Starting phenix.real_space_refine on Thu Jul 31 21:50:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7e_27228/07_2025/8d7e_27228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7e_27228/07_2025/8d7e_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_27228/07_2025/8d7e_27228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7e_27228/07_2025/8d7e_27228.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7e_27228/07_2025/8d7e_27228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7e_27228/07_2025/8d7e_27228.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.04, per 1000 atoms: 0.67 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.38 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: 2.73 Time building geometry restraints manager: 2.76 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.330 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:72.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.000 TRP C 293 HIS 0.002 0.000 HIS D 207 PHE 0.004 0.001 PHE F 126 TYR 0.018 0.001 TYR C 276 ARG 0.002 0.000 ARG D 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 4) link_NAG-ASN : angle 1.18497 ( 12) link_BETA1-4 : bond 0.00351 ( 4) link_BETA1-4 : angle 0.75390 ( 12) hydrogen bonds : bond 0.27192 ( 274) hydrogen bonds : angle 10.34248 ( 771) SS BOND : bond 0.00257 ( 13) SS BOND : angle 0.58746 ( 26) covalent geometry : bond 0.00235 ( 9194) covalent geometry : angle 0.49202 (12533) *********************** 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 : 1.495 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: 0.8835 (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: 1.5702 time to fit residues: 266.0875 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 : 1.552 ------------------------------------------------------------------------------- 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 94 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 57 ASN F 77 ASN F 175 GLN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108925 restraints weight = 11126.494| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.30 r_work: 0.3114 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- 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: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9215 Z= 0.288 Angle : 0.750 10.137 12583 Z= 0.380 Chirality : 0.051 0.201 1418 Planarity : 0.006 0.055 1593 Dihedral : 4.819 47.034 1405 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 6.01 % Allowed : 17.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.24), residues: 1131 helix: -3.56 (0.55), residues: 29 sheet: -0.19 (0.22), residues: 519 loop : -1.36 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 101 HIS 0.010 0.003 HIS C 99 PHE 0.020 0.002 PHE F 100 TYR 0.019 0.003 TYR F 95 ARG 0.006 0.001 ARG G 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 4) link_NAG-ASN : angle 1.84835 ( 12) link_BETA1-4 : bond 0.00401 ( 4) link_BETA1-4 : angle 1.45605 ( 12) hydrogen bonds : bond 0.04795 ( 274) hydrogen bonds : angle 6.84184 ( 771) SS BOND : bond 0.00799 ( 13) SS BOND : angle 1.37710 ( 26) covalent geometry : bond 0.00709 ( 9194) covalent geometry : angle 0.74567 (12533) *********************** 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 169 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 109 time to evaluate : 0.893 Fit side-chains REVERT: C 283 LYS cc_start: 0.6887 (tttm) cc_final: 0.6621 (tttp) REVERT: C 290 TRP cc_start: 0.8249 (m100) cc_final: 0.7948 (m100) REVERT: G 18 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8089 (ttm170) REVERT: G 148 GLN cc_start: 0.7828 (mt0) cc_final: 0.7456 (mt0) REVERT: G 155 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7624 (mp) REVERT: F 21 SER cc_start: 0.8912 (m) cc_final: 0.8668 (t) REVERT: E 79 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8206 (mp10) REVERT: E 108 LYS cc_start: 0.8343 (tttp) cc_final: 0.7842 (ttmm) REVERT: E 172 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.7951 (p) REVERT: D 155 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8059 (mt-10) REVERT: D 187 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8560 (t) outliers start: 60 outliers final: 35 residues processed: 158 average time/residue: 1.1686 time to fit residues: 198.7633 Evaluate side-chains 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ASP 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 18 ARG Chi-restraints excluded: chain G residue 95 SER 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 135 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 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 85 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 0.0370 chunk 97 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS C 119 ASN F 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113743 restraints weight = 11162.643| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.25 r_work: 0.3158 