.015 0.002 TYR B 49 PHE 0.017 0.002 PHE D 108 TRP 0.013 0.002 TRP D 111 HIS 0.006 0.002 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 ( 7010) covalent geometry : angle 0.65396 / 0.34 ( 9563) SS BOND : bond 0.00517 / 0.41 ( 13) SS BOND : angle 1.33457 / 0.72 ( 26) hydrogen bonds : bond 0.03602 / 2.27 ( 273) hydrogen bonds : angle 6.18272 / 4.34 ( 810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7715 (ptmm) REVERT: B 79 GLU cc_start: 0.7480 (mp0) cc_final: 0.7163 (mp0) REVERT: B 81 GLU cc_start: 0.8272 (pt0) cc_final: 0.7909 (pt0) REVERT: B 108 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7281 (ptm-80) REVERT: B 143 ASP cc_start: 0.7655 (m-30) cc_final: 0.7447 (m-30) REVERT: B 169 LYS cc_start: 0.7442 (mtpp) cc_final: 0.6612 (tmmm) REVERT: D 45 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7379 (mppt) REVERT: D 83 LYS cc_start: 0.8209 (mttt) cc_final: 0.7637 (mppt) REVERT: D 142 SER cc_start: 0.8445 (p) cc_final: 0.8064 (m) REVERT: D 209 LYS cc_start: 0.8496 (mmpt) cc_final: 0.8182 (mmtm) REVERT: E 52 ASP cc_start: 0.7454 (m-30) cc_final: 0.6666 (t0) REVERT: E 53 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7205 (ttm110) REVERT: E 188 LYS cc_start: 0.8449 (mttt) cc_final: 0.8201 (mtpp) REVERT: E 191 ARG cc_start: 0.8159 (mtm180) cc_final: 0.7934 (mmp-170) REVERT: E 196 GLN cc_start: 0.8411 (tt0) cc_final: 0.8185 (mt0) outliers start: 38 outliers final: 21 residues processed: 152 average time/residue: 0.4709 time to fit residues: 75.9557 Evaluate side-chains 142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 ASN Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 68 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 5 GLN D 41 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS E 41 GLN E 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119484 restraints weight = 7989.068| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.71 r_work: 0.3259 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7023 Z= 0.196 Angle : 0.585 7.099 9589 Z= 0.303 Chirality : 0.044 0.162 1087 Planarity : 0.005 0.049 1223 Dihedral : 5.048 56.850 983 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.46 % Favored : 97.32 % Rotamer: Outliers : 6.27 % Allowed : 16.75 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.28), residues: 896 helix: -0.01 (0.70), residues: 52 sheet: 0.92 (0.25), residues: 415 loop : 0.49 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.011 0.002 TYR E 2 PHE 0.014 0.002 PHE D 108 TRP 0.014 0.002 TRP A 47 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 ( 7010) covalent geometry : angle 0.58257 / 0.30 ( 9563) SS BOND : bond 0.00387 / 0.32 ( 13) SS BOND : angle 1.09090 / 0.71 ( 26) hydrogen bonds : bond 0.03772 / 2.44 ( 273) hydrogen bonds : angle 5.91962 / 4.15 ( 810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 0.250 Fit side-chains REVERT: B 9 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.8033 (p) REVERT: B 79 GLU cc_start: 0.7362 (mp0) cc_final: 0.7083 (mp0) REVERT: B 108 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7472 (ptm-80) REVERT: D 45 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7483 (mppt) REVERT: D 48 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: D 53 ILE cc_start: 0.8620 (tp) cc_final: 0.8304 (mt) REVERT: D 83 LYS cc_start: 0.8323 (mttt) cc_final: 0.7504 (mptt) REVERT: D 88 THR cc_start: 0.8248 (p) cc_final: 0.8008 (t) REVERT: D 142 SER cc_start: 0.8384 (p) cc_final: 0.8078 (m) REVERT: D 209 LYS cc_start: 0.8589 (mmpt) cc_final: 0.8365 (mmpt) REVERT: D 214 LYS cc_start: 0.7976 (tttm) cc_final: 0.7692 (tttt) REVERT: E 52 ASP cc_start: 0.7592 (m-30) cc_final: 0.6893 (t0) REVERT: E 53 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7275 (ttm110) REVERT: E 188 LYS cc_start: 0.8694 (mttt) cc_final: 0.8365 (mtpp) REVERT: E 191 