Starting phenix.real_space_refine on Fri Jul 3 12:24:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s0n_54416/07_2026/9s0n_54416_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s0n_54416/07_2026/9s0n_54416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s0n_54416/07_2026/9s0n_54416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s0n_54416/07_2026/9s0n_54416.map" model { file = "/net/cci-nas-00/data/ceres_data/9s0n_54416/07_2026/9s0n_54416_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s0n_54416/07_2026/9s0n_54416_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 3 5.21 5 S 62 5.16 5 C 8610 2.51 5 N 2333 2.21 5 O 2617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13650 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain breaks: 1 Chain: "a" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2220 Classifications: {'peptide': 279} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 268} Chain: "b" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2220 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain: "c" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2220 Classifications: {'peptide': 279} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 268} Chain: "d" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2173 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Chain: "e" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2173 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "f" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2220 Classifications: {'peptide': 279} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 268} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1' AGS a 401 " occ=0.00 ... (29 atoms not shown) pdb=" S1G AGS a 401 " occ=0.00 residue: pdb="MG MG a 402 " occ=0.00 residue: pdb=" C1' AGS b 401 " occ=0.00 ... (29 atoms not shown) pdb=" S1G AGS b 401 " occ=0.00 residue: pdb="MG MG b 402 " occ=0.00 residue: pdb=" C1' AGS f 401 " occ=0.00 ... (29 atoms not shown) pdb=" S1G AGS f 401 " occ=0.00 residue: pdb="MG MG f 402 " occ=0.00 Time building chain proxies: 2.62, per 1000 atoms: 0.19 Number of scatterers: 13650 At special positions: 0 Unit cell: (83.325, 127.05, 121.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 25 15.00 Mg 3 11.99 O 2617 8.00 N 2333 7.00 C 8610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 475.3 milliseconds 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3134 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 51.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'a' and resid 18 through 35 Processing helix chain 'a' and resid 38 through 46 Processing helix chain 'a' and resid 46 through 54 removed outlier: 3.709A pdb=" N TYR a 50 " --> pdb=" O ASP a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 78 removed outlier: 3.563A pdb=" N SER a 61 " --> pdb=" O SER a 57 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS a 64 " --> pdb=" O ARG a 60 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY a 71 " --> pdb=" O LEU a 67 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR a 77 " --> pdb=" O ILE a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 85 Processing helix chain 'a' and resid 92 through 95 Processing helix chain 'a' and resid 96 through 105 Processing helix chain 'a' and resid 108 through 121 Processing helix chain 'a' and resid 139 through 151 removed outlier: 3.718A pdb=" N VAL a 151 " --> pdb=" O ILE a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 166 through 170 removed outlier: 3.884A pdb=" N VAL a 170 " --> pdb=" O ASN a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 195 removed outlier: 4.700A pdb=" N GLU a 188 " --> pdb=" O ALA a 184 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER a 189 " --> pdb=" O LYS a 185 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 243 Processing helix chain 'a' and resid 255 through 259 removed outlier: 4.336A pdb=" N GLY a 259 " --> pdb=" O HIS a 256 " (cutoff:3.500A) Processing helix chain 'a' and resid 262 through 276 Processing helix chain 'b' and resid 18 through 35 Processing helix chain 'b' and resid 38 through 46 Processing helix chain 'b' and resid 46 through 54 Processing helix chain 'b' and resid 56 through 78 removed outlier: 4.204A pdb=" N LYS b 64 " --> pdb=" O ARG b 60 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 85 Processing helix chain 'b' and resid 96 through 105 Processing helix chain 'b' and resid 108 through 121 Processing helix chain 'b' and resid 139 through 151 removed outlier: 3.696A pdb=" N VAL b 151 " --> pdb=" O ILE b 147 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 195 removed outlier: 3.778A pdb=" N ALA b 192 " --> pdb=" O GLU b 188 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 243 Processing helix chain 'b' and resid 262 through 276 Processing helix chain 'c' and resid 18 through 35 Processing helix chain 'c' and resid 38 through 46 Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 56 through 78 removed outlier: 4.424A pdb=" N LYS c 64 " --> pdb=" O ARG c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 85 removed outlier: 3.768A pdb=" N TYR c 83 " --> pdb=" O THR c 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 105 Processing helix chain 'c' and resid 108 through 121 Processing helix chain 'c' and resid 138 through 151 removed outlier: 3.697A pdb=" N VAL c 151 " --> pdb=" O ILE c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 195 removed outlier: 3.737A pdb=" N ALA c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 237 through 243 Processing helix chain 'c' and resid 262 through 276 Processing helix chain 'd' and resid 19 through 28 removed outlier: 3.822A pdb=" N ARG d 23 " --> pdb=" O LYS d 19 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 35 Processing helix chain 'd' and resid 38 through 46 Processing helix chain 'd' and resid 46 through 55 removed outlier: 3.760A pdb=" N TYR d 50 " --> pdb=" O ASP d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 Processing helix chain 'd' and resid 62 through 70 Processing helix chain 'd' and resid 71 through 78 Processing helix chain 'd' and resid 80 through 85 Processing helix chain 'd' and resid 96 through 105 Processing helix chain 'd' and resid 108 through 121 Processing helix chain 'd' and resid 124 through 127 Processing helix chain 'd' and resid 139 through 151 removed outlier: 3.765A pdb=" N VAL d 151 " --> pdb=" O ILE d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 164 through 170 removed outlier: 4.056A pdb=" N ASP d 168 " --> pdb=" O PRO d 165 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL d 170 " --> pdb=" O ASN d 167 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 194 removed outlier: 3.861A pdb=" N ALA d 192 " --> pdb=" O GLU d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 237 through 243 removed outlier: 3.589A pdb=" N ASP d 243 " --> pdb=" O GLN d 239 " (cutoff:3.500A) Processing helix chain 'd' and resid 262 through 276 Processing helix chain 'e' and resid 18 through 35 Processing helix chain 'e' and resid 38 through 46 Processing helix chain 'e' and resid 46 through 54 Processing helix chain 'e' and resid 56 through 78 removed outlier: 3.932A pdb=" N LYS e 64 " --> pdb=" O ARG e 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 85 removed outlier: 3.908A pdb=" N TYR e 83 " --> pdb=" O THR e 79 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 95 Processing helix chain 'e' and resid 96 through 105 Processing helix chain 'e' and resid 108 through 121 Processing helix chain 'e' and resid 124 through 127 Processing helix chain 'e' and resid 142 through 151 removed outlier: 3.598A pdb=" N VAL e 151 " --> pdb=" O ILE e 147 " (cutoff:3.500A) Processing helix chain 'e' and resid 166 through 170 removed outlier: 4.149A pdb=" N VAL e 170 " --> pdb=" O ASN e 167 " (cutoff:3.500A) Processing helix chain 'e' and resid 186 through 194 removed outlier: 4.123A pdb=" N ALA e 190 " --> pdb=" O VAL e 186 " (cutoff:3.500A) Processing helix chain 'e' and resid 234 through 236 No H-bonds generated for 'chain 'e' and resid 234 through 236' Processing helix chain 'e' and resid 237 through 245 removed outlier: 3.559A pdb=" N GLN e 242 " --> pdb=" O GLN e 238 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP e 243 " --> pdb=" O GLN e 239 " (cutoff:3.500A) Processing helix chain 'e' and resid 255 through 259 removed outlier: 3.570A pdb=" N GLY e 259 " --> pdb=" O HIS e 256 " (cutoff:3.500A) Processing helix chain 'e' and resid 262 through 276 Processing helix chain 'f' and resid 18 through 35 Processing helix chain 'f' and resid 38 through 46 Processing helix chain 'f' and resid 46 through 54 Processing helix chain 'f' and resid 56 through 78 removed outlier: 4.249A pdb=" N LYS f 64 " --> pdb=" O ARG f 60 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY f 71 " --> pdb=" O LEU f 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR f 77 " --> pdb=" O ILE f 73 " (cutoff:3.500A) Processing helix chain 'f' and resid 80 through 85 Processing helix chain 'f' and resid 96 through 105 Processing helix chain 'f' and resid 108 through 121 Processing helix chain 'f' and resid 139 through 151 removed outlier: 3.585A pdb=" N VAL f 151 " --> pdb=" O ILE f 147 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 170 removed outlier: 4.245A pdb=" N VAL f 170 " --> pdb=" O ASN f 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 186 through 195 removed outlier: 3.818A pdb=" N ALA f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) Processing helix chain 'f' and resid 237 through 243 Processing helix chain 'f' and resid 262 through 276 Processing sheet with id=AA1, first strand: chain 'a' and resid 154 through 156 removed outlier: 6.187A pdb=" N GLY a 155 " --> pdb=" O TRP a 176 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE a 175 " --> pdb=" O ILE a 217 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR a 219 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP a 177 " --> pdb=" O THR a 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 200 through 203 removed outlier: 4.057A pdb=" N GLN a 203 " --> pdb=" O SER a 207 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER a 207 " --> pdb=" O GLN a 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 227 through 228 Processing sheet with id=AA4, first strand: chain 'b' and resid 154 through 156 removed outlier: 6.098A pdb=" N GLY b 155 " --> pdb=" O TRP b 176 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE b 175 " --> pdb=" O ILE b 217 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR b 219 " --> pdb=" O ILE b 175 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP b 177 " --> pdb=" O THR b 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 200 through 203 removed outlier: 5.977A pdb=" N VAL b 201 " --> pdb=" O SER b 208 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER b 208 " --> pdb=" O VAL b 201 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN b 203 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 227 through 229 removed outlier: 3.507A pdb=" N THR b 234 " --> pdb=" O VAL b 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 154 through 156 removed outlier: 6.311A pdb=" N GLY c 155 " --> pdb=" O TRP c 176 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE c 175 " --> pdb=" O ILE c 217 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR c 219 " --> pdb=" O ILE c 175 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP c 177 " --> pdb=" O THR c 219 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE c 130 " --> pdb=" O VAL c 218 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N SER c 220 " --> pdb=" O ILE c 130 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU c 132 " --> pdb=" O SER c 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 200 through 203 removed outlier: 