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9215 Z= 0.102 Angle : 0.526 7.902 12583 Z= 0.267 Chirality : 0.043 0.148 1418 Planarity : 0.004 0.041 1593 Dihedral : 4.024 25.292 1401 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.40 % Allowed : 20.42 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1131 helix: -3.45 (0.56), residues: 29 sheet: 0.23 (0.23), residues: 519 loop : -0.93 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 101 HIS 0.004 0.001 HIS D 171 PHE 0.011 0.001 PHE C 125 TYR 0.020 0.001 TYR D 152 ARG 0.003 0.000 ARG C 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 4) link_NAG-ASN : angle 1.28785 ( 12) link_BETA1-4 : bond 0.00259 ( 4) link_BETA1-4 : angle 1.21721 ( 12) hydrogen bonds : bond 0.03176 ( 274) hydrogen bonds : angle 5.99524 ( 771) SS BOND : bond 0.00329 ( 13) SS BOND : angle 0.62766 ( 26) covalent geometry : bond 0.00234 ( 9194) covalent geometry : angle 0.52386 (12533) *********************** 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 144 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.951 Fit side-chains REVERT: C 237 SER cc_start: 0.5953 (OUTLIER) cc_final: 0.5722 (t) REVERT: C 283 LYS cc_start: 0.7075 (tttm) cc_final: 0.6781 (tttp) REVERT: G 18 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8143 (ttm170) REVERT: G 71 ASP cc_start: 0.8202 (m-30) cc_final: 0.7892 (m-30) REVERT: G 148 GLN cc_start: 0.7774 (mt0) cc_final: 0.7475 (mt0) REVERT: G 155 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7605 (mp) REVERT: F 99 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: F 184 SER cc_start: 0.9181 (m) cc_final: 0.8943 (t) REVERT: F 196 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7261 (tttt) REVERT: E 108 LYS cc_start: 0.8348 (tttp) cc_final: 0.7787 (ttmm) REVERT: E 172 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8009 (p) REVERT: D 43 LYS cc_start: 0.8539 (mttp) cc_final: 0.8325 (mttt) REVERT: D 105 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: D 163 SER cc_start: 0.7352 (OUTLIER) cc_final: 0.7034 (p) REVERT: D 217 ARG cc_start: 0.6095 (tpt-90) cc_final: 0.5723 (tpp80) outliers start: 44 outliers final: 20 residues processed: 133 average time/residue: 1.5121 time to fit residues: 215.2977 Evaluate side-chains 118 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 237 SER 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 F residue 2 VAL Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 30 SER 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 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 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 70 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112395 restraints weight = 11118.203| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.22 r_work: 0.3144 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3087 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= 0.115 Angle : 0.558 8.739 12583 Z= 0.275 Chirality : 0.044 0.187 1418 Planarity : 0.004 0.040 1593 Dihedral : 4.177 26.503 1401 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.50 % Allowed : 21.42 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1131 helix: -3.28 (0.57), residues: 29 sheet: 0.45 (0.23), residues: 519 loop : -0.70 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 101 HIS 0.005 0.001 HIS C 99 PHE 0.009 0.001 PHE F 100 TYR 0.025 0.001 TYR D 152 ARG 0.002 0.000 ARG G 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 4) link_NAG-ASN : angle 1.63200 ( 12) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 1.83811 ( 12) hydrogen bonds : bond 0.02772 ( 274) hydrogen bonds : angle 5.66734 ( 771) SS BOND : bond 0.00404 ( 13) SS BOND : angle 0.76483 ( 26) covalent geometry : bond 0.00281 ( 9194) covalent geometry : angle 0.55256 (12533) *********************** 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 139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.882 Fit side-chains REVERT: C 237 SER cc_start: 0.5999 (OUTLIER) cc_final: 0.5794 (t) REVERT: G 18 ARG cc_start: 0.8466 (ttm110) cc_final: 0.8163 (ttm170) REVERT: G 148 GLN cc_start: 0.7763 (mt0) cc_final: 0.7546 (mt0) REVERT: G 155 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7622 (mp) REVERT: F 99 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: F 184 SER cc_start: 0.9193 (m) cc_final: 0.8965 (t) REVERT: F 196 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7275 (tttt) REVERT: E 108 LYS cc_start: 0.8364 (tttp) cc_final: 0.7798 (ttmm) REVERT: E 172 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.7965 (p) REVERT: D 43 LYS cc_start: 0.8556 (mttp) cc_final: 0.8275 (mttt) REVERT: D 163 SER cc_start: 0.7378 (OUTLIER) cc_final: 0.7064 (p) REVERT: D 217 ARG cc_start: 0.6081 (tpt-90) cc_final: 0.5677 (tpp80) outliers start: 45 outliers final: 31 residues processed: 128 average time/residue: 1.0744 time to fit residues: 147.9626 Evaluate side-chains 126 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 