Starting phenix.real_space_refine on Tue Aug 4 22:45:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ov_75894/08_2026/11ov_75894.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ov_75894/08_2026/11ov_75894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11ov_75894/08_2026/11ov_75894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ov_75894/08_2026/11ov_75894.map" model { file = "/net/cci-nas-00/data/ceres_data/11ov_75894/08_2026/11ov_75894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ov_75894/08_2026/11ov_75894.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 48 5.16 5 C 4445 2.51 5 N 1178 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6981 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1815 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 14, 'TRANS': 214} Chain: "B" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1519 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 13, 'TRANS': 178} Chain breaks: 1 Chain: "C" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1856 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 1 Chain: "h" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain: "l" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 1.46, per 1000 atoms: 0.21 Number of scatterers: 6981 At special positions: 0 Unit cell: (92.96, 104.58, 87.98, 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 48 16.00 O 1310 8.00 N 1178 7.00 C 4445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 98 " distance=2.03 Simple disulfide: pdb=" SG CYS h 105 " - pdb=" SG CYS h 110 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.04 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: 0.30 Conformation dependent library (CDL) restraints added in 346.7 milliseconds 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 21 sheets defined 7.7% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.517A pdb=" N GLN B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.778A pdb=" N ILE B 172 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.924A pdb=" N GLU C 65 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 66 " --> pdb=" O GLY C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 66' Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 144 through 149 removed outlier: 4.013A pdb=" N LEU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.693A pdb=" N GLN C 247 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'h' and resid 53 through 57 Processing helix chain 'h' and resid 89 through 93 removed outlier: 3.659A pdb=" N THR h 93 " --> pdb=" O THR h 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 75 removed outlier: 5.542A pdb=" N LEU A 68 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET A 241 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 70 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 72 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 removed outlier: 4.719A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA A 248 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.191A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.191A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 81 removed outlier: 6.448A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.761A pdb=" N GLU B 238 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.632A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR C 151 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 170 through 171 removed outlier: 6.277A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 3 through 7 removed outlier: 3.804A pdb=" N LEU h 18 " --> pdb=" O MET h 85 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET h 85 " --> pdb=" O LEU h 18 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN h 84 " --> pdb=" O ILE h 71 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE h 71 " --> pdb=" O GLN h 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 3 through 7 removed outlier: 3.804A pdb=" N LEU h 18 " --> pdb=" O MET h 85 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET h 85 " --> pdb=" O LEU h 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'h' and resid 60 through 62 removed outlier: 3.694A pdb=" N GLU h 61 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR h 50 " --> pdb=" O