4.350A pdb=" N GLN c 203 " --> pdb=" O SER c 207 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER c 207 " --> pdb=" O GLN c 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 227 through 228 Processing sheet with id=AB1, first strand: chain 'd' and resid 154 through 157 removed outlier: 6.316A pdb=" N ILE d 175 " --> pdb=" O ILE d 217 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR d 219 " --> pdb=" O ILE d 175 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TRP d 177 " --> pdb=" O THR d 219 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE d 130 " --> pdb=" O VAL d 218 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER d 220 " --> pdb=" O ILE d 130 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU d 132 " --> pdb=" O SER d 220 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE d 246 " --> pdb=" O THR d 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 199 through 203 removed outlier: 3.949A pdb=" N VAL d 199 " --> pdb=" O ILE d 211 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN d 203 " --> pdb=" O SER d 207 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER d 207 " --> pdb=" O GLN d 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'e' and resid 155 through 157 removed outlier: 6.364A pdb=" N GLY e 155 " --> pdb=" O TRP e 176 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE e 175 " --> pdb=" O ILE e 217 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE e 130 " --> pdb=" O VAL e 216 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR e 129 " --> pdb=" O PHE e 246 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE e 248 " --> pdb=" O THR e 129 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP e 131 " --> pdb=" O PHE e 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'e' and resid 200 through 201 Processing sheet with id=AB5, first strand: chain 'f' and resid 154 through 156 removed outlier: 6.077A pdb=" N GLY f 155 " --> pdb=" O TRP f 176 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE f 175 " --> pdb=" O ILE f 217 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR f 219 " --> pdb=" O ILE f 175 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TRP f 177 " --> pdb=" O THR f 219 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE f 130 " --> pdb=" O VAL f 218 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 200 through 203 removed outlier: 4.311A pdb=" N GLN f 203 " --> pdb=" O SER f 207 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER f 207 " --> pdb=" O GLN f 203 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 227 through 229 564 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 4350 1.35 - 1.48: 3686 1.48 - 1.62: 5866 1.62 - 1.75: 0 1.75 - 1.89: 98 Bond restraints: 14000 Sorted by residual: bond pdb=" O3B AGS a 401 " pdb=" PB AGS a 401 " ideal model delta sigma weight residual 1.673 1.531 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" O3B AGS b 401 " pdb=" PB AGS b 401 " ideal model delta sigma weight residual 1.673 1.532 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" O3B AGS f 401 " pdb=" PB AGS f 401 " ideal model delta sigma weight residual 1.673 1.543 0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" O3A AGS a 401 " pdb=" PA AGS a 401 " ideal model delta sigma weight residual 1.664 1.536 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" O3A AGS b 401 " pdb=" PA AGS b 401 " ideal model delta sigma weight residual 1.664 1.540 0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 13995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 18379 2.74 - 5.48: 570 5.48 - 8.22: 57 8.22 - 10.96: 28 10.96 - 13.70: 5 Bond angle restraints: 19039 Sorted by residual: angle pdb=" CB HIS a 237 " pdb=" CG HIS a 237 " pdb=" CD2 HIS a 237 " ideal model delta sigma weight residual 131.20 124.54 6.66 1.30e+00 5.92e-01 2.63e+01 angle pdb=" O5' DG H 101 " pdb=" C5' DG H 101 " pdb=" C4' DG H 101 " ideal model delta sigma weight residual 109.40 113.26 -3.86 8.00e-01 1.56e+00 2.33e+01 angle pdb=" N LYS b 140 " pdb=" CA LYS b 140 " pdb=" C LYS b 140 " ideal model delta sigma weight residual 111.36 116.57 -5.21 1.09e+00 8.42e-01 2.29e+01 angle pdb=" CB HIS b 149 " pdb=" CG HIS b 149 " pdb=" CD2 HIS b 149 " ideal model delta sigma weight residual 131.20 125.01 6.19 1.30e+00 5.92e-01 2.27e+01 angle pdb=" C4' DT H 28 " pdb=" O4' DT H 28 " pdb=" C1' DT H 28 " ideal model delta sigma weight residual 110.10 105.38 4.72 1.00e+00 1.00e+00 2.22e+01 ... (remaining 19034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.70: 8067 34.70 - 69.40: 244 69.40 - 104.10: 25 104.10 - 138.79: 0 138.79 - 173.49: 3 Dihedral angle restraints: 8339 sinusoidal: 3506 harmonic: 4833 Sorted by residual: dihedral pdb=" C THR f 137 " pdb=" N THR f 137 " pdb=" CA THR f 137 " pdb=" CB THR f 137 " ideal model delta harmonic sigma weight residual -122.00 -137.04 15.04 0 2.50e+00 1.60e-01 3.62e+01 dihedral pdb=" N THR f 137 " pdb=" C THR f 137 " pdb=" CA THR f 137 " pdb=" CB THR f 137 " ideal model delta harmonic sigma weight residual 123.40 135.84 -12.44 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" O1A AGS f 401 " pdb=" O3A AGS f 401 " pdb=" PA AGS f 401 " pdb=" PB AGS f 401 " ideal model delta sinusoidal sigma weight residual 82.37 -104.35 -173.28 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1916 0.109 - 0.217: 127 0.217 - 0.326: 11 0.326 - 0.434: 16 0.434 - 0.543: 3 Chirality restraints: 2073 Sorted by residual: chirality pdb=" CA THR f 137 " pdb=" N THR f 137 " pdb=" C THR f 137 " pdb=" CB THR f 137 " both_signs ideal model delta sigma weight residual False 2.53 1.98 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" P DT H 24 " pdb=" OP1 DT H 24 " pdb=" OP2 DT H 24 " pdb=" O5' DT H 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" P DA H 98 " pdb=" OP1 DA H 98 " pdb=" OP2 DA H 98 " pdb=" O5' DA H 98 " both_signs ideal model delta sigma weight residual True 