24 ARG Chi-restraints excluded: chain G residue 34 LEU 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 196 LYS 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 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 83 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 163 SER 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 1 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 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 F 77 ASN E 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107348 restraints weight = 11173.922| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.26 r_work: 0.3071 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 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 = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9215 Z= 0.196 Angle : 0.628 10.523 12583 Z= 0.315 Chirality : 0.046 0.167 1418 Planarity : 0.005 0.041 1593 Dihedral : 4.643 26.608 1401 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.61 % Allowed : 21.12 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1131 helix: -3.25 (0.60), residues: 29 sheet: 0.50 (0.23), residues: 523 loop : -0.71 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 101 HIS 0.007 0.001 HIS C 99 PHE 0.014 0.002 PHE F 100 TYR 0.024 0.002 TYR D 152 ARG 0.003 0.001 ARG G 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 4) link_NAG-ASN : angle 1.71161 ( 12) link_BETA1-4 : bond 0.00172 ( 4) link_BETA1-4 : angle 1.71146 ( 12) hydrogen bonds : bond 0.03126 ( 274) hydrogen bonds : angle 5.83629 ( 771) SS BOND : bond 0.00566 ( 13) SS BOND : angle 1.07852 ( 26) covalent geometry : bond 0.00485 ( 9194) covalent geometry : angle 0.62306 (12533) *********************** 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 148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 92 time to evaluate : 1.029 Fit side-chains REVERT: G 71 ASP cc_start: 0.8160 (m-30) cc_final: 0.7834 (m-30) REVERT: G 148 GLN cc_start: 0.7815 (mt0) cc_final: 0.7583 (mt0) REVERT: G 155 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7622 (mp) REVERT: F 99 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: F 184 SER cc_start: 0.9190 (m) cc_final: 0.8959 (t) REVERT: F 196 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7262 (tttt) REVERT: E 24 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.6761 (mtm110) REVERT: E 108 LYS cc_start: 0.8360 (tttp) cc_final: 0.8096 (ttmp) REVERT: E 141 TYR cc_start: 0.8471 (t80) cc_final: 0.8157 (t80) REVERT: E 171 ASP cc_start: 0.8253 (m-30) cc_final: 0.7997 (m-30) REVERT: E 172 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.7922 (p) REVERT: E 214 GLU cc_start: 0.5432 (OUTLIER) cc_final: 0.4776 (tp30) REVERT: D 163 SER cc_start: 0.7451 (OUTLIER) cc_final: 0.7153 (p) REVERT: D 217 ARG cc_start: 0.6081 (tpt-90) cc_final: 0.5712 (tpp80) outliers start: 56 outliers final: 40 residues processed: 137 average time/residue: 1.1204 time to fit residues: 165.2320 Evaluate side-chains 134 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 88 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 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 95 SER 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 154 VAL 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 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 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 50 ILE 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 158 THR Chi-restraints excluded: chain D residue 163 SER 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 9 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.144987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111021 restraints weight = 11054.712| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.24 r_work: 0.3086 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 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 = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3529 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= 0.114 Angle : 0.563 8.856 12583 Z= 0.278 Chirality : 0.044 0.193 1418 Planarity : 0.004 0.041 1593 Dihedral : 4.385 26.700 1401 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.11 % Allowed : 21.