GLU h 61 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR h 35 " --> pdb=" O CYS h 99 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL h 37 " --> pdb=" O TYR h 97 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER h 117 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY h 102 " --> pdb=" O LEU h 115 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU h 115 " --> pdb=" O GLY h 102 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE h 104 " --> pdb=" O SER h 113 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER h 113 " --> pdb=" O PHE h 104 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LEU h 106 " --> pdb=" O TYR h 111 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR h 111 " --> pdb=" O LEU h 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 60 through 62 removed outlier: 3.694A pdb=" N GLU h 61 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR h 50 " --> pdb=" O GLU h 61 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR h 35 " --> pdb=" O CYS h 99 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL h 37 " --> pdb=" O TYR h 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.571A pdb=" N GLU l 105 " --> pdb=" O LEU l 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR l 102 " --> pdb=" O TYR l 86 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR l 86 " --> pdb=" O THR l 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'l' and resid 53 through 54 removed outlier: 3.952A pdb=" N ASN l 53 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR l 49 " --> pdb=" O ASN l 53 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 66 through 67 removed outlier: 3.512A pdb=" N SER l 67 " --> pdb=" O ASP l 70 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 513 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: 1.05 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2143 1.34 - 1.46: 1660 1.46 - 1.58: 3279 1.58 - 1.70: 4 1.70 - 1.83: 75 Bond restraints: 7161 Sorted by residual: bond pdb=" CA PRO A 253 " pdb=" C PRO A 253 " ideal model delta sigma weight residual 1.517 1.493 0.024 6.70e-03 2.23e+04 1.26e+01 bond pdb=" CA SER A 261 " pdb=" CB SER A 261 " ideal model delta sigma weight residual 1.534 1.483 0.051 1.77e-02 3.19e+03 8.33e+00 bond pdb=" CA ALA A 263 " pdb=" CB ALA A 263 " ideal model delta sigma weight residual 1.537 1.500 0.037 1.41e-02 5.03e+03 6.95e+00 bond pdb=" CA ALA A 265 " pdb=" CB ALA A 265 " ideal model delta sigma weight residual 1.531 1.492 0.039 1.57e-02 4.06e+03 6.08e+00 bond pdb=" CA PRO A 253 " pdb=" CB PRO A 253 " ideal model delta sigma weight residual 1.539 1.517 0.022 9.30e-03 1.16e+04 5.72e+00 ... (remaining 7156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 9581 4.37 - 8.74: 135 8.74 - 13.11: 20 13.11 - 17.48: 3 17.48 - 21.85: 3 Bond angle restraints: 9742 Sorted by residual: angle pdb=" CB MET B 222 " pdb=" CG MET B 222 " pdb=" SD MET B 222 " ideal model delta sigma weight residual 112.70 134.55 -21.85 3.00e+00 1.11e-01 5.31e+01 angle pdb=" CB LYS h 67 " pdb=" CG LYS h 67 " pdb=" CD LYS h 67 " ideal model delta sigma weight residual 111.30 125.85 -14.55 2.30e+00 1.89e-01 4.00e+01 angle pdb=" CB MET B 147 " pdb=" CG MET B 147 " pdb=" SD MET B 147 " ideal model delta sigma weight residual 112.70 131.32 -18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" CB MET B 193 " pdb=" CG MET B 193 " pdb=" SD MET B 193 " ideal model delta sigma weight residual 112.70 130.46 -17.76 3.00e+00 1.11e-01 3.51e+01 angle pdb=" CA GLU A 227 " pdb=" CB GLU A 227 " pdb=" CG GLU A 227 " ideal model delta sigma weight residual 114.10 125.78 -11.68 2.00e+00 2.50e-01 3.41e+01 ... (remaining 9737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 3531 16.50 - 33.00: 493 33.00 - 49.50: 161 49.50 - 66.00: 21 66.00 - 82.50: 7 Dihedral angle restraints: 4213 sinusoidal: 1632 harmonic: 2581 Sorted by residual: dihedral pdb=" CA ARG C 176 " pdb=" C ARG C 176 " pdb=" N MET C 177 " pdb=" CA MET C 177 " ideal model delta harmonic sigma weight residual 180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CB CYS l 23 " pdb=" SG CYS l 23 " pdb=" SG CYS l 88 " pdb=" CB CYS l 88 " ideal model delta sinusoidal sigma weight residual -86.00 -38.95 -47.05 