2.34 -2.78 -0.44 2.00e-01 2.50e+01 4.95e+00 ... (remaining 2070 not shown) Planarity restraints: 2357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP c 177 " -0.039 2.00e-02 2.50e+03 3.96e-02 3.92e+01 pdb=" CG TRP c 177 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP c 177 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP c 177 " 0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP c 177 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP c 177 " 0.044 2.00e-02 2.50e+03 pdb=" CE3 TRP c 177 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 177 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 177 " -0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP c 177 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS b 149 " 0.067 2.00e-02 2.50e+03 4.94e-02 3.67e+01 pdb=" CG HIS b 149 " -0.080 2.00e-02 2.50e+03 pdb=" ND1 HIS b 149 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 HIS b 149 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS b 149 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS b 149 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AGS f 401 " 0.078 2.00e-02 2.50e+03 3.16e-02 2.74e+01 pdb=" C2 AGS f 401 " -0.015 2.00e-02 2.50e+03 pdb=" C4 AGS f 401 " -0.021 2.00e-02 2.50e+03 pdb=" C5 AGS f 401 " -0.007 2.00e-02 2.50e+03 pdb=" C6 AGS f 401 " 0.019 2.00e-02 2.50e+03 pdb=" C8 AGS f 401 " -0.024 2.00e-02 2.50e+03 pdb=" N1 AGS f 401 " 0.009 2.00e-02 2.50e+03 pdb=" N3 AGS f 401 " -0.029 2.00e-02 2.50e+03 pdb=" N6 AGS f 401 " 0.036 2.00e-02 2.50e+03 pdb=" N7 AGS f 401 " -0.019 2.00e-02 2.50e+03 pdb=" N9 AGS f 401 " -0.027 2.00e-02 2.50e+03 ... (remaining 2354 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 11 2.47 - 3.08: 9557 3.08 - 3.69: 20634 3.69 - 4.29: 30952 4.29 - 4.90: 50315 Nonbonded interactions: 111469 Sorted by model distance: nonbonded pdb=" O1A AGS b 401 " pdb="MG MG b 402 " model vdw 1.868 2.170 nonbonded pdb=" OG1 THR b 141 " pdb="MG MG b 402 " model vdw 1.906 2.170 nonbonded pdb=" O2B AGS a 401 " pdb="MG MG a 402 " model vdw 1.919 2.170 nonbonded pdb=" OG1 THR f 141 " pdb="MG MG f 402 " model vdw 1.921 2.170 nonbonded pdb=" O2B AGS f 401 " pdb="MG MG f 402 " model vdw 1.929 2.170 ... (remaining 111464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 12 through 203 or resid 207 through 227 or resid 234 throu \ gh 288)) selection = (chain 'b' and (resid 12 through 203 or resid 207 through 227 or resid 234 throu \ gh 288)) selection = (chain 'c' and (resid 12 through 203 or resid 207 through 227 or resid 234 throu \ gh 288)) selection = (chain 'd' and (resid 12 through 203 or resid 207 through 288)) selection = (chain 'e' and (resid 12 through 227 or resid 234 through 288)) selection = (chain 'f' and (resid 12 through 203 or resid 207 through 227 or resid 234 throu \ gh 288)) } 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.070 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 14000 Z= 0.367 Angle : 1.098 13.703 19039 Z= 0.635 Chirality : 0.071 0.543 2073 Planarity : 0.008 0.111 2357 Dihedral : 16.361 173.493 5205 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 0.84 % Allowed : 7.53 % Favored : 91.63 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1642 helix: -0.13 (0.18), residues: 748 sheet: 0.52 (0.37), residues: 205 loop : -0.11 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.004 ARG f 244 TYR 0.031 0.005 TYR d 107 PHE 0.028 0.002 PHE f 258 TRP 0.066 0.005 TRP c 177 HIS 0.007 0.001 HIS b 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.37 (14000) covalent geometry : angle 1.09766 / 0.63 (19039) hydrogen bonds : bond 0.18740 / 18.53 ( 564) hydrogen bonds : angle 6.61222 / 6.17 ( 1635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 185 LYS cc_start: 0.9253 (tttp) cc_final: 0.8739 (tttm) REVERT: b 252 ARG cc_start: 0.8796 (tpp80) cc_final: 0.8570 (tpp80) REVERT: c 25 MET cc_start: 0.9143 (mtp) cc_final: 0.8741 (mtm) REVERT: c 68 ASP cc_start: 0.8583 (t70) cc_final: 0.8204 (t0) REVERT: c 162 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8263 (mm-30) REVERT: c 179 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: c 181 LYS cc_start: 0.8469 (ptmt) cc_final: 0.8268 (ptmt) REVERT: c 224 MET cc_start: 0.8623 (tpt) cc_final: 0.8217 (tpt) REVERT: c 281 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8233 (mt-10) REVERT: d 272 TRP cc_start: 0.6980 (t-100) cc_final: 0.6733 (t-100) REVERT: e 17 ARG cc_start: 0.9101 (mmm-85) cc_final: 0.8877 (mmt90) REVERT: e 97 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8670 (mtp-110) REVERT: e 149 HIS cc_start: 0.9286 (m90) cc_final: 0.8925 (m-70) REVERT: e 154 TYR cc_start: 0.8860 (p90) cc_final: 0.8448 (p90) REVERT: e 178 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7201 (pp20) REVERT: e 250 LEU cc_start: 0.7304 (tp) cc_final: 0.6757 (tp) REVERT: f 198 LYS cc_start: 0.8337 (tptt) cc_final: 0.8031 (tmmt) REVERT: f 241 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7701 (mm) outliers start: 12 outliers final: 6 residues processed: 162 average time/residue: 0.1229 time to fit residues: 27.5120 Evaluate side-chains 136 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 159 TRP Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain c residue 154 TYR Chi-restraints excluded: chain c residue 179 GLU Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 97 ARG Chi-restraints excluded: chain e residue 158 ASN Chi-restraints excluded: chain e residue 178 GLU Chi-restraints excluded: chain f residue 241 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 167 ASN c 221 ASN d 69 ASN ** e 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.138454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094826 restraints weight = 27905.623| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.37 r_work: 0.3219 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14000 Z= 0.167 Angle : 0.599 7.015 19039 Z= 0.326 Chirality : 0.047 0.340 2073 Planarity : 0.004 0.036 2357 Dihedral : 14.556 176.603 2057 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.19 % Favored : 97.75 % Rotamer: Outliers : 1.67 % Allowed : 7.46 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1642 helix: 1.01 (0.19), residues: 749 sheet: 0.75 (0.38), residues: 197 loop : -0.15 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 252 TYR 0.014 0.002 TYR c 99 PHE 0.019 0.002 PHE b 246 TRP 0.019 0.001 TRP e 176 HIS 0.004 0.001 HIS b 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (14000) covalent geometry : angle 0.59878 / 0.33 (19039) hydrogen bonds : bond 0.05449 / 5.26 ( 564) hydrogen bonds : angle 4.89792 / 4.59 ( 1635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 185 LYS cc_start: 0.9331 (tttp) cc_final: 0.8842 (tttm) REVERT: b 252 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8619 (tpp80) REVERT: c 25 MET cc_start: 0.9068 (mtp) cc_final: 0.8579 (mtm) REVERT: c 162 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8211 (mm-30) REVERT: c 178 GLU cc_start: 0.7948 (tp30) cc_final: 0.7157 (mt-10) REVERT: c 179 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: c 181 LYS cc_start: 0.8582 (ptmt) cc_final: 0.8110 (ptmm) REVERT: c 224 MET cc_start: 0.8662 (tpt) cc_final: 0.8148 (tpt) REVERT: c 281 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8242 (mt-10) REVERT: d 41 GLN cc_start: 0.8820 (mt0) cc_final: 0.8556 (mt0) REVERT: e 17 ARG cc_start: 0.9174 (mmm-85) cc_final: 0.8943 (mpt-90) REVERT: e 98 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8469 (pt) REVERT: e 149 HIS cc_start: 0.9244 (m90) cc_final: 0.8904 (m-70) REVERT: e 176 TRP cc_start: 0.7656 (t60) cc_final: 0.7410 (t60) REVERT: e 250 LEU cc_start: 0.7412 (tp) cc_final: 0.6847 (tp) REVERT: f 210 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6966 (pt0) outliers start: 24 outliers final: 12 residues processed: 151 average time/residue: 0.1247 time to fit residues: 26.7831 Evaluate side-chains 128 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 159 TRP Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 245 MET Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain c residue 154 TYR Chi-restraints excluded: chain c residue 179 GLU Chi-restraints excluded: chain c residue 219 THR Chi-restraints excluded: chain c residue 221 ASN Chi-restraints excluded: chain d residue 246 PHE Chi-restraints excluded: chain e residue 98 ILE Chi-restraints excluded: chain e residue 158 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 158 ASN d 96 ASN d 276 HIS ** e 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.139187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095906 restraints weight = 27741.692| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.38 r_work: 0.3234 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14000 Z= 0.123 Angle : 0.531 6.716 19039 Z= 0.287 Chirality : 0.045 0.339 2073 Planarity : 0.003 0.034 2357 Dihedral : 13.932 176.643 2045 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 1.26 % Allowed : 8.09 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1642 helix: 1.28 (0.19), residues: 760 sheet: 0.73 (0.38), residues: 199 loop : -0.14 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG f 252 TYR 0.013 0.001 TYR a 285 PHE 0.014 0.001 PHE e 246 TRP 0.018 0.001 TRP d 272 HIS 0.006 0.001 HIS e 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (14000) covalent geometry : angle 0.53081 / 0.29 (19039) hydrogen bonds : bond 0.04233 / 4.06 ( 564) hydrogen bonds : angle 4.50377 / 4.19 ( 1635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 212 ASP cc_start: 0.8673 (m-30) cc_final: 0.8356 (m-30) REVERT: b 185 LYS cc_start: 0.9308 (tttp) cc_final: 0.8826 (tttm) REVERT: b 252 ARG cc_start: 0.8812 (tpp80) cc_final: 0.8609 (tpp80) REVERT: c 25 MET cc_start: 0.9023 (mtp) cc_final: 0.8560 (mtm) REVERT: c 162 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8190 (mm-30) REVERT: c 178 GLU cc_start: 0.8016 (tp30) cc_final: 0.7315 (mt-10) REVERT: c 224 MET cc_start: 0.8676 (tpt) cc_final: 0.8158 (tpt) REVERT: d 41 GLN cc_start: 0.8812 (mt0) cc_final: 0.8574 (mt0) REVERT: d 245 MET cc_start: -0.0986 (tpp) cc_final: -0.1212 (mmt) REVERT: e 98 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8389 (pt) REVERT: e 117 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7799 (pp) REVERT: e 149 HIS cc_start: 0.9271 (m90) cc_final: 0.8923 (m-70) REVERT: e 168 ASP cc_start: 0.8962 (t0) cc_final: 0.8632 (t70) outliers start: 18 outliers final: 11 residues processed: 147 average time/residue: 0.1265 time to fit residues: 25.9893 Evaluate side-chains 133 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 221 ASN Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain c residue 221 ASN Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 246 PHE Chi-restraints excluded: chain e residue 98 ILE Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain f residue 182 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 3 optimal weight: 0.0980 chunk 120 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 158 ASN e 237 HIS f 167 ASN f 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.139088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095800 restraints weight = 27528.241| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.31 r_work: 0.3241 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14000 Z= 0.115 Angle : 0.503 6.312 19039 Z= 0.272 Chirality : 0.044 0.341 2073 Planarity : 0.003 0.032 2357 Dihedral : 13.443 176.728 2036 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 1.46 % Allowed : 8.58 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.21), residues: 1642 helix: 1.44 (0.19), residues: 758 sheet: 0.68 (0.38), residues: 201 loop : -0.17 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 271 TYR 0.012 0.001 TYR b 107 PHE 0.013 0.001 PHE e 246 TRP 0.036 0.001 TRP e 176 HIS 