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1131 helix: -3.15 (0.61), residues: 29 sheet: 0.56 (0.23), residues: 531 loop : -0.56 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 101 HIS 0.004 0.001 HIS C 99 PHE 0.009 0.001 PHE E 99 TYR 0.025 0.001 TYR D 152 ARG 0.006 0.000 ARG G 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 4) link_NAG-ASN : angle 2.90091 ( 12) link_BETA1-4 : bond 0.00389 ( 4) link_BETA1-4 : angle 1.97611 ( 12) hydrogen bonds : bond 0.02643 ( 274) hydrogen bonds : angle 5.53252 ( 771) SS BOND : bond 0.00380 ( 13) SS BOND : angle 0.78669 ( 26) covalent geometry : bond 0.00277 ( 9194) covalent geometry : angle 0.55269 (12533) *********************** 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 141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 90 time to evaluate : 1.022 Fit side-chains REVERT: G 71 ASP cc_start: 0.8209 (m-30) cc_final: 0.7907 (m-30) REVERT: G 155 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7604 (mp) REVERT: F 99 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: F 184 SER cc_start: 0.9188 (m) cc_final: 0.8943 (t) REVERT: F 196 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7381 (tttt) REVERT: E 106 GLU cc_start: 0.8305 (pt0) cc_final: 0.7946 (pt0) REVERT: E 171 ASP cc_start: 0.8277 (m-30) cc_final: 0.8046 (m-30) REVERT: E 172 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8032 (p) REVERT: E 214 GLU cc_start: 0.5366 (OUTLIER) cc_final: 0.4745 (tp30) REVERT: D 43 LYS cc_start: 0.8595 (mttp) cc_final: 0.8345 (mttt) REVERT: D 112 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: D 163 SER cc_start: 0.7434 (OUTLIER) cc_final: 0.7143 (p) REVERT: D 217 ARG cc_start: 0.6119 (tpt-90) cc_final: 0.5722 (tpp80) outliers start: 51 outliers final: 38 residues processed: 130 average time/residue: 1.0054 time to fit residues: 141.7216 Evaluate side-chains 131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 86 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 34 LEU 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 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 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 76 SER 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 50 ILE 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 112 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 163 SER 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 88 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 107 optimal weight: 0.0000 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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 = 0.144336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110097 restraints weight = 11184.444| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.22 r_work: 0.3102 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- 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: 0.8411 moved from start: 0.3648 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= 0.134 Angle : 0.593 10.280 12583 Z= 0.291 Chirality : 0.045 0.200 1418 Planarity : 0.005 0.041 1593 Dihedral : 4.522 26.158 1401 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.61 % Allowed : 21.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1131 helix: -2.95 (0.63), residues: 29 sheet: 0.64 (0.23), residues: 531 loop : -0.50 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 101 HIS 0.005 0.001 HIS C 99 PHE 0.009 0.001 PHE E 99 TYR 0.022 0.001 TYR D 152 ARG 0.005 0.000 ARG G 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 4) link_NAG-ASN : angle 4.10199 ( 12) link_BETA1-4 : bond 0.00409 ( 4) link_BETA1-4 : angle 2.18500 ( 12) hydrogen bonds : bond 0.02702 ( 274) hydrogen bonds : angle 5.47722 ( 771) SS BOND : bond 0.00431 ( 13) SS BOND : angle 0.84547 ( 26) covalent geometry : bond 0.00330 ( 9194) covalent geometry : angle 0.57487 (12533) *********************** 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 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 89 time to evaluate : 0.928 Fit side-chains REVERT: G 71 ASP cc_start: 0.8208 (m-30) cc_final: 0.7921 (m-30) REVERT: G 155 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7630 (mp) REVERT: F 99 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: F 109 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: F 184 SER cc_start: 0.9176 (m) cc_final: 0.8963 (t) REVERT: F 196 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7389 (tttt) REVERT: E 106 GLU cc_start: 0.8361 (pt0) cc_final: 0.7970 (pt0) REVERT: E 171 ASP cc_start: 0.8303 (m-30) cc_final: 0.8067 (m-30) REVERT: E 172 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8032 (p) REVERT: D 43 LYS cc_start: 0.8603 (mttp) cc_final: 0.8358 (mttt) REVERT: D 112 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: D 163 SER cc_start: 0.7466 (OUTLIER) cc_final: 0.7177 (p) REVERT: D 217 ARG cc_start: 0.6161 (tpt-90) cc_final: 0.5751 (tpp80) outliers start: 56 outliers final: 43 residues processed: 133 average time/residue: 0.9584 time to fit residues: 139.0258 Evaluate side-chains 138 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 88 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 GLU 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 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 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 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 50 ILE 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 112 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 163 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 F 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112332 restraints weight = 11258.894| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.20 r_work: 0.3162 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9215 Z= 0.092 Angle : 0.578 16.610 12583 Z= 0.276 Chirality : 0.043 0.230 1418 Planarity : 0.004 0.041 1593 Dihedral : 4.412 32.608 1401 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.01 % Allowed : 22.