Starting phenix.real_space_refine on Wed Mar 4 13:13:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7e_27228/03_2026/8d7e_27228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7e_27228/03_2026/8d7e_27228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7e_27228/03_2026/8d7e_27228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7e_27228/03_2026/8d7e_27228.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7e_27228/03_2026/8d7e_27228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7e_27228/03_2026/8d7e_27228.cif" } resolution = 2.93 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6044 atoms to isotropic. 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 34 5.16 5 C 5654 2.51 5 N 1512 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "G GLU 166": not complete - not flipped Residue "G GLU 166": not complete - not flipped Residue "E GLU 166": not complete - not flipped Residue "E GLU 166": not complete - not flipped Time to flip 79 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8959 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "G" Number of atoms: 1649 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1649 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Chain: "F" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1654 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 206} Chain: "E" Number of atoms: 1646 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1646 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1639 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.91, per 1000 atoms: 0.21 Number of scatterers: 8959 At special positions: 0 Unit cell: (84.15, 125.8, 165.75, 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 34 16.00 O 1759 8.00 N 1512 7.00 C 5654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 215 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 215 " - pdb=" SG CYS D 134 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 1 " - " ASN C 190 " " NAG B 1 " - " ASN C 70 " " NAG H 1 " - " ASN C 60 " " NAG I 1 " - " ASN C 142 " Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 263.3 milliseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 26 sheets defined 6.4% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'G' and resid 29 through 32 removed outlier: 3.925A pdb=" N SER G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.205A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 184 through 188 removed outlier: 3.631A pdb=" N GLU G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 184 through 188' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.590A pdb=" N THR F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.856A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 194 removed outlier: 4.055A pdb=" N GLY F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 194' Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.059A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.602A pdb=" N LEU E 126 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 127' Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.560A pdb=" N HIS E 190 " --> pdb=" O ASP E 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.576A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 37 removed outlier: 6.108A pdb=" N HIS C 32 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N HIS C 104 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN C 34 " --> pdb=" O HIS C 104 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY C 106 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU C 36 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU C 97 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS C 91 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS C 99 " --> pdb=" O CYS C 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.682A pdb=" N VAL C 42 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 73 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 117 removed outlier: 3.544A pdb=" N HIS C 130 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 150 through 151 removed outlier: 3.699A pdb=" N HIS C 147 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR C 140 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 211 through 213 removed outlier: 3.569A pdb=" N VAL C 211 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 225 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 224 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS C 265 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AA8, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.547A pdb=" N SER G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA G 19 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE G 72 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.583A pdb=" N TYR G 88 " --> pdb=" O TYR G 37 