0.006 0.001 HIS e 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (14000) covalent geometry : angle 0.50346 / 0.27 (19039) hydrogen bonds : bond 0.03681 / 3.52 ( 564) hydrogen bonds : angle 4.30640 / 4.00 ( 1635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: a 212 ASP cc_start: 0.8639 (m-30) cc_final: 0.8330 (m-30) REVERT: b 178 GLU cc_start: 0.7606 (tp30) cc_final: 0.7395 (tp30) REVERT: b 185 LYS cc_start: 0.9304 (tttp) cc_final: 0.8834 (tttm) REVERT: b 219 THR cc_start: 0.8986 (m) cc_final: 0.8630 (p) REVERT: c 25 MET cc_start: 0.8970 (mtp) cc_final: 0.8515 (mtm) REVERT: c 162 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8182 (mm-30) REVERT: c 178 GLU cc_start: 0.7979 (tp30) cc_final: 0.7266 (mm-30) REVERT: c 181 LYS cc_start: 0.8638 (ptmt) cc_final: 0.8432 (ptmt) REVERT: c 224 MET cc_start: 0.8689 (tpt) cc_final: 0.8163 (tpt) REVERT: d 41 GLN cc_start: 0.8799 (mt0) cc_final: 0.8541 (mt0) REVERT: e 98 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8365 (pt) REVERT: e 117 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7829 (pp) REVERT: e 149 HIS cc_start: 0.9260 (m90) cc_final: 0.8928 (m-70) REVERT: e 168 ASP cc_start: 0.8925 (t0) cc_final: 0.8617 (t70) REVERT: e 237 HIS cc_start: 0.7396 (t70) cc_final: 0.7103 (t-170) REVERT: e 250 LEU cc_start: 0.7429 (tp) cc_final: 0.7052 (tp) outliers start: 21 outliers final: 13 residues processed: 142 average time/residue: 0.1306 time to fit residues: 25.8291 Evaluate side-chains 131 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 221 ASN Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 246 PHE Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 98 ILE Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain f residue 182 MET Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 219 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 106 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 140 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 158 ASN d 54 ASN ** e 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.134816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091274 restraints weight = 28197.757| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.35 r_work: 0.3153 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14000 Z= 0.235 Angle : 0.596 8.904 19039 Z= 0.320 Chirality : 0.048 0.353 2073 Planarity : 0.004 0.096 2357 Dihedral : 13.403 175.763 2036 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 2.02 % Allowed : 9.41 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1642 helix: 1.14 (0.19), residues: 762 sheet: 0.62 (0.38), residues: 199 loop : -0.29 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG e 252 TYR 0.015 0.002 TYR d 50 PHE 0.020 0.002 PHE b 246 TRP 0.021 0.001 TRP e 176 HIS 0.009 0.001 HIS e 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 (14000) covalent geometry : angle 0.59644 / 0.32 (19039) hydrogen bonds : bond 0.04300 / 4.14 ( 564) hydrogen bonds : angle 4.47373 / 4.22 ( 1635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 219 THR cc_start: 0.9034 (m) cc_final: 0.8549 (p) REVERT: c 25 MET cc_start: 0.9034 (mtp) cc_final: 0.8545 (mtm) REVERT: c 154 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8377 (p90) REVERT: c 162 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8244 (mm-30) REVERT: c 178 GLU cc_start: 0.8037 (tp30) cc_final: 0.7227 (mt-10) REVERT: c 179 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: c 181 LYS cc_start: 0.8598 (ptmt) cc_final: 0.8339 (ptmm) REVERT: c 185 LYS cc_start: 0.9351 (mmmt) cc_final: 0.9011 (tptp) REVERT: c 221 ASN cc_start: 0.8481 (t0) cc_final: 0.8268 (t0) REVERT: c 224 MET cc_start: 0.8546 (tpt) cc_final: 0.7934 (tpt) REVERT: d 41 GLN cc_start: 0.8769 (mt0) cc_final: 0.8386 (mt0) REVERT: e 117 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7978 (pp) REVERT: e 149 HIS cc_start: 0.9262 (m90) cc_final: 0.8924 (m-70) REVERT: e 168 ASP cc_start: 0.8866 (t0) cc_final: 0.8530 (t70) REVERT: e 250 LEU cc_start: 0.7429 (tp) cc_final: 0.6862 (tp) outliers start: 29 outliers final: 20 residues processed: 147 average time/residue: 0.1154 time to fit residues: 24.5250 Evaluate side-chains 145 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 221 ASN Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain c residue 154 TYR Chi-restraints excluded: chain c residue 179 GLU Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 246 PHE Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 97 ARG Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 182 MET Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 219 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 16 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 100 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.137151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093795 restraints weight = 27754.326| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.39 r_work: 0.3203 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14000 Z= 0.108 Angle : 0.507 6.342 19039 Z= 0.271 Chirality : 0.044 0.338 2073 Planarity : 0.003 0.034 2357 Dihedral : 13.173 177.501 2036 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 1.60 % Allowed : 10.25 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1642 helix: 1.43 (0.19), residues: 762 sheet: 0.57 (0.38), residues: 201 loop : -0.20 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 252 TYR 0.014 0.001 TYR e 99 PHE 0.012 0.001 PHE e 246 TRP 0.036 0.001 TRP e 176 HIS 0.008 0.001 HIS e 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (14000) covalent geometry : angle 0.50746 / 0.27 (19039) hydrogen bonds : bond 0.03465 / 3.32 ( 564) hydrogen bonds : angle 4.22273 / 3.92 ( 1635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: b 178 GLU cc_start: 0.7828 (tp30) cc_final: 0.7462 (tp30) REVERT: b 185 LYS cc_start: 0.9311 (tttp) cc_final: 0.8700 (tttm) REVERT: b 219 THR cc_start: 0.8972 (m) cc_final: 0.8671 (p) REVERT: c 25 MET cc_start: 0.9045 (mtp) cc_final: 0.8554 (mtm) REVERT: c 154 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8364 (p90) REVERT: c 162 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8252 (mm-30) REVERT: c 178 GLU cc_start: 0.8004 (tp30) cc_final: 0.7214 (mt-10) REVERT: c 181 LYS cc_start: 0.8590 (ptmt) cc_final: 0.8273 (ptmm) REVERT: c 224 MET cc_start: 0.8505 (tpt) cc_final: 0.7955 (tpt) REVERT: e 117 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7806 (pp) REVERT: e 149 HIS cc_start: 0.9250 (m90) cc_final: 0.8905 (m-70) REVERT: e 168 ASP cc_start: 0.8918 (t0) cc_final: 0.8543 (t70) REVERT: e 178 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6502 (pm20) REVERT: e 250 LEU cc_start: 0.7501 (tp) cc_final: 0.6691 (tp) REVERT: f 142 ASN cc_start: 0.7452 (OUTLIER) cc_final: 0.7144 (t0) outliers start: 23 outliers final: 16 residues processed: 141 average time/residue: 0.1106 time to fit residues: 22.5585 Evaluate side-chains 138 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 221 ASN Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 154 TYR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 246 PHE Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 97 ARG Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 178 GLU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 142 ASN Chi-restraints excluded: chain f residue 182 MET Chi-restraints excluded: chain f residue 219 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 161 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 0.0270 chunk 71 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN f 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.137938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094628 restraints weight = 27736.861| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.38 r_work: 0.3218 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14000 Z= 0.104 Angle : 0.489 6.419 19039 Z= 0.261 Chirality : 0.044 0.346 2073 Planarity : 0.003 0.034 2357 Dihedral : 12.976 176.888 2036 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 1.32 % Allowed : 10.67 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1642 helix: 1.57 (0.19), residues: 756 sheet: 0.51 (0.38), residues: 201 loop : -0.17 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 253 TYR 0.016 0.001 TYR d 50 PHE 0.012 0.001 PHE d 246 TRP 0.023 0.001 TRP e 176 HIS 0.006 0.001 HIS e 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (14000) covalent geometry : angle 0.48913 / 0.26 (19039) hydrogen bonds : bond 0.03180 / 3.03 ( 564) hydrogen bonds : angle 4.10091 / 3.75 ( 1635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: b 178 GLU cc_start: 0.7813 (tp30) cc_final: 0.7310 (tp30) REVERT: b 185 LYS cc_start: 0.9299 (tttp) cc_final: 0.8720 (tttm) REVERT: b 219 THR cc_start: 0.8962 (m) cc_final: 0.8618 (p) REVERT: c 25 MET cc_start: 0.9031 (mtp) cc_final: 0.8517 (mtm) REVERT: c 154 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8370 (p90) REVERT: c 162 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8142 (mm-30) REVERT: c 178 GLU cc_start: 0.7982 (tp30) cc_final: 0.7187 (mt-10) REVERT: c 181 LYS cc_start: 0.8561 (ptmt) cc_final: 0.8317 (ptmt) REVERT: c 185 LYS cc_start: 0.9353 (mmmt) cc_final: 0.9009 (tptp) REVERT: c 224 MET cc_start: 0.8487 (tpt) cc_final: 0.7881 (tpt) REVERT: e 117 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7796 (pp) REVERT: e 149 HIS cc_start: 0.9232 (m90) cc_final: 0.8879 (m-70) REVERT: e 168 ASP cc_start: 0.8893 (t0) cc_final: 0.8531 (t70) REVERT: e 250 LEU cc_start: 0.7368 (tp) cc_final: 0.6777 (tp) REVERT: f 253 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7968 (ttm-80) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.1308 time to fit residues: 26.3071 Evaluate side-chains 136 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 GLU Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 221 ASN Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain c residue 154 TYR Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 97 ARG Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 182 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 0.0030 chunk 155 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 158 ASN ** b 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** e 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.137797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094516 restraints weight = 27669.536| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.40 r_work: 0.3207 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14000 Z= 0.108 Angle : 0.493 7.818 19039 Z= 0.261 Chirality : 0.043 0.349 2073 Planarity : 0.003 0.035 2357 Dihedral : 12.893 176.958 2036 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 1.67 % Allowed : 10.60 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1642 helix: 1.64 (0.19), residues: 756 sheet: 0.50 (0.38), residues: 201 loop : -0.15 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 97 TYR 0.013 0.001 TYR b 107 PHE 0.012 0.001 PHE d 246 TRP 0.044 0.001 TRP e 176 HIS 0.005 0.001 HIS e 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (14000) covalent geometry : angle 0.49301 / 0.26 (19039) hydrogen bonds : bond 0.03135 / 3.00 ( 564) hydrogen bonds : angle 4.05531 / 3.71 ( 1635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.559 Fit side-chains REVERT: b 178 GLU cc_start: 0.7827 (tp30) cc_final: 0.7372 (tp30) REVERT: b 185 LYS cc_start: 0.9293 (tttp) cc_final: 0.8740 (tttm) REVERT: b 219 THR cc_start: 0.8929 (m) cc_final: 0.8681 (p) REVERT: c 25 MET cc_start: 0.8998 (mtp) cc_final: 0.8505 (mtm) REVERT: c 162 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8204 (mm-30) REVERT: c 178 GLU cc_start: 0.7966 (tp30) cc_final: 0.7178 (mt-10) REVERT: c 181 LYS cc_start: 0.8572 (ptmt) cc_final: 0.8337 (ptmt) REVERT: c 185 LYS cc_start: 0.9369 (mmmt) cc_final: 