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8050 (mmp-170) outliers start: 49 outliers final: 28 residues processed: 162 average time/residue: 0.4856 time to fit residues: 83.2976 Evaluate side-chains 149 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 ASN Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 55 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 73 optimal weight: 0.0270 chunk 83 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 GLN E 6 GLN E 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.177265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122933 restraints weight = 8009.283| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.74 r_work: 0.3306 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7023 Z= 0.104 Angle : 0.516 6.819 9589 Z= 0.268 Chirality : 0.042 0.151 1087 Planarity : 0.004 0.045 1223 Dihedral : 4.769 58.546 983 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.34 % Favored : 97.54 % Rotamer: Outliers : 3.58 % Allowed : 20.08 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.95 (0.29), residues: 896 helix: 0.17 (0.73), residues: 51 sheet: 0.91 (0.26), residues: 421 loop : 0.54 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 39 TYR 0.014 0.001 TYR C 40 PHE 0.010 0.001 PHE D 80 TRP 0.010 0.001 TRP A 47 HIS 0.002 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 7010) covalent geometry : angle 0.51492 / 0.27 ( 9563) SS BOND : bond 0.00284 / 0.23 ( 13) SS BOND : angle 0.84316 / 0.55 ( 26) hydrogen bonds : bond 0.02752 / 1.80 ( 273) hydrogen bonds : angle 5.39118 / 3.78 ( 810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.263 Fit side-chains REVERT: B 9 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7876 (p) REVERT: B 79 GLU cc_start: 0.7399 (mp0) cc_final: 0.7150 (mp0) REVERT: B 108 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7444 (ptm-80) REVERT: C 31 ASN cc_start: 0.7864 (t0) cc_final: 0.7257 (t0) REVERT: D 45 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7786 (mtmt) REVERT: D 53 ILE cc_start: 0.8565 (tp) cc_final: 0.8258 (mt) REVERT: D 83 LYS cc_start: 0.8288 (mttt) cc_final: 0.7473 (mptt) REVERT: D 88 THR cc_start: 0.8200 (p) cc_final: 0.7969 (t) REVERT: D 142 SER cc_start: 0.8406 (p) cc_final: 0.8111 (m) REVERT: D 214 LYS cc_start: 0.7919 (tttm) cc_final: 0.7709 (tttt) REVERT: E 52 ASP cc_start: 0.7490 (m-30) cc_final: 0.6822 (t0) REVERT: E 53 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7239 (ttm110) REVERT: E 62 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.8025 (m) REVERT: E 188 LYS cc_start: 0.8496 (mttt) cc_final: 0.8200 (mtpp) REVERT: E 191 ARG cc_start: 0.8233 (mtm180) cc_final: 0.8025 (mmp-170) REVERT: E 205 GLU cc_start: 0.7976 (tp30) cc_final: 0.7742 (tp30) outliers start: 28 outliers final: 16 residues processed: 140 average time/residue: 0.5073 time to fit residues: 75.1807 Evaluate side-chains 131 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 5 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.177158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123069 restraints weight = 8016.645| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.72 r_work: 0.3306 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7023 Z= 0.104 Angle : 0.511 6.638 9589 Z= 0.264 Chirality : 0.042 0.149 1087 Planarity : 0.004 0.044 1223 Dihedral : 4.603 55.106 982 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Rotamer: Outliers : 3.84 % Allowed : 20.20 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.99 (0.29), residues: 896 helix: 0.22 (0.73), residues: 52 sheet: 0.98 (0.26), residues: 411 loop : 0.54 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.010 0.001 TYR D 34 PHE 0.010 0.001 PHE D 80 TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 7010) covalent geometry : angle 0.50982 / 0.26 ( 9563) SS BOND : bond 0.00282 / 0.22 ( 13) SS BOND : angle 0.72616 / 0.45 ( 26) hydrogen bonds : bond 0.02664 / 1.74 ( 273) hydrogen bonds : angle 5.14500 / 3.60 ( 810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.276 Fit side-chains REVERT: B 9 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7886 (p) REVERT: B 79 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: B 105 GLU cc_start: 0.7416 (pt0) cc_final: 0.7175 (pt0) REVERT: B 149 LYS cc_start: 0.6111 (mttp) cc_final: 0.5570 (mppt) REVERT: B 169 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7214 (pttp) REVERT: C 31 ASN cc_start: 0.7902 (t0) cc_final: 0.7288 (t0) REVERT: D 34 TYR cc_start: 0.8115 (m-10) cc_final: 0.7907 (m-10) REVERT: D 45 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7742 (mtmt) REVERT: D 53 ILE cc_start: 0.8615 (tp) cc_final: 0.8322 (mt) REVERT: D 83 LYS cc_start: 0.8293 (mttt) cc_final: 0.7477 (mptt) REVERT: D 88 THR cc_start: 0.8161 (p) cc_final: 0.7944 (t) REVERT: D 101 ASP cc_start: 0.8646 (m-30) cc_final: 0.8359 (m-30) REVERT: D 142 SER cc_start: 0.8423 (p) cc_final: 0.8131 (m) REVERT: D 209 LYS cc_start: 0.8625 (mmpt) cc_final: 0.8188 (mmtm) REVERT: E 52 ASP cc_start: 0.7521 (m-30) cc_final: 0.6830 (t0) REVERT: E 53 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7339 (mtm110) REVERT: E 62 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.8020 (m) REVERT: E 188 LYS cc_start: 0.8503 (mttt) cc_final: 0.8186 (mtpp) outliers start: 30 outliers final: 17 residues processed: 137 average time/residue: 0.5358 time to fit residues: 77.5219 Evaluate side-chains 135 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120492 restraints weight = 8059.202| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.72 r_work: 0.3276 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7023 Z= 0.141 Angle : 0.537 6.404 9589 Z= 0.277 Chirality : 0.042 0.151 1087 Planarity : 0.005 0.078 1223 Dihedral : 4.692 55.258 982 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.46 % Favored : 97.43 % Rotamer: Outliers : 4.35 % Allowed : 19.95 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.96 (0.28), residues: 896 helix: 0.22 (0.73), residues: 52 sheet: 1.03 (0.26), residues: 404 loop : 0.43 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 108 TYR 0.010 0.001 TYR D 96 PHE 0.010 0.001 PHE D 80 TRP 0.011 0.001 TRP A 47 HIS 0.002 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 7010) covalent geometry : angle 0.53569 / 0.28 ( 9563) SS BOND : bond 0.00336 / 0.26 ( 13) SS BOND : angle 0.81120 / 0.49 ( 26) hydrogen bonds : bond 0.02751 / 1.80 ( 273) hydrogen bonds : angle 5.15350 / 3.61 ( 810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.263 Fit side-chains REVERT: B 9 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7963 (p) REVERT: B 105 GLU cc_start: 0.7497 (pt0) cc_final: 0.7252 (pt0) REVERT: B 107 LYS cc_start: 0.7822 (tttp) cc_final: 0.7071 (ttpp) REVERT: B 149 LYS cc_start: 0.6182 (mttp) cc_final: 0.5710 (mppt) REVERT: B 169 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7228 (tmmt) REVERT: C 31 ASN cc_start: 0.7921 (t0) cc_final: 0.7318 (t0) REVERT: D 45 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7771 (mtmt) REVERT: D 53 ILE cc_start: 0.8627 (tp) cc_final: 0.8335 (mt) REVERT: D 83 LYS cc_start: 0.8367 (mttt) cc_final: 0.7552 (mptt) REVERT: D 88 THR cc_start: 0.8165 (p) cc_final: 0.7949 (t) REVERT: D 142 SER cc_start: 0.8419 (p) cc_final: 0.8134 (m) REVERT: D 209 LYS cc_start: 0.8607 (mmpt) cc_final: 0.8140 (mmtm) REVERT: D 218 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7165 (ttm170) REVERT: E 52 ASP cc_start: 0.7550 (m-30) cc_final: 0.6865 (t0) REVERT: E 53 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7348 (ttm110) REVERT: E 62 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.8084 (m) REVERT: E 188 LYS cc_start: 0.8539 (mttt) cc_final: 0.8222 (mtpp) outliers start: 34 