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AB2, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.557A pdb=" N ASN G 138 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 146 through 150 removed outlier: 4.099A pdb=" N LYS G 146 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR G 198 " --> pdb=" O LYS G 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.562A pdb=" N ALA F 92 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 97 " --> pdb=" O HIS F 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS F 35 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N MET F 34 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 124 through 128 removed outlier: 6.474A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 124 through 128 removed outlier: 6.474A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 155 through 158 removed outlier: 3.784A pdb=" N THR F 155 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP F 203 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS F 200 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 7 removed outlier: 11.818A pdb=" N CYS E 23 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N THR E 74 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N ALA E 25 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 12.016A pdb=" N THR E 72 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N GLN E 27 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP E 70 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.576A pdb=" N LEU E 11 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.511A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 146 through 150 removed outlier: 3.763A pdb=" N LYS E 150 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.930A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS D 96 " --> pdb=" O TRP D 110 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP D 110 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA D 98 " --> pdb=" O GLN D 108 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.930A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 127 through 131 removed outlier: 3.652A pdb=" N SER D 187 " --> pdb=" O CYS D 147 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.231A pdb=" N TYR D 201 " --> pdb=" O VAL D 218 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 771 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: 1.36 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: 1.21 - 1.33: 2662 1.33 - 1.46: 1935 1.46 - 1.58: 4555 1.58 - 1.70: 0 1.70 - 1.82: 42 Bond restraints: 9194 Sorted by residual: bond pdb=" C ILE C 278 " pdb=" O ILE C 278 " ideal model delta sigma weight residual 1.236 1.211 0.025 1.04e-02 9.25e+03 5.72e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C ARG D 16 " pdb=" O ARG D 16 " ideal model delta sigma weight residual 1.234 1.215 0.020 1.28e-02 6.10e+03 2.36e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 ... (remaining 9189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 12276 1.50 - 3.00: 227 3.00 - 4.50: 25 4.50 - 6.00: 2 6.00 - 7.50: 3 Bond angle restraints: 12533 Sorted by residual: angle pdb=" N ALA C 296 " pdb=" CA ALA C 296 " pdb=" C ALA C 296 " ideal model delta sigma weight residual 107.88 112.34 -4.46 1.41e+00 5.03e-01 1.00e+01 angle pdb=" CA CYS C 154 " pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " ideal model delta sigma weight residual 114.40 121.59 -7.19 2.30e+00 1.89e-01 9.77e+00 angle pdb=" N LYS D 208 " pdb=" CA LYS D 208 " pdb=" C LYS D 208 " ideal model delta sigma weight residual 109.81 116.48 -6.67 2.21e+00 2.05e-01 9.11e+00 angle pdb=" C HIS F 204 " pdb=" N LYS F 205 " pdb=" CA LYS F 205 " ideal model delta sigma weight residual 120.09 123.47 -3.38 1.25e+00 6.40e-01 7.31e+00 angle pdb=" C LYS D 208 " pdb=" N PRO D 209 " pdb=" CA PRO D 209 " ideal model delta sigma weight residual 118.97 116.39 2.58 1.04e+00 9.25e-01 6.15e+00 ... (remaining 12528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 5495 33.93 - 67.86: 73 67.86 - 101.80: 10 101.80 - 135.73: 1 135.73 - 169.66: 1 Dihedral angle restraints: 5580 sinusoidal: 2260 harmonic: 3320 Sorted by residual: dihedral pdb=" CB GLU E 166 " pdb=" CG GLU E 166 " pdb=" CD GLU E 166 " pdb=" OE1 GLU E 166 " ideal model delta sinusoidal sigma weight residual 0.00 169.66 -169.66 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CB CYS G 215 " pdb=" SG CYS G 215 " pdb=" SG CYS F 131 " pdb=" CB CYS F 131 " ideal model delta sinusoidal sigma weight residual -86.00 -49.68 -36.32 1 1.00e+01 1.00e-02 1.86e+01 dihedral pdb=" CB GLU G 166 " pdb=" CG GLU G 166 " pdb=" CD GLU G 166 " pdb=" OE1 GLU G 166 " ideal model delta sinusoidal sigma weight residual 0.00 104.32 -104.32 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 5577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1230 0.057 - 0.113: 177 0.113 - 0.170: 9 0.170 - 0.226: 0 0.226 - 