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1131 helix: -2.81 (0.66), residues: 29 sheet: 0.70 (0.23), residues: 524 loop : -0.35 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 101 HIS 0.002 0.001 HIS C 99 PHE 0.011 0.001 PHE C 141 TYR 0.022 0.001 TYR D 152 ARG 0.005 0.000 ARG G 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 4) link_NAG-ASN : angle 5.99441 ( 12) link_BETA1-4 : bond 0.00407 ( 4) link_BETA1-4 : angle 2.16715 ( 12) hydrogen bonds : bond 0.02460 ( 274) hydrogen bonds : angle 5.26712 ( 771) SS BOND : bond 0.00308 ( 13) SS BOND : angle 0.60760 ( 26) covalent geometry : bond 0.00215 ( 9194) covalent geometry : angle 0.54386 (12533) *********************** 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 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 87 time to evaluate : 0.885 Fit side-chains REVERT: G 71 ASP cc_start: 0.8120 (m-30) cc_final: 0.7840 (m-30) REVERT: G 155 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7576 (mp) REVERT: F 99 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: F 184 SER cc_start: 0.9153 (m) cc_final: 0.8907 (t) REVERT: E 106 GLU cc_start: 0.8301 (pt0) cc_final: 0.7923 (pt0) REVERT: E 155 LEU cc_start: 0.7681 (tm) cc_final: 0.7428 (tt) REVERT: E 172 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8002 (p) REVERT: E 214 GLU cc_start: 0.5263 (OUTLIER) cc_final: 0.4464 (tp30) REVERT: D 43 LYS cc_start: 0.8544 (mttp) cc_final: 0.8288 (mttt) REVERT: D 163 SER cc_start: 0.7529 (OUTLIER) cc_final: 0.7261 (p) REVERT: D 217 ARG cc_start: 0.6076 (tpt-90) cc_final: 0.5663 (tpp80) outliers start: 50 outliers final: 38 residues processed: 127 average time/residue: 1.0251 time to fit residues: 140.9005 Evaluate side-chains 128 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 85 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 G residue 14 SER Chi-restraints excluded: chain G residue 34 LEU 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 6 GLU 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 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 199 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 76 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 163 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 94 optimal weight: 4.9990 overall best weight: 1.3960 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.143592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107897 restraints weight = 11184.312| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.20 r_work: 0.3080 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 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 = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9215 Z= 0.165 Angle : 0.613 12.451 12583 Z= 0.302 Chirality : 0.047 0.408 1418 Planarity : 0.005 0.041 1593 Dihedral : 4.752 37.104 1401 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.11 % Allowed : 22.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1131 helix: -2.72 (0.67), residues: 29 sheet: 0.64 (0.23), residues: 533 loop : -0.35 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 101 HIS 0.006 0.001 HIS C 99 PHE 0.010 0.001 PHE F 100 TYR 0.026 0.002 TYR D 152 ARG 0.005 0.000 ARG G 55 Details of bonding type rmsd link_NAG-ASN : bond 0.01737 ( 4) link_NAG-ASN : angle 4.42547 ( 12) link_BETA1-4 : bond 0.00324 ( 4) link_BETA1-4 : angle 1.68091 ( 12) hydrogen bonds : bond 0.02777 ( 274) hydrogen bonds : angle 5.45899 ( 771) SS BOND : bond 0.00499 ( 13) SS BOND : angle 0.91038 ( 26) covalent geometry : bond 0.00406 ( 9194) covalent geometry : angle 0.59554 (12533) *********************** 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 136 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 85 time to evaluate : 0.932 Fit side-chains REVERT: G 71 ASP cc_start: 0.8201 (m-30) cc_final: 0.7893 (m-30) REVERT: G 155 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7616 (mp) REVERT: F 99 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: F 109 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: F 184 SER cc_start: 0.9169 (m) cc_final: 0.8951 (t) REVERT: E 106 GLU cc_start: 0.8371 (pt0) cc_final: 0.7991 (pt0) REVERT: E 155 LEU cc_start: 0.7742 (tm) cc_final: 0.7455 (tt) REVERT: E 172 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.7956 (p) REVERT: E 214 GLU cc_start: 0.5239 (OUTLIER) cc_final: 0.4423 (tp30) REVERT: D 43 LYS cc_start: 0.8556 (mttp) cc_final: 0.8342 (mttt) REVERT: D 112 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7168 (pm20) REVERT: D 163 SER cc_start: 0.7579 (OUTLIER) cc_final: 0.7304 (p) REVERT: D 217 ARG cc_start: 0.6112 (tpt-90) cc_final: 