outliers final: 20 residues processed: 142 average time/residue: 0.5024 time to fit residues: 75.5227 Evaluate side-chains 139 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.0470 chunk 21 optimal weight: 0.5980 overall best weight: 0.9284 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.174714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121859 restraints weight = 8102.678| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.63 r_work: 0.3279 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7023 Z= 0.139 Angle : 0.544 9.038 9589 Z= 0.278 Chirality : 0.043 0.153 1087 Planarity : 0.005 0.065 1223 Dihedral : 4.734 54.817 982 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Rotamer: Outliers : 5.24 % Allowed : 19.82 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.92 (0.28), residues: 896 helix: 0.17 (0.73), residues: 52 sheet: 1.01 (0.26), residues: 404 loop : 0.41 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.012 0.001 TYR D 34 PHE 0.010 0.001 PHE D 80 TRP 0.017 0.001 TRP A 157 HIS 0.002 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7010) covalent geometry : angle 0.54380 / 0.28 ( 9563) SS BOND : bond 0.00376 / 0.27 ( 13) SS BOND : angle 0.71738 / 0.46 ( 26) hydrogen bonds : bond 0.02765 / 1.81 ( 273) hydrogen bonds : angle 5.15611 / 3.59 ( 810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8105 (mtpt) REVERT: B 9 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.8148 (p) REVERT: B 105 GLU cc_start: 0.7657 (pt0) cc_final: 0.7414 (pt0) REVERT: B 107 LYS cc_start: 0.7940 (tttp) cc_final: 0.7446 (ttpp) REVERT: B 149 LYS cc_start: 0.6262 (mttp) cc_final: 0.5786 (mppt) REVERT: B 169 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7417 (tmmt) REVERT: C 31 ASN cc_start: 0.8034 (t0) cc_final: 0.7364 (t0) REVERT: D 34 TYR cc_start: 0.8122 (m-10) cc_final: 0.7843 (m-10) REVERT: D 45 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7896 (mtmt) REVERT: D 48 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: D 53 ILE cc_start: 0.8655 (tp) cc_final: 0.8362 (mt) REVERT: D 88 THR cc_start: 0.8210 (p) cc_final: 0.8006 (t) REVERT: D 110 TYR cc_start: 0.8071 (m-80) cc_final: 0.7782 (m-80) REVERT: D 142 SER cc_start: 0.8408 (p) cc_final: 0.8126 (m) REVERT: E 52 ASP cc_start: 0.7630 (m-30) cc_final: 0.6990 (t0) REVERT: E 53 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7343 (ttm110) REVERT: E 62 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8096 (m) REVERT: E 188 LYS cc_start: 0.8662 (mttt) cc_final: 0.8339 (mtpp) outliers start: 41 outliers final: 24 residues processed: 145 average time/residue: 0.5043 time to fit residues: 77.6341 Evaluate side-chains 144 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 66 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 73 optimal weight: 0.0050 chunk 74 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 77 optimal weight: 0.0470 chunk 81 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.176415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123058 restraints weight = 8085.382| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.67 r_work: 0.3300 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7023 Z= 0.108 Angle : 0.542 7.264 9589 Z= 0.277 Chirality : 0.042 0.148 1087 Planarity : 0.005 0.061 1223 Dihedral : 4.598 53.255 982 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.46 % Favored : 97.43 % Rotamer: Outliers : 4.48 % Allowed : 20.59 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.96 (0.29), residues: 896 helix: 0.31 (0.74), residues: 52 sheet: 1.03 (0.26), residues: 404 loop : 0.42 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.022 0.001 TYR D 55 PHE 0.010 0.001 PHE D 80 TRP 0.016 0.001 TRP A 157 HIS 0.002 0.000 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7010) covalent geometry : angle 0.54146 / 0.28 ( 9563) SS BOND : bond 0.00307 / 0.23 ( 13) SS BOND : angle 0.58740 / 0.37 ( 26) hydrogen bonds : bond 0.02578 / 1.69 ( 273) hydrogen bonds : angle 5.01534 / 3.51 ( 810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: B 9 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.8101 (p) REVERT: B 105 GLU cc_start: 0.7631 (pt0) cc_final: 0.7399 (pt0) REVERT: B 107 LYS cc_start: 0.7892 (tttp) cc_final: 0.7136 (ttpp) REVERT: B 149 LYS cc_start: 0.6236 (mttp) cc_final: 0.5768 (mppt) REVERT: B 169 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7435 (tmmt) REVERT: C 31 ASN cc_start: 0.8041 (t0) cc_final: 0.7373 (t0) REVERT: D 34 TYR cc_start: 0.8103 (m-10) cc_final: 0.7890 (m-10) REVERT: D 53 ILE cc_start: 0.8662 (tp) cc_final: 0.8370 (mt) REVERT: D 88 THR cc_start: 0.8243 (p) cc_final: 0.8034 (t) REVERT: D 110 TYR cc_start: 0.8062 (m-80) cc_final: 0.7795 (m-80) REVERT: D 142 SER cc_start: 0.8395 (p) cc_final: 0.8125 (m) REVERT: D 209 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8256 (mmtm) REVERT: D 218 ARG cc_start: 0.7657 (ptm160) cc_final: 0.7232 (ttm170) REVERT: E 49 ASP cc_start: 0.6556 (OUTLIER) cc_final: 0.6354 (p0) REVERT: E 53 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7376 (ttm110) REVERT: E 62 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.8050 (m) REVERT: E 188 LYS cc_start: 0.8649 (mttt) cc_final: 0.8324 (mtpp) outliers start: 35 outliers final: 23 residues processed: 135 average time/residue: 0.5041 time to fit residues: 72.1695 Evaluate side-chains 139 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116476 restraints weight = 8046.666| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.70 r_work: 0.3216 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7023 Z= 0.195 Angle : 0.605 7.817 9589 Z= 0.310 Chirality : 0.044 0.158 1087 Planarity : 0.005 0.057 1223 Dihedral : 5.042 56.997 982 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.12 % Favored : 96.76 % Rotamer: Outliers : 4.48 % Allowed : 20.97 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.76 (0.28), residues: 896 helix: 0.40 (0.76), residues: 47 sheet: 0.87 (0.26), residues: 406 loop : 0.28 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 108 TYR 0.012 0.002 TYR D 96 PHE 0.012 0.002 PHE A 103 TRP 0.013 0.002 TRP A 47 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 7010) covalent geometry : angle 0.60339 / 0.31 ( 9563) SS BOND : bond 0.00488 / 0.38 ( 13) SS BOND : angle 1.09978 / 0.78 ( 26) hydrogen bonds : bond 0.02970 / 1.93 ( 273) hydrogen bonds : angle 5.42008 / 3.76 ( 810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 45 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7691 (tttp) REVERT: B 105 GLU cc_start: 0.7798 (pt0) cc_final: 0.7548 (pt0) REVERT: B 149 LYS cc_start: 0.6282 (mttp) cc_final: 0.5812 (mppt) REVERT: B 169 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7525 (tmmt) REVERT: C 31 ASN cc_start: 0.8059 (t0) cc_final: 0.7407 (t0) REVERT: D 45 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7888 (mtmt) REVERT: D 48 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: D 88 THR cc_start: 0.8206 (p) cc_final: 0.7998 (t) REVERT: D 110 TYR cc_start: 0.8077 (m-80) cc_final: 0.7760 (m-80) REVERT: D 142 SER cc_start: 0.8446 (p) cc_final: 0.8176 (m) REVERT: D 209 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8215 (mmtm) REVERT: D 218 ARG cc_start: 0.7788 (ptm160) cc_final: 0.7255 (ttm-80) REVERT: E 25 ASN cc_start: 0.7836 (t0) cc_final: 0.7574 (m-40) REVERT: E 26 ASN cc_start: 0.8557 (t0) cc_final: 0.7977 (t0) REVERT: E 49 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6602 (p0) REVERT: E 53 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7492 (ttm110) REVERT: E 62 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8184 (m) REVERT: E 188 LYS cc_start: 0.8675 (mttt) cc_final: 0.8349 (mtpp) outliers start: 35 