0.283: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA LYS D 208 " pdb=" N LYS D 208 " pdb=" C LYS D 208 " pdb=" CB LYS D 208 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ILE C 278 " pdb=" N ILE C 278 " pdb=" C ILE C 278 " pdb=" CB ILE C 278 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1415 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 95 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO E 96 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 153 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO D 154 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 154 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 154 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 95 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO G 96 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 96 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 96 " -0.017 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1916 2.79 - 3.31: 7168 3.31 - 3.84: 14328 3.84 - 4.37: 16082 4.37 - 4.90: 29061 Nonbonded interactions: 68555 Sorted by model distance: nonbonded pdb=" OH TYR G 37 " pdb=" OE1 GLN G 90 " model vdw 2.257 3.040 nonbonded pdb=" OD1 ASP F 73 " pdb=" OG SER F 75 " model vdw 2.260 3.040 nonbonded pdb=" O HIS C 83 " pdb=" OH TYR C 87 " model vdw 2.294 3.040 nonbonded pdb=" O PRO D 192 " pdb=" OG SER D 195 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP D 54 " pdb=" OG SER D 56 " model vdw 2.334 3.040 ... (remaining 68550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'D' and (resid 1 through 9 or resid 11 through 22 or resid 24 through 30 \ or resid 34 through 39 or resid 41 through 48 or resid 51 or resid 54 through 55 \ or resid 58 or resid 60 or resid 62 through 78 or resid 81 through 87 or resid \ 89 through 91 or resid 94 through 97 or resid 103 or resid 107 or resid 110 thro \ ugh 114 or resid 116 through 220)) selection = (chain 'F' and (resid 1 through 9 or resid 11 through 22 or resid 24 through 30 \ or resid 34 through 39 or resid 41 through 48 or resid 51 or resid 54 through 55 \ or resid 58 or resid 60 or resid 62 through 78 or resid 81 through 87 or resid \ 89 through 91 or resid 94 through 97 or resid 101 or resid 104 or resid 107 thro \ ugh 111 or resid 113 through 132 or resid 139 through 217)) } ncs_group { reference = (chain 'E' and (resid 2 or resid 5 through 8 or resid 11 through 12 or resid 14 \ or resid 16 or resid 18 or resid 20 or resid 23 through 28 or resid 30 through 3 \ 3 or resid 35 through 41 or resid 43 through 44 or resid 46 through 49 or resid \ 51 through 53 or resid 57 or resid 59 or resid 61 through 76 or resid 78 or resi \ d 80 through 84 or resid 86 through 90 or resid 93 or resid 95 or resid 98 throu \ gh 103 or resid 106 through 215)) selection = (chain 'G' and (resid 2 or resid 5 through 8 or resid 11 through 12 or resid 14 \ or resid 16 or resid 18 or resid 20 or resid 23 through 28 or resid 30 through 3 \ 1 or resid 33 through 34 or resid 36 through 42 or resid 44 through 45 or resid \ 47 through 50 or resid 52 through 54 or resid 58 or resid 60 or resid 62 through \ 77 or resid 79 or resid 81 through 85 or resid 87 through 91 or resid 94 or res \ id 96 or resid 98 through 103 or resid 106 through 215)) } 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=0.00 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.730 Find NCS groups from input model: 0.130 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 0.047 9215 Z= 0.123 Angle : 0.494 7.496 12583 Z= 0.264 Chirality : 0.041 0.283 1418 Planarity : 0.004 0.038 1593 Dihedral : 11.955 169.662 3407 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.70 % Allowed : 16.62 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.23), residues: 1131 helix: -4.06 (0.45), residues: 28 sheet: -0.79 (0.23), residues: 494 loop : -1.98 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 16 TYR 0.018 0.001 TYR C 276 PHE 0.004 0.001 PHE F 126 TRP 0.005 0.000 TRP C 293 HIS 0.002 0.000 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9194) covalent geometry : angle 0.49202 (12533) SS BOND : bond 0.00257 ( 13) SS BOND : angle 0.58746 ( 26) hydrogen bonds : bond 0.27192 ( 274) hydrogen bonds : angle 10.34248 ( 771) link_BETA1-4 : bond 0.00351 ( 4) link_BETA1-4 : angle 0.75390 ( 12) link_NAG-ASN : bond 0.00133 ( 4) link_NAG-ASN : angle 1.18497 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.343 Fit side-chains REVERT: C 169 MET cc_start: 0.6823 (mmt) cc_final: 0.6535 (mmt) REVERT: C 243 PHE cc_start: 0.7714 (t80) cc_final: 0.7507 (t80) REVERT: G 104 LYS cc_start: 0.8834 (tttt) cc_final: 0.8570 (tttp) REVERT: G 148 GLN cc_start: 0.7470 (mt0) cc_final: 0.7252 (mt0) REVERT: E 108 LYS cc_start: 0.8203 (tttp) cc_final: 0.7838 (ttmm) REVERT: D 152 TYR cc_start: 0.7418 (p90) cc_final: 0.7206 (p90) REVERT: D 160 SER cc_start: 