0.5661 (tpp80) outliers start: 51 outliers final: 41 residues processed: 125 average time/residue: 0.9711 time to fit residues: 131.6056 Evaluate side-chains 132 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 84 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG 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 6 GLU 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 109 GLN 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 199 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 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 50 ILE 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 112 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 158 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.144350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107626 restraints weight = 11217.302| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.32 r_work: 0.3106 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 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 = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3805 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= 0.133 Angle : 0.582 12.409 12583 Z= 0.287 Chirality : 0.045 0.333 1418 Planarity : 0.004 0.041 1593 Dihedral : 4.648 36.496 1401 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.60 % Allowed : 22.72 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1131 helix: -2.69 (0.67), residues: 29 sheet: 0.65 (0.23), residues: 533 loop : -0.32 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 101 HIS 0.005 0.001 HIS C 99 PHE 0.009 0.001 PHE C 141 TYR 0.027 0.001 TYR D 152 ARG 0.004 0.000 ARG G 55 Details of bonding type rmsd link_NAG-ASN : bond 0.01549 ( 4) link_NAG-ASN : angle 4.22945 ( 12) link_BETA1-4 : bond 0.00276 ( 4) link_BETA1-4 : angle 1.62542 ( 12) hydrogen bonds : bond 0.02611 ( 274) hydrogen bonds : angle 5.39701 ( 771) SS BOND : bond 0.00414 ( 13) SS BOND : angle 0.77964 ( 26) covalent geometry : bond 0.00325 ( 9194) covalent geometry : angle 0.56490 (12533) ********************** 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 130 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 0.763 Fit side-chains REVERT: G 71 ASP cc_start: 0.8125 (m-30) cc_final: 0.7818 (m-30) REVERT: G 155 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7599 (mp) REVERT: F 99 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: F 184 SER cc_start: 0.9136 (m) cc_final: 0.8916 (t) REVERT: E 106 GLU cc_start: 0.8317 (pt0) cc_final: 0.7922 (pt0) REVERT: E 155 LEU cc_start: 0.7712 (tm) cc_final: 0.7428 (tt) REVERT: E 172 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.7903 (p) REVERT: E 214 GLU cc_start: 0.5258 (OUTLIER) cc_final: 0.4499 (tp30) REVERT: D 43 LYS cc_start: 0.8505 (mttp) cc_final: 0.8271 (mttt) REVERT: D 112 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: D 163 SER cc_start: 0.7562 (OUTLIER) cc_final: 0.7319 (p) REVERT: D 217 ARG cc_start: 0.6032 (tpt-90) cc_final: 0.5626 (tpp80) outliers start: 46 outliers final: 38 residues processed: 121 average time/residue: 1.2558 time to fit residues: 164.0290 Evaluate side-chains 127 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG 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 6 GLU 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 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 199 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 76 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 163 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 20 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.143203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107350 restraints weight = 11227.579| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.38 r_work: 0.3093 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 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 = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9215 Z= 0.167 Angle : 0.617 12.130 12583 Z= 0.305 Chirality : 0.046 0.347 1418 Planarity : 0.005 0.041 1593 Dihedral : 4.811 37.629 1401 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.70 % Allowed : 22.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1131 helix: -2.95 (0.56), residues: 35 sheet: 0.64 (0.23), residues: 532 loop : -0.35 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 101 HIS 0.006 0.001 HIS C 99 PHE 0.010 0.001 PHE F 29 TYR 0.026 0.002 TYR D 152 ARG 0.005 0.001 ARG G 55 Details of bonding type rmsd link_NAG-ASN : bond 0.01414 ( 4) link_NAG-ASN : angle 4.12681 ( 12) link_BETA1-4 : bond 0.00219 ( 4) link_BETA1-4 : angle 1.61000 ( 12) hydrogen bonds : bond 0.02784 ( 274) hydrogen bonds : angle 5.49869 ( 771) SS BOND : bond 0.00546 ( 13) SS BOND : angle 1.07866 ( 26) covalent geometry : bond 0.00414 ( 9194) covalent geometry : angle 0.60082 (12533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9263.21 seconds wall clock time: 168 minutes 31.21 seconds (10111.21 seconds total)