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS h 22 " pdb=" SG CYS h 22 " pdb=" SG CYS h 98 " pdb=" CB CYS h 98 " ideal model delta sinusoidal sigma weight residual -86.00 -46.70 -39.30 1 1.00e+01 1.00e-02 2.17e+01 ... (remaining 4210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 837 0.059 - 0.119: 195 0.119 - 0.178: 38 0.178 - 0.238: 8 0.238 - 0.297: 3 Chirality restraints: 1081 Sorted by residual: chirality pdb=" CG LEU h 115 " pdb=" CB LEU h 115 " pdb=" CD1 LEU h 115 " pdb=" CD2 LEU h 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA ASN B 88 " pdb=" N ASN B 88 " pdb=" C ASN B 88 " pdb=" CB ASN B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1078 not shown) Planarity restraints: 1249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP l 35 " 0.019 2.00e-02 2.50e+03 2.42e-02 1.47e+01 pdb=" CG TRP l 35 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP l 35 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP l 35 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP l 35 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP l 35 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP l 35 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP l 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP l 35 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP l 35 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 255 " -0.319 9.50e-02 1.11e+02 1.43e-01 1.25e+01 pdb=" NE ARG A 255 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 255 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 255 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 255 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 273 " -0.057 5.00e-02 4.00e+02 8.61e-02 1.18e+01 pdb=" N PRO A 274 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.048 5.00e-02 4.00e+02 ... (remaining 1246 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1678 2.79 - 3.32: 5792 3.32 - 3.85: 11632 3.85 - 4.37: 13143 4.37 - 4.90: 23094 Nonbonded interactions: 55339 Sorted by model distance: nonbonded pdb=" OG1 THR B 171 " pdb=" O GLU C 50 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A 76 " pdb=" O ASN A 226 " model vdw 2.319 3.040 nonbonded pdb=" O SER B 223 " pdb=" OG SER B 223 " model vdw 2.323 3.040 nonbonded pdb=" O SER h 87 " pdb=" OG SER h 87 " model vdw 2.329 3.040 nonbonded pdb=" O THR l 74 " pdb=" OG1 THR l 74 " model vdw 2.333 3.040 ... (remaining 55334 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: 21.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.030 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 7164 Z= 0.269 Angle : 1.239 21.851 9748 Z= 0.624 Chirality : 0.056 0.297 1081 Planarity : 0.008 0.143 1249 Dihedral : 16.951 82.497 2548 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.17 % Allowed : 34.77 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.27), residues: 883 helix: -3.53 (0.53), residues: 44 sheet: -0.24 (0.34), residues: 263 loop : -1.76 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 272 TYR 0.021 0.002 TYR C 133 PHE 0.038 0.002 PHE h 70 TRP 0.062 0.003 TRP l 35 HIS 0.003 0.001 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.27 ( 7161) covalent geometry : angle 1.23860 / 0.62 ( 9742) SS BOND : bond 0.00480 / 0.18 ( 3) SS BOND : angle 1.93820 / 1.07 ( 6) hydrogen bonds : bond 0.22237 / 14.45 ( 162) hydrogen bonds : angle 8.72470 / 5.84 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7862 (tp30) cc_final: 0.7569 (tp30) REVERT: A 241 MET cc_start: 0.9104 (ttp) cc_final: 0.8475 (tmm) REVERT: A 259 TYR cc_start: 0.8805 (m-80) cc_final: 0.8603 (m-80) REVERT: A 260 MET cc_start: 0.9116 (ttp) cc_final: 0.8811 (ttm) REVERT: B 31 TYR cc_start: 0.6816 (p90) cc_final: 0.6540 (p90) REVERT: B 33 CYS cc_start: 0.8287 (m) cc_final: 0.7990 (m) REVERT: B 162 ASP cc_start: 0.9125 (m-30) cc_final: 0.8884 (m-30) REVERT: C 160 GLN cc_start: 0.8825 (tt0) cc_final: 0.8412 (tt0) REVERT: C 205 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7204 (tp30) REVERT: h 85 MET cc_start: 0.2817 (mpp) cc_final: 0.2229 (ppp) outliers start: 32 outliers final: 26 residues processed: 173 average time/residue: 0.4556 time to fit residues: 83.4348 Evaluate side-chains 167 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain h residue 