0.8110 (p) cc_final: 0.7870 (t) REVERT: D 183 TYR cc_start: 0.8060 (m-80) cc_final: 0.7828 (m-80) REVERT: D 188 VAL cc_start: 0.8354 (t) cc_final: 0.8135 (m) outliers start: 7 outliers final: 3 residues processed: 157 average time/residue: 0.5644 time to fit residues: 94.7268 Evaluate side-chains 104 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain E residue 78 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0040 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 HIS C 100 GLN C 119 ASN C 209 ASN G 27 GLN G 148 GLN F 1 GLN F 57 ASN F 77 ASN F 175 GLN F 201 ASN E 27 GLN E 34 ASN E 148 GLN D 77 ASN D 99 GLN D 178 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115224 restraints weight = 11115.073| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.03 r_work: 0.3172 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9215 Z= 0.218 Angle : 0.689 9.236 12583 Z= 0.347 Chirality : 0.048 0.187 1418 Planarity : 0.006 0.052 1593 Dihedral : 4.502 49.930 1405 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.21 % Allowed : 18.12 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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: -1.22 (0.24), residues: 1131 helix: -3.50 (0.57), residues: 29 sheet: -0.14 (0.22), residues: 519 loop : -1.26 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 62 TYR 0.016 0.002 TYR F 95 PHE 0.016 0.002 PHE G 119 TRP 0.020 0.002 TRP F 101 HIS 0.009 0.002 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 9194) covalent geometry : angle 0.68504 (12533) SS BOND : bond 0.00696 ( 13) SS BOND : angle 1.27950 ( 26) hydrogen bonds : bond 0.03849 ( 274) hydrogen bonds : angle 6.55878 ( 771) link_BETA1-4 : bond 0.00660 ( 4) link_BETA1-4 : angle 1.31786 ( 12) link_NAG-ASN : bond 0.00261 ( 4) link_NAG-ASN : angle 1.58210 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 108 time to evaluate : 0.358 Fit side-chains REVERT: C 169 MET cc_start: 0.6810 (mmt) cc_final: 0.6508 (mmt) REVERT: C 283 LYS cc_start: 0.6914 (tttm) cc_final: 0.6584 (tttp) REVERT: C 290 TRP cc_start: 0.8265 (m100) cc_final: 0.8029 (m100) REVERT: G 148 GLN cc_start: 0.7784 (mt0) cc_final: 0.7467 (mt0) REVERT: G 155 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7538 (mp) REVERT: F 21 SER cc_start: 0.8930 (m) cc_final: 0.8710 (t) REVERT: E 108 LYS cc_start: 0.8337 (tttp) cc_final: 0.7851 (ttmm) REVERT: E 172 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.7931 (p) REVERT: D 155 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7978 (mt-10) REVERT: D 217 ARG cc_start: 0.6171 (tpt-90) cc_final: 0.5545 (tpp-160) outliers start: 52 outliers final: 29 residues processed: 149 average time/residue: 0.5594 time to fit residues: 88.8531 Evaluate side-chains 129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 200 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 256 HIS F 77 ASN F 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110721 restraints weight = 11126.597| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.13 r_work: 0.3085 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9215 Z= 0.167 Angle : 0.590 8.883 12583 Z= 0.299 Chirality : 0.045 0.156 1418 Planarity : 0.005 0.040 1593 Dihedral : 4.261 26.613 1401 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.11 % Allowed : 18.82 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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 (0.25), residues: 1131 helix: -3.43 (0.54), residues: 29 sheet: 0.24 (0.23), residues: 517 loop : -0.96 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 109 TYR 0.018 0.002 TYR D 152 PHE 0.011 0.002 PHE E 99 TRP 0.016 0.001 TRP F 101 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9194) covalent geometry : angle 0.58664 (12533) SS BOND : bond 0.00557 ( 13) SS BOND : angle 0.91093 ( 26) hydrogen bonds : bond 0.03699 ( 274) hydrogen bonds : angle 6.13862 ( 771) link_BETA1-4 : bond 0.00240 ( 4) link_BETA1-4 : angle 1.35770 ( 12) link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 1.53562 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 97 time to evaluate : 0.359 Fit side-chains REVERT: C 237 SER cc_start: 0.6085 (OUTLIER) cc_final: 0.5837 (t) REVERT: C 283 LYS cc_start: 0.7175 (tttm) cc_final: 0.6835 (tttp) REVERT: C 290 TRP cc_start: 0.8309 (m100) cc_final: 0.8056 (m100) REVERT: G 71 ASP cc_start: 0.8276 (m-30) cc_final: 0.8037 (m-30) REVERT: G 148 GLN cc_start: 0.7827 (mt0) cc_final: 0.7595 (mt0) REVERT: G 155 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7622 (mp) REVERT: F 21 SER cc_start: 0.8965 (m) cc_final: 0.8761 (t) REVERT: F 196 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7325 (tttt) REVERT: E 108 LYS cc_start: 0.8408 (tttp) cc_final: 0.7856 (ttmm) REVERT: E 172 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8007 (p) REVERT: D 34 MET cc_start: 0.9366 (mmt) cc_final: 0.9040 (mmm) REVERT: D 43 LYS cc_start: 0.8590 (mttp) cc_final: 0.8361 (mttt) REVERT: D 105 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: D 217 ARG cc_start: 0.6223 (tpt-90) cc_final: 0.5834 (tpp80) outliers start: 61 outliers final: 38 residues processed: 143 average time/residue: 0.5347 time to fit residues: 81.9541 Evaluate side-chains 136 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 93 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN F 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111298 restraints weight = 11188.643| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.22 r_work: 0.3091 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9215 Z= 0.126 Angle : 0.564 8.787 12583 Z= 0.281 Chirality : 0.044 0.165 1418 Planarity : 0.004 0.040 1593 Dihedral : 4.227 27.670 1401 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.81 % Allowed : 20.22 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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: -0.40 (0.25), residues: 1131 helix: -3.19 (0.57), residues: 29 sheet: 0.49 (0.23), residues: 512 loop : -0.77 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 110 TYR 0.022 0.001 TYR D 152 PHE 0.009 0.001 PHE C 141 TRP 0.015 0.001 TRP F 101 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9194) covalent geometry : angle 0.55902 (12533) SS BOND : bond 0.00427 ( 13) SS BOND : angle 0.84383 ( 26) hydrogen bonds : bond 0.02802 ( 274) hydrogen bonds : angle 5.77352 ( 771) link_BETA1-4 : bond 0.00180 ( 4) link_BETA1-4 : angle 1.56368 ( 12) link_NAG-ASN : bond 0.00773 ( 4) link_NAG-ASN : angle 1.68314 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 91 time to evaluate : 0.315 Fit side-chains REVERT: C 283 LYS cc_start: 0.7190 (tttm) cc_final: 0.6922 (tttp) REVERT: C 290 TRP cc_start: 0.8294 (m100) cc_final: 0.8029 (m100) REVERT: G 71 ASP cc_start: 0.8242 (m-30) cc_final: 0.7959 (m-30) REVERT: G 148 GLN cc_start: 0.7800 (mt0) cc_final: 0.7597 (mt0) REVERT: G 155 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7633 (mp) REVERT: F 99 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: F 184 SER cc_start: 0.9200 (m) cc_final: 0.8983 (t) REVERT: F 196 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7334 (tttt) REVERT: E 108 LYS cc_start: 0.8404 (tttp) cc_final: 0.7857 (ttmm) REVERT: E 172 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8051 (p) REVERT: D 34 MET cc_start: 0.9368 (mmt) cc_final: 0.9088 (mmm) REVERT: D 43 LYS cc_start: 0.8603 (mttp) cc_final: 0.8387 (mttt) REVERT: D 163 SER cc_start: 0.7376 (OUTLIER) cc_final: 0.7068 (p) REVERT: D 217 ARG cc_start: 0.6189 (tpt-90) cc_final: 0.5800 (tpp80) outliers start: 58 outliers final: 42 residues processed: 138 average time/residue: 0.4658 time to fit residues: 69.2699 Evaluate side-chains 133 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 86 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 200 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110515 restraints weight = 11206.424| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.21 r_work: 0.3079 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9215 Z= 0.139 Angle : 0.575 9.066 12583 Z= 0.287 Chirality : 0.044 0.157 1418 Planarity : 0.005 0.040 1593 Dihedral : 4.362 26.908 1401 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.61 % Allowed : 20.32 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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: -0.25 (0.25), residues: 1131 helix: -3.12 (0.60), residues: 29 sheet: 0.54 (0.23), residues: 525 loop : -0.64 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 18 TYR 0.023 0.001 TYR D 152 PHE 0.009 0.001 PHE E 99 TRP 0.015 0.001 TRP F 101 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9194) covalent geometry : angle 0.56845 (12533) SS BOND : bond 0.00447 ( 13) SS BOND : angle 0.90907 ( 26) hydrogen bonds : bond 0.02822 ( 274) hydrogen bonds : angle 5.59830 ( 771) link_BETA1-4 : bond 0.00271 ( 4) link_BETA1-4 : angle 1.75896 ( 12) link_NAG-ASN : bond 0.00614 ( 4) link_NAG-ASN : angle 2.04746 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 89 time to evaluate : 0.388 Fit side-chains REVERT: C 283 LYS cc_start: 0.7157 (tttm) cc_final: 0.6865 (tttp) REVERT: C 290 TRP cc_start: 0.8312 (m100) cc_final: 0.8064 (m100) REVERT: G 71 ASP cc_start: 0.8239 (m-30) cc_final: 0.7959 (m-30) REVERT: G 155 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7619 (mp) REVERT: F 99 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: F 184 SER cc_start: 0.9197 (m) cc_final: 0.8977 (t) REVERT: F 196 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7358 (tttt) REVERT: E 108 LYS cc_start: 0.8411 (tttp) cc_final: 0.7852 (ttmm) REVERT: E 171 ASP cc_start: 0.8285 (m-30) cc_final: 0.8051 (m-30) REVERT: E 172 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8058 (p) REVERT: E 214 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.4790 (tp30) REVERT: D 34 MET cc_start: 0.9367 (mmt) cc_final: 0.9063 (mmm) REVERT: D 43 LYS cc_start: 0.8603 (mttp) cc_final: 0.8341 (mttt) REVERT: D 105 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: D 163 SER cc_start: 0.7399 (OUTLIER) cc_final: 0.7108 (p) REVERT: D 217 ARG cc_start: 0.6156 (tpt-90) cc_final: 0.5789 (tpp80) outliers start: 66 outliers final: 45 residues processed: 144 average time/residue: 0.4817 time to fit residues: 75.0048 Evaluate side-chains 140 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 88 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN E 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106164 restraints weight = 11181.295| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.16 r_work: 0.3051 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 9215 Z= 0.228 Angle : 0.673 9.964 12583 Z= 0.334 Chirality : 0.048 0.259 1418 Planarity : 0.005 0.040 1593 Dihedral : 5.158 27.630 1401 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.61 % Allowed : 20.42 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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: -0.31 (0.25), residues: 1131 helix: -3.06 (0.61), residues: 29 sheet: 0.55 (0.23), residues: 526 loop : -0.74 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 109 TYR 0.022 0.002 TYR D 152 PHE 0.015 0.002 PHE F 100 TRP 0.020 0.002 TRP F 101 HIS 0.008 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 9194) covalent geometry : angle 0.66312 (12533) SS BOND : bond 0.00637 ( 13) SS BOND : angle 1.14022 ( 26) hydrogen bonds : bond 0.03192 ( 274) hydrogen bonds : angle 5.85360 ( 771) link_BETA1-4 : bond 0.00580 ( 4) link_BETA1-4 : angle 2.01975 ( 12) link_NAG-ASN : bond 0.00284 ( 4) link_NAG-ASN : angle 2.84671 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 94 time to evaluate : 0.347 Fit side-chains REVERT: C 283 LYS cc_start: 0.7066 (tttm) cc_final: 0.6823 (tttp) REVERT: C 290 TRP cc_start: 0.8388 (m100) cc_final: 0.8094 (m100) REVERT: G 71 ASP cc_start: 0.8194 (m-30) cc_final: 0.7871 (m-30) REVERT: G 155 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7640 (mp) REVERT: F 99 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: F 196 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7387 (tttt) REVERT: E 24 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.6892 (mtm110) REVERT: E 106 GLU cc_start: 0.8371 (pt0) cc_final: 0.7946 (pt0) REVERT: E 171 ASP cc_start: 0.8295 (m-30) cc_final: 0.8072 (m-30) REVERT: E 172 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.7989 (p) REVERT: D 34 MET cc_start: 0.9390 (mmt) cc_final: 0.9081 (mmm) REVERT: D 105 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: D 163 SER cc_start: 0.7499 (OUTLIER) cc_final: 0.7206 (p) REVERT: D 217 ARG cc_start: 0.6121 (tpt-90) cc_final: 0.5711 (tpp80) outliers start: 66 outliers final: 48 residues processed: 147 average time/residue: 0.4667 time to fit residues: 74.2097 Evaluate side-chains 146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 92 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108577 restraints weight = 11228.805| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.18 r_work: 0.3086 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9215 Z= 0.125 Angle : 0.597 10.506 12583 Z= 0.293 Chirality : 0.045 0.226 1418 Planarity : 0.004 0.041 1593 Dihedral : 4.728 27.153 1401 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.81 % Allowed : 21.92 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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: -0.19 (0.25), residues: 1131 helix: -2.90 (0.65), residues: 29 sheet: 0.54 (0.23), residues: 526 loop : -0.56 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 214 TYR 0.021 0.001 TYR D 152 PHE 0.009 0.001 PHE E 99 TRP 0.016 0.001 TRP F 101 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9194) covalent geometry : angle 0.57858 (12533) SS BOND : bond 0.00437 ( 13) SS BOND : angle 0.88840 ( 26) hydrogen bonds : bond 0.02677 ( 274) hydrogen bonds : angle 5.57100 ( 771) link_BETA1-4 : bond 0.00267 ( 4) link_BETA1-4 : angle 2.09477 ( 12) link_NAG-ASN : bond 0.00360 ( 4) link_NAG-ASN : angle 4.29456 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 86 time to evaluate : 0.302 Fit side-chains REVERT: C 283 LYS cc_start: 0.7053 (tttm) cc_final: 0.6784 (tttp) REVERT: C 290 TRP cc_start: 0.8355 (m100) cc_final: 0.8040 (m100) REVERT: G 71 ASP cc_start: 0.8164 (m-30) cc_final: 0.7862 (m-30) REVERT: G 155 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7622 (mp) REVERT: F 99 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: F 184 SER cc_start: 0.9189 (m) cc_final: 0.8947 (t) REVERT: F 196 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7387 (tttt) REVERT: E 106 GLU cc_start: 0.8381 (pt0) cc_final: 