outliers final: 21 residues processed: 132 average time/residue: 0.5154 time to fit residues: 71.9908 Evaluate side-chains 132 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.171371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118212 restraints weight = 8003.223| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.67 r_work: 0.3236 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7023 Z= 0.154 Angle : 0.581 7.435 9589 Z= 0.297 Chirality : 0.043 0.153 1087 Planarity : 0.005 0.058 1223 Dihedral : 4.887 54.857 982 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Rotamer: Outliers : 3.58 % Allowed : 22.12 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.73 (0.29), residues: 896 helix: 0.46 (0.77), residues: 47 sheet: 0.82 (0.26), residues: 407 loop : 0.29 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.017 0.001 TYR D 34 PHE 0.010 0.001 PHE D 80 TRP 0.013 0.001 TRP A 47 HIS 0.002 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 7010) covalent geometry : angle 0.57886 / 0.30 ( 9563) SS BOND : bond 0.00379 / 0.28 ( 13) SS BOND : angle 1.04184 / 0.81 ( 26) hydrogen bonds : bond 0.02724 / 1.77 ( 273) hydrogen bonds : angle 5.27066 / 3.68 ( 810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.279 Fit side-chains REVERT: B 9 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8124 (p) REVERT: B 45 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7666 (tttp) REVERT: B 105 GLU cc_start: 0.7688 (pt0) cc_final: 0.7398 (pt0) REVERT: B 107 LYS cc_start: 0.8098 (tttp) cc_final: 0.7388 (ttpp) REVERT: B 169 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7609 (tmmt) REVERT: C 31 ASN cc_start: 0.8073 (t0) cc_final: 0.7391 (t0) REVERT: D 45 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7816 (mtmt) REVERT: D 53 ILE cc_start: 0.8626 (tp) cc_final: 0.8312 (mp) REVERT: D 88 THR cc_start: 0.8180 (p) cc_final: 0.7974 (t) REVERT: D 110 TYR cc_start: 0.7995 (m-80) cc_final: 0.7677 (m-80) REVERT: D 142 SER cc_start: 0.8437 (p) cc_final: 0.8164 (m) REVERT: D 209 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8210 (mmtm) REVERT: D 218 ARG cc_start: 0.7696 (ptm160) cc_final: 0.7171 (ttt-90) REVERT: E 26 ASN cc_start: 0.8568 (t0) cc_final: 0.8000 (t0) REVERT: E 49 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6550 (p0) REVERT: E 53 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7474 (ttm110) REVERT: E 62 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.8101 (m) REVERT: E 188 LYS cc_start: 0.8642 (mttt) cc_final: 0.8299 (mtpp) outliers start: 28 outliers final: 21 residues processed: 124 average time/residue: 0.5106 time to fit residues: 66.9688 Evaluate side-chains 124 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.171959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118671 restraints weight = 8004.425| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.69 r_work: 0.3252 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7023 Z= 0.132 Angle : 0.562 7.479 9589 Z= 0.289 Chirality : 0.043 0.152 1087 Planarity : 0.005 0.057 1223 Dihedral : 4.822 53.799 982 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 4.09 % Allowed : 21.61 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.71 (0.29), residues: 896 helix: 0.55 (0.77), residues: 47 sheet: 0.78 (0.26), residues: 409 loop : 0.28 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.013 0.001 TYR D 34 PHE 0.010 0.001 PHE D 80 TRP 0.013 0.001 TRP A 157 HIS 0.002 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 7010) covalent geometry : angle 0.56071 / 0.29 ( 9563) SS BOND : bond 0.00363 / 0.27 ( 13) SS BOND : angle 0.91963 / 0.69 ( 26) hydrogen bonds : bond 0.02672 / 1.75 ( 273) hydrogen bonds : angle 5.16319 / 3.60 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2774.95 seconds wall clock time: 48 minutes 7.47 seconds (2887.47 seconds total)