22 CYS Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain l residue 21 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.105455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.071991 restraints weight = 16597.603| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.01 r_work: 0.2937 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7164 Z= 0.182 Angle : 0.688 9.783 9748 Z= 0.341 Chirality : 0.045 0.191 1081 Planarity : 0.005 0.065 1249 Dihedral : 6.558 49.990 996 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.82 % Allowed : 29.43 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.28), residues: 883 helix: -2.90 (0.58), residues: 52 sheet: 0.01 (0.34), residues: 257 loop : -1.44 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 272 TYR 0.015 0.001 TYR B 102 PHE 0.009 0.001 PHE A 74 TRP 0.020 0.001 TRP h 36 HIS 0.002 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 7161) covalent geometry : angle 0.68789 / 0.34 ( 9742) SS BOND : bond 0.00447 / 0.18 ( 3) SS BOND : angle 1.22543 / 0.65 ( 6) hydrogen bonds : bond 0.03637 / 2.37 ( 162) hydrogen bonds : angle 5.34733 / 3.64 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8425 (tp30) REVERT: A 75 GLU cc_start: 0.8223 (tp30) cc_final: 0.7754 (tp30) REVERT: B 31 TYR cc_start: 0.7224 (p90) cc_final: 0.6988 (p90) REVERT: B 33 CYS cc_start: 0.8640 (m) cc_final: 0.8293 (m) REVERT: B 116 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6318 (pmtt) REVERT: C 160 GLN cc_start: 0.8727 (tt0) cc_final: 0.8369 (tt0) REVERT: C 205 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: h 70 PHE cc_start: 0.5998 (m-80) cc_final: 0.5619 (m-80) REVERT: h 85 MET cc_start: 0.3264 (mpp) cc_final: 0.2306 (mmp) outliers start: 37 outliers final: 19 residues processed: 169 average time/residue: 0.5078 time to fit residues: 90.8099 Evaluate side-chains 158 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain l residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN B 205 ASN C 152 HIS l 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.066686 restraints weight = 16402.058| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.88 r_work: 0.2830 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7164 Z= 0.244 Angle : 0.719 10.975 9748 Z= 0.356 Chirality : 0.045 0.175 1081 Planarity : 0.005 0.051 1249 Dihedral : 5.949 53.842 977 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 6.77 % Allowed : 27.34 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.28), residues: 883 helix: -2.58 (0.63), residues: 53 sheet: -0.31 (0.32), residues: 284 loop : -1.22 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 103 TYR 0.018 0.002 TYR B 159 PHE 0.014 0.002 PHE h 82 TRP 0.024 0.002 TRP h 47 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 ( 7161) covalent geometry : angle 0.71817 / 0.36 ( 9742) SS BOND : bond 0.00265 / 0.12 ( 3) SS BOND : angle 1.15548 / 0.49 ( 6) hydrogen bonds : bond 0.03637 / 2.37 ( 162) hydrogen bonds : angle 4.99435 / 3.41 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8405 (tp30) REVERT: A 75 GLU cc_start: 0.8331 (tp30) cc_final: 0.7912 (tp30) REVERT: A 271 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8055 (tp30) REVERT: B 31 TYR cc_start: 0.7488 (p90) cc_final: 0.7193 (p90) REVERT: B 116 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6742 (pmtt) REVERT: B 150 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8312 (tm-30) REVERT: C 160 GLN cc_start: 0.8740 (tt0) cc_final: 0.8420 (tt0) REVERT: C 205 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7401 (tp30) REVERT: h 70 PHE cc_start: 0.6792 (m-80) cc_final: 0.6413 (m-80) REVERT: h 91 GLU cc_start: 0.9123 (tp30) cc_final: 0.8751 (mp0) REVERT: l 33 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6593 (tp) REVERT: l 45 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8284 (ptmm) outliers start: 52 outliers final: 21 residues processed: 181 average time/residue: 0.4471 time to fit residues: 85.8855 Evaluate side-chains 162 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 115 LEU Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 162 HIS h 39 GLN l 6 GLN l 38 GLN l 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.100674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.068460 