0.7993 (pt0) REVERT: E 155 LEU cc_start: 0.7677 (tm) cc_final: 0.7389 (tt) REVERT: E 172 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.7973 (p) REVERT: E 214 GLU cc_start: 0.5429 (OUTLIER) cc_final: 0.4848 (tp30) REVERT: D 34 MET cc_start: 0.9327 (mmt) cc_final: 0.9092 (mmm) REVERT: D 105 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: D 112 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: D 163 SER cc_start: 0.7558 (OUTLIER) cc_final: 0.7287 (p) REVERT: D 217 ARG cc_start: 0.6064 (tpt-90) cc_final: 0.5680 (tpp80) outliers start: 58 outliers final: 44 residues processed: 131 average time/residue: 0.4717 time to fit residues: 66.7209 Evaluate side-chains 138 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 86 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106094 restraints weight = 11252.347| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.31 r_work: 0.3051 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9215 Z= 0.204 Angle : 0.678 16.149 12583 Z= 0.330 Chirality : 0.047 0.213 1418 Planarity : 0.005 0.041 1593 Dihedral : 5.137 35.356 1401 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.41 % Allowed : 21.02 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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: -0.28 (0.25), residues: 1131 helix: -3.02 (0.57), residues: 35 sheet: 0.48 (0.23), residues: 536 loop : -0.60 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 109 TYR 0.019 0.002 TYR F 95 PHE 0.012 0.002 PHE F 100 TRP 0.018 0.002 TRP F 101 HIS 0.007 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 9194) covalent geometry : angle 0.64677 (12533) SS BOND : bond 0.00590 ( 13) SS BOND : angle 1.17260 ( 26) hydrogen bonds : bond 0.03016 ( 274) hydrogen bonds : angle 5.71749 ( 771) link_BETA1-4 : bond 0.00319 ( 4) link_BETA1-4 : angle 2.46321 ( 12) link_NAG-ASN : bond 0.00241 ( 4) link_NAG-ASN : angle 6.01436 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 88 time to evaluate : 0.343 Fit side-chains REVERT: C 283 LYS cc_start: 0.7066 (tttm) cc_final: 0.6852 (tttp) REVERT: C 290 TRP cc_start: 0.8388 (m100) cc_final: 0.8112 (m100) REVERT: G 71 ASP cc_start: 0.8180 (m-30) cc_final: 0.7862 (m-30) REVERT: G 155 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7658 (mp) REVERT: F 99 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: F 109 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: F 184 SER cc_start: 0.9229 (m) cc_final: 0.8976 (t) REVERT: F 196 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7421 (tttt) REVERT: E 106 GLU cc_start: 0.8405 (pt0) cc_final: 0.7980 (pt0) REVERT: E 155 LEU cc_start: 0.7696 (tm) cc_final: 0.7395 (tt) REVERT: E 172 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.7996 (p) REVERT: E 214 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.4844 (tp30) REVERT: D 34 MET cc_start: 0.9379 (mmt) cc_final: 0.9083 (mmm) REVERT: D 105 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: D 163 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7309 (p) REVERT: D 217 ARG cc_start: 0.6086 (tpt-90) cc_final: 0.5657 (tpp80) outliers start: 64 outliers final: 51 residues processed: 140 average time/residue: 0.4551 time to fit residues: 68.8640 Evaluate side-chains 147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 88 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107594 restraints weight = 11156.198| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.29 r_work: 0.3101 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9215 Z= 0.132 Angle : 0.594 12.724 12583 Z= 0.293 Chirality : 0.046 0.430 1418 Planarity : 0.004 0.042 1593 Dihedral : 4.964 39.543 1401 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 6.01 % Allowed : 21.72 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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: -0.16 (0.26), residues: 1131 helix: -2.92 (0.59), residues: 35 sheet: 0.55 (0.23), residues: 536 loop : -0.51 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 214 TYR 0.019 0.001 TYR D 152 PHE 0.009 0.001 PHE E 99 TRP 0.017 0.001 TRP F 101 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9194) covalent geometry : angle 0.57545 (12533) SS BOND : bond 0.00421 ( 13) SS BOND : angle 0.88598 ( 26) hydrogen bonds : bond 0.02698 ( 274) hydrogen bonds : angle 5.55051 ( 771) link_BETA1-4 : bond 0.00185 ( 4) link_BETA1-4 : angle 1.72493 ( 12) link_NAG-ASN : bond 0.01599 ( 4) link_NAG-ASN : angle 4.36542 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 85 time to evaluate : 0.346 Fit side-chains REVERT: C 283 LYS cc_start: 0.7068 (tttm) cc_final: 0.6800 (tttp) REVERT: C 290 TRP cc_start: 0.8367 (m100) cc_final: 0.8029 (m100) REVERT: G 71 ASP cc_start: 0.8090 (m-30) cc_final: 0.7794 (m-30) REVERT: G 148 GLN cc_start: 0.7902 (mt0) cc_final: 0.7589 (mt0) REVERT: G 155 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7617 (mp) REVERT: F 13 GLN cc_start: 0.8680 (tt0) cc_final: 0.8455 (mt0) REVERT: F 99 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: F 184 SER cc_start: 0.9170 (m) cc_final: 0.8915 (t) REVERT: F 196 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7415 (tttt) REVERT: E 106 GLU cc_start: 0.8347 (pt0) cc_final: 0.7918 (pt0) REVERT: E 155 LEU cc_start: 0.7670 (tm) cc_final: 0.7370 (tt) REVERT: E 172 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.7970 (p) REVERT: E 214 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.4816 (tp30) REVERT: D 34 MET cc_start: 0.9306 (mmt) cc_final: 0.9021 (mmm) REVERT: D 105 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: D 163 SER cc_start: 0.7538 (OUTLIER) cc_final: 0.7301 (p) REVERT: D 217 ARG cc_start: 0.6056 (tpt-90) cc_final: 0.5672 (tpp80) outliers start: 60 outliers final: 49 residues processed: 134 average time/residue: 0.4635 time to fit residues: 67.1279 Evaluate side-chains 140 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 84 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.0570 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106311 restraints weight = 11198.634| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.36 r_work: 0.3083 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9215 Z= 0.182 Angle : 0.632 12.319 12583 Z= 0.314 Chirality : 0.047 0.363 1418 Planarity : 0.005 0.042 1593 Dihedral : 5.093 38.933 1401 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.91 % Allowed : 21.72 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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: -0.23 (0.25), residues: 1131 helix: -2.94 (0.58), residues: 35 sheet: 0.46 (0.22), residues: 538 loop : -0.51 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 109 TYR 0.018 0.002 TYR D 152 PHE 0.011 0.002 PHE C 141 TRP 0.018 0.002 TRP F 101 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 9194) covalent geometry : angle 0.61588 (12533) SS BOND : bond 0.00525 ( 13) SS BOND : angle 1.06926 ( 26) hydrogen bonds : bond 0.02892 ( 274) hydrogen bonds : angle 5.64537 ( 771) link_BETA1-4 : bond 0.00271 ( 4) link_BETA1-4 : angle 1.77726 ( 12) link_NAG-ASN : bond 0.01599 ( 4) link_NAG-ASN : angle 4.19860 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 85 time to evaluate : 0.272 Fit side-chains REVERT: C 283 LYS cc_start: 0.7150 (tttm) cc_final: 0.6943 (tttp) REVERT: C 290 TRP cc_start: 0.8399 (m100) cc_final: 0.8124 (m100) REVERT: G 71 ASP cc_start: 0.8190 (m-30) cc_final: 0.7893 (m-30) REVERT: G 155 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7661 (mp) REVERT: F 99 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: F 184 SER cc_start: 0.9189 (m) cc_final: 0.8935 (t) REVERT: F 196 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7483 (tttt) REVERT: E 106 GLU cc_start: 0.8387 (pt0) cc_final: 0.7990 (pt0) REVERT: E 155 LEU cc_start: 0.7688 (tm) cc_final: 0.7383 (tt) REVERT: E 172 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8072 (p) REVERT: E 214 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.4789 (tp30) REVERT: D 34 MET cc_start: 0.9389 (mmt) cc_final: 0.9097 (mmm) REVERT: D 105 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: D 163 SER cc_start: 0.7537 (OUTLIER) cc_final: 0.7305 (p) REVERT: D 217 ARG cc_start: 0.6143 (tpt-90) cc_final: 0.5712 (tpp80) outliers start: 59 outliers final: 48 residues processed: 133 average time/residue: 0.4697 time to fit residues: 67.3290 Evaluate side-chains 140 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 85 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108329 restraints weight = 11040.015| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.36 r_work: 0.3090 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9215 Z= 0.121 Angle : 0.577 12.244 12583 Z= 0.286 Chirality : 0.045 0.365 1418 Planarity : 0.004 0.042 1593 Dihedral : 4.762 37.354 1401 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.51 % Allowed : 22.32 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % 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: -0.10 (0.26), residues: 1131 helix: -2.88 (0.59), residues: 35 sheet: 0.54 (0.23), residues: 540 loop : -0.42 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 214 TYR 0.019 0.001 TYR D 152 PHE 0.009 0.001 PHE C 125 TRP 0.015 0.001 TRP F 101 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9194) covalent geometry : angle 0.56023 (12533) SS BOND : bond 0.00389 ( 13) SS BOND : angle 0.81878 ( 26) hydrogen bonds : bond 0.02569 ( 274) hydrogen bonds : angle 5.43495 ( 771) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 1.56592 ( 12) link_NAG-ASN : bond 0.01513 ( 4) link_NAG-ASN : angle 4.12240 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.09 seconds wall clock time: 60 minutes 39.28 seconds (3639.28 seconds total)