restraints weight = 16400.991| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.87 r_work: 0.2872 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7164 Z= 0.133 Angle : 0.667 10.575 9748 Z= 0.327 Chirality : 0.043 0.159 1081 Planarity : 0.004 0.044 1249 Dihedral : 5.669 50.795 975 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.34 % Allowed : 29.17 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.28), residues: 883 helix: -2.53 (0.62), residues: 53 sheet: -0.22 (0.32), residues: 282 loop : -1.13 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG l 24 TYR 0.017 0.001 TYR h 111 PHE 0.012 0.001 PHE h 82 TRP 0.025 0.001 TRP l 35 HIS 0.002 0.000 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7161) covalent geometry : angle 0.66674 / 0.33 ( 9742) SS BOND : bond 0.00297 / 0.15 ( 3) SS BOND : angle 0.75856 / 0.37 ( 6) hydrogen bonds : bond 0.02821 / 1.84 ( 162) hydrogen bonds : angle 4.67803 / 3.19 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8346 (tp30) REVERT: A 75 GLU cc_start: 0.8351 (tp30) cc_final: 0.7934 (tp30) REVERT: A 260 MET cc_start: 0.9031 (ttp) cc_final: 0.8768 (mtp) REVERT: B 31 TYR cc_start: 0.7459 (p90) cc_final: 0.7149 (p90) REVERT: B 116 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6748 (pmtt) REVERT: B 150 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8290 (tm-30) REVERT: C 160 GLN cc_start: 0.8702 (tt0) cc_final: 0.8410 (tt0) REVERT: C 205 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7399 (tp30) REVERT: h 34 MET cc_start: 0.8054 (mmt) cc_final: 0.7576 (mmm) REVERT: h 91 GLU cc_start: 0.9094 (tp30) cc_final: 0.8786 (mp0) REVERT: l 33 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7125 (tp) REVERT: l 45 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8452 (ptmm) REVERT: l 71 PHE cc_start: 0.3196 (m-10) cc_final: 0.2939 (m-10) REVERT: l 79 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8757 (mm110) REVERT: l 82 ASP cc_start: 0.8209 (m-30) cc_final: 0.7727 (m-30) REVERT: l 86 TYR cc_start: 0.8494 (m-10) cc_final: 0.8186 (m-10) outliers start: 41 outliers final: 23 residues processed: 171 average time/residue: 0.5322 time to fit residues: 96.0050 Evaluate side-chains 165 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 98 CYS Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 0.0010 chunk 63 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN h 39 GLN l 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.099358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067228 restraints weight = 16305.018| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.89 r_work: 0.2848 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7164 Z= 0.171 Angle : 0.681 10.617 9748 Z= 0.333 Chirality : 0.043 0.142 1081 Planarity : 0.004 0.045 1249 Dihedral : 5.600 49.019 975 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.86 % Allowed : 28.91 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.29), residues: 883 helix: -2.38 (0.63), residues: 54 sheet: -0.27 (0.31), residues: 289 loop : -1.02 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 176 TYR 0.016 0.001 TYR h 111 PHE 0.012 0.001 PHE A 91 TRP 0.015 0.001 TRP h 47 HIS 0.002 0.000 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 7161) covalent geometry : angle 0.68128 / 0.33 ( 9742) SS BOND : bond 0.00309 / 0.13 ( 3) SS BOND : angle 0.62443 / 0.32 ( 6) hydrogen bonds : bond 0.02780 / 1.82 ( 162) hydrogen bonds : angle 4.60712 / 3.14 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: A 75 GLU cc_start: 0.8369 (tp30) cc_final: 0.7944 (tp30) REVERT: B 31 TYR cc_start: 0.7546 (p90) cc_final: 0.7245 (p90) REVERT: B 150 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8304 (tm-30) REVERT: C 54 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8899 (mt-10) REVERT: C 160 GLN cc_start: 0.8725 (tt0) cc_final: 0.8404 (tt0) REVERT: C 205 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: h 34 MET cc_start: 0.8257 (mmt) cc_final: 0.7840 (mmm) REVERT: h 85 MET cc_start: 0.2416 (mmp) cc_final: 0.1769 (mmm) REVERT: h 91 GLU cc_start: 0.9164 (tp30) cc_final: 0.8841 (mp0) REVERT: l 33 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7024 (tp) REVERT: l 45 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8315 (ptmm) REVERT: l 71 PHE cc_start: 0.3531 (m-10) cc_final: 0.3254 (m-10) REVERT: l 79 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8664 (mm110) REVERT: l 82 ASP cc_start: 0.7944 (m-30) cc_final: 0.7699 (m-30) outliers start: 45 outliers final: 31 residues processed: 179 average time/residue: 0.4956 time to fit residues: 93.9981 Evaluate side-chains 178 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 98 CYS Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 39 GLN l 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.098681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.067146 restraints weight = 16336.693| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.81 r_work: 0.2846 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7164 Z= 0.161 Angle : 0.690 11.756 9748 Z= 0.335 Chirality : 0.043 0.138 1081 Planarity : 0.004 0.041 1249 Dihedral : 5.511 47.339 975 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.73 % Allowed : 29.17 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.28), residues: 883 helix: -2.42 (0.62), residues: 54 sheet: -0.19 (0.32), residues: 277 loop : -1.01 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 176 TYR 0.015 0.001 TYR h 111 PHE 0.013 0.001 PHE A 91 TRP 0.018 0.001 TRP h 47 HIS 0.002 0.000 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 7161) covalent geometry : angle 0.68986 / 0.34 ( 9742) SS BOND : bond 0.00313 / 0.14 ( 3) SS BOND : angle 0.61409 / 0.31 ( 6) hydrogen bonds : bond 0.02710 / 1.78 ( 162) hydrogen bonds : angle 4.52800 / 3.08 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: A 75 GLU cc_start: 0.8356 (tp30) cc_final: 0.7929 (tp30) REVERT: B 31 TYR cc_start: 0.7561 (p90) cc_final: 0.7222 (p90) REVERT: B 150 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8293 (tm-30) REVERT: C 160 GLN cc_start: 0.8721 (tt0) cc_final: 0.8403 (tt0) REVERT: C 205 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: h 34 MET cc_start: 0.8460 (mmt) cc_final: 0.8141 (mmm) REVERT: h 91 GLU cc_start: 0.9205 (tp30) cc_final: 0.8888 (mp0) REVERT: h 98 CYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7506 (p) REVERT: l 33 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7082 (tp) REVERT: l 45 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8374 (ptmm) REVERT: l 79 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8646 (mm110) outliers start: 44 outliers final: 27 residues processed: 175 average time/residue: 0.4481 time to fit residues: 83.0346 Evaluate side-chains 175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 98 CYS Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 0.0670 chunk 6 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 83 optimal weight: 0.4980 overall best weight: 2.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN h 39 GLN l 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.066517 restraints weight = 16200.338| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.81 r_work: 0.2844 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7164 Z= 0.161 Angle : 0.716 12.963 9748 Z= 0.347 Chirality : 0.043 0.150 1081 Planarity : 0.004 0.041 1249 Dihedral : 5.439 48.435 975 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.34 % Allowed : 31.12 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.29), residues: 883 helix: -2.28 (0.64), residues: 54 sheet: -0.13 (0.32), residues: 277 loop : -0.97 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG l 61 TYR 0.017 0.001 TYR h 111 PHE 0.013 0.001 PHE A 91 TRP 0.024 0.001 TRP h 47 HIS 0.002 0.000 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 7161) covalent geometry : angle 0.71601 / 0.35 ( 9742) SS BOND : bond 0.00310 / 0.14 ( 3) SS BOND : angle 0.58000 / 0.29 ( 6) hydrogen bonds : bond 0.02683 / 1.75 ( 162) hydrogen bonds : angle 4.45877 / 3.03 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: A 75 GLU cc_start: 0.8389 (tp30) cc_final: 0.7953 (tp30) REVERT: A 103 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9389 (tm) REVERT: B 31 TYR cc_start: 0.7584 (p90) cc_final: 0.7243 (p90) REVERT: B 150 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8293 (tm-30) REVERT: C 160 GLN cc_start: 0.8726 (tt0) cc_final: 0.8427 (tt0) REVERT: C 205 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7439 (tp30) REVERT: h 34 MET cc_start: 0.8633 (mmt) cc_final: 0.8284 (mmm) REVERT: h 85 MET cc_start: 0.2949 (mmp) cc_final: 0.2354 (mmm) REVERT: h 91 GLU cc_start: 0.9240 (tp30) cc_final: 0.9028 (mp0) REVERT: h 98 CYS cc_start: 0.8359 (t) cc_final: 0.7772 (p) REVERT: l 33 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7176 (tp) REVERT: l 45 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8536 (ptmm) REVERT: l 79 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8733 (mm110) outliers start: 41 outliers final: 29 residues processed: 179 average time/residue: 0.4864 time to fit residues: 92.2358 Evaluate side-chains 182 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 60 THR Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN C 57 ASN h 39 GLN l 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064295 restraints weight = 16575.152| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.82 r_work: 0.2796 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7164 Z= 0.207 Angle : 0.744 13.326 9748 Z= 0.361 Chirality : 0.044 0.134 1081 Planarity : 0.004 0.042 1249 Dihedral : 5.512 48.260 975 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.08 % Allowed : 31.77 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.29), residues: 883 helix: -2.33 (0.63), residues: 54 sheet: -0.11 (0.32), residues: 280 loop : -0.88 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 176 TYR 0.019 0.001 TYR C 133 PHE 0.014 0.001 PHE h 82 TRP 0.035 0.002 TRP l 35 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 ( 7161) covalent geometry : angle 0.74375 / 0.36 ( 9742) SS BOND : bond 0.00579 / 0.22 ( 3) SS BOND : angle 0.54233 / 0.28 ( 6) hydrogen bonds : bond 0.02858 / 1.89 ( 162) hydrogen bonds : angle 4.59618 / 3.13 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: A 60 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8697 (mm-30) REVERT: A 75 GLU cc_start: 0.8408 (tp30) cc_final: 0.7995 (tp30) REVERT: B 31 TYR cc_start: 0.7640 (p90) cc_final: 0.7300 (p90) REVERT: B 150 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 205 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: h 34 MET cc_start: 0.8664 (mmt) cc_final: 0.8288 (mmm) REVERT: h 91 GLU cc_start: 0.9339 (tp30) cc_final: 0.9129 (mp0) REVERT: h 98 CYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8050 (p) REVERT: l 33 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7143 (tp) REVERT: l 45 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8567 (ptmm) REVERT: l 79 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8577 (mm110) REVERT: l 86 TYR cc_start: 0.8579 (m-10) cc_final: 0.8324 (m-10) outliers start: 39 outliers final: 26 residues processed: 182 average time/residue: 0.4524 time to fit residues: 87.2985 Evaluate side-chains 183 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 98 CYS Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 39 GLN l 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063587 restraints weight = 16501.243| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.74 r_work: 0.2783 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7164 Z= 0.222 Angle : 0.785 14.967 9748 Z= 0.381 Chirality : 0.044 0.159 1081 Planarity : 0.004 0.043 1249 Dihedral : 5.557 48.405 975 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.04 % Allowed : 33.07 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.28), residues: 883 helix: -2.39 (0.62), residues: 55 sheet: -0.09 (0.31), residues: 288 loop : -0.93 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 176 TYR 0.020 0.001 TYR C 133 PHE 0.016 0.001 PHE A 91 TRP 0.036 0.002 TRP h 47 HIS 0.002 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 ( 7161) covalent geometry : angle 0.78546 / 0.38 ( 9742) SS BOND : bond 0.00365 / 0.14 ( 3) SS BOND : angle 0.62046 / 0.34 ( 6) hydrogen bonds : bond 0.02876 / 1.87 ( 162) hydrogen bonds : angle 4.59172 / 3.12 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: A 75 GLU cc_start: 0.8410 (tp30) cc_final: 0.7998 (tp30) REVERT: B 31 TYR cc_start: 0.7680 (p90) cc_final: 0.7339 (p90) REVERT: B 150 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8369 (tm-30) REVERT: C 205 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7447 (tp30) REVERT: h 34 MET cc_start: 0.8722 (mmt) cc_final: 0.8380 (mmm) REVERT: h 98 CYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7828 (p) REVERT: l 24 ARG cc_start: 0.7991 (mmm160) cc_final: 0.7440 (ttm-80) REVERT: l 33 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7222 (tp) REVERT: l 45 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8571 (ptmm) REVERT: l 79 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8571 (mm110) REVERT: l 89 GLN cc_start: 0.8682 (tt0) cc_final: 0.8203 (tt0) outliers start: 31 outliers final: 21 residues processed: 180 average time/residue: 0.4476 time to fit residues: 85.2525 Evaluate side-chains 180 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 98 CYS Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 62 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 40.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 39 GLN l 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.064225 restraints weight = 16442.339| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.73 r_work: 0.2799 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7164 Z= 0.180 Angle : 0.793 15.674 9748 Z= 0.384 Chirality : 0.044 0.149 1081 Planarity : 0.004 0.046 1249 Dihedral : 5.294 48.425 973 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.78 % Allowed : 33.98 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.28), residues: 883 helix: -2.31 (0.63), residues: 55 sheet: -0.12 (0.30), residues: 293 loop : -0.93 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 176 TYR 0.020 0.001 TYR B 102 PHE 0.025 0.001 PHE h 82 TRP 0.042 0.002 TRP h 47 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 7161) covalent geometry : angle 0.79355 / 0.38 ( 9742) SS BOND : bond 0.00219 / 0.08 ( 3) SS BOND : angle 0.58436 / 0.33 ( 6) hydrogen bonds : bond 0.02756 / 1.81 ( 162) hydrogen bonds : angle 4.54662 / 3.08 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8423 (tp30) REVERT: A 75 GLU cc_start: 0.8432 (tp30) cc_final: 0.8016 (tp30) REVERT: B 31 TYR cc_start: 0.7679 (p90) cc_final: 0.7348 (p90) REVERT: B 150 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8361 (tm-30) REVERT: C 177 MET cc_start: 0.8295 (pmm) cc_final: 0.7962 (pmm) REVERT: C 205 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: h 34 MET cc_start: 0.8695 (mmt) cc_final: 0.8341 (mmm) REVERT: h 98 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7809 (p) REVERT: l 24 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7448 (ttm-80) REVERT: l 33 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7171 (tp) REVERT: l 79 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8464 (mm110) REVERT: l 82 ASP cc_start: 0.7855 (m-30) cc_final: 0.7570 (m-30) REVERT: l 89 GLN cc_start: 0.8678 (tt0) cc_final: 0.8329 (tt0) outliers start: 29 outliers final: 22 residues processed: 179 average time/residue: 0.4753 time to fit residues: 90.1178 Evaluate side-chains 183 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 98 CYS Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 80 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 39 GLN l 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.063459 restraints weight = 16553.884| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.72 r_work: 0.2786 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7164 Z= 0.203 Angle : 0.805 17.270 9748 Z= 0.387 Chirality : 0.044 0.137 1081 Planarity : 0.004 0.041 1249 Dihedral : 5.323 48.719 973 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.91 % Allowed : 34.24 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.28), residues: 883 helix: -2.34 (0.63), residues: 55 sheet: -0.08 (0.30), residues: 293 loop : -0.95 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 176 TYR 0.020 0.002 TYR C 133 PHE 0.017 0.001 PHE A 91 TRP 0.040 0.002 TRP h 47 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 7161) covalent geometry : angle 0.80493 / 0.39 ( 9742) SS BOND : bond 0.00228 / 0.09 ( 3) SS BOND : angle 0.56450 / 0.32 ( 6) hydrogen bonds : bond 0.02826 / 1.84 ( 162) hydrogen bonds : angle 4.54394 / 3.08 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2962.08 seconds wall clock time: 51 minutes 17.50 seconds (3077.50 seconds total)