0.9040 (tptp) REVERT: c 224 MET cc_start: 0.8500 (tpt) cc_final: 0.7900 (tpt) REVERT: e 117 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7827 (pp) REVERT: e 149 HIS cc_start: 0.9241 (m90) cc_final: 0.8884 (m-70) REVERT: e 178 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6315 (pm20) REVERT: e 245 MET cc_start: 0.7465 (tmm) cc_final: 0.6803 (tmm) REVERT: e 250 LEU cc_start: 0.7389 (tp) cc_final: 0.6785 (tp) REVERT: f 253 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7929 (ttm-80) outliers start: 24 outliers final: 16 residues processed: 140 average time/residue: 0.1372 time to fit residues: 27.0860 Evaluate side-chains 136 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 GLU Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 221 ASN Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 178 GLU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 182 MET Chi-restraints excluded: chain f residue 183 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 142 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 158 ASN ** b 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 110 GLN ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** f 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.136046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092608 restraints weight = 27938.672| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.39 r_work: 0.3173 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14000 Z= 0.156 Angle : 0.525 10.046 19039 Z= 0.277 Chirality : 0.045 0.355 2073 Planarity : 0.003 0.035 2357 Dihedral : 12.875 176.699 2036 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 1.60 % Allowed : 11.16 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1642 helix: 1.57 (0.19), residues: 756 sheet: 0.48 (0.38), residues: 199 loop : -0.18 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG a 252 TYR 0.013 0.001 TYR b 107 PHE 0.014 0.002 PHE c 248 TRP 0.023 0.001 TRP e 176 HIS 0.007 0.001 HIS e 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (14000) covalent geometry : angle 0.52481 / 0.28 (19039) hydrogen bonds : bond 0.03398 / 3.27 ( 564) hydrogen bonds : angle 4.11865 / 3.79 ( 1635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.543 Fit side-chains REVERT: b 178 GLU cc_start: 0.7882 (tp30) cc_final: 0.7298 (tp30) REVERT: b 185 LYS cc_start: 0.9335 (tttp) cc_final: 0.8745 (tttm) REVERT: b 219 THR cc_start: 0.8947 (m) cc_final: 0.8598 (p) REVERT: c 25 MET cc_start: 0.8991 (mtp) cc_final: 0.8508 (mtm) REVERT: c 162 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8243 (mm-30) REVERT: c 178 GLU cc_start: 0.7977 (tp30) cc_final: 0.7129 (mt-10) REVERT: c 179 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: c 181 LYS cc_start: 0.8545 (ptmt) cc_final: 0.8300 (ptmt) REVERT: c 185 LYS cc_start: 0.9363 (mmmt) cc_final: 0.9050 (tptp) REVERT: c 224 MET cc_start: 0.8443 (tpt) cc_final: 0.7816 (tpt) REVERT: e 97 ARG cc_start: 0.8944 (ptp-170) cc_final: 0.8700 (ptm160) REVERT: e 117 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7883 (pp) REVERT: e 149 HIS cc_start: 0.9236 (m90) cc_final: 0.8878 (m-70) REVERT: e 166 PHE cc_start: 0.8297 (m-80) cc_final: 0.8023 (m-80) REVERT: e 178 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6955 (pp20) REVERT: e 245 MET cc_start: 0.7542 (tmm) cc_final: 0.6908 (tmm) REVERT: e 250 LEU cc_start: 0.7387 (tp) cc_final: 0.6761 (tp) outliers start: 23 outliers final: 17 residues processed: 138 average time/residue: 0.1457 time to fit residues: 28.3217 Evaluate side-chains 139 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 GLU Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 221 ASN Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain c residue 179 GLU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 98 ILE Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 178 GLU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 182 MET Chi-restraints excluded: chain f residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 35 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 89 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.140709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097803 restraints weight = 27622.268| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.39 r_work: 0.3185 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14000 Z= 0.120 Angle : 0.506 9.661 19039 Z= 0.266 Chirality : 0.044 0.349 2073 Planarity : 0.003 0.036 2357 Dihedral : 12.772 177.921 2036 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer: Outliers : 1.39 % Allowed : 11.58 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1642 helix: 1.60 (0.19), residues: 762 sheet: 0.35 (0.38), residues: 197 loop : -0.17 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG a 252 TYR 0.014 0.001 TYR d 50 PHE 0.011 0.001 PHE d 246 TRP 0.054 0.001 TRP e 176 HIS 0.014 0.001 HIS e 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14000) covalent geometry : angle 0.50563 / 0.27 (19039) hydrogen bonds : bond 0.03205 / 3.08 ( 564) hydrogen bonds : angle 4.08296 / 3.74 ( 1635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.576 Fit side-chains REVERT: b 178 GLU cc_start: 0.7867 (tp30) cc_final: 0.7384 (tp30) REVERT: b 185 LYS cc_start: 0.9325 (tttp) cc_final: 0.8755 (tttm) REVERT: b 219 THR cc_start: 0.8926 (m) cc_final: 0.8644 (p) REVERT: c 25 MET cc_start: 0.8982 (mtp) cc_final: 0.8543 (mtm) REVERT: c 162 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8259 (mm-30) REVERT: c 178 GLU cc_start: 0.7972 (tp30) cc_final: 0.7173 (mt-10) REVERT: c 181 LYS cc_start: 0.8574 (ptmt) cc_final: 0.8303 (ptmt) REVERT: c 185 LYS cc_start: 0.9378 (mmmt) cc_final: 0.9070 (tptp) REVERT: c 224 MET cc_start: 0.8408 (tpt) cc_final: 0.7803 (tpt) REVERT: c 281 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8132 (mt-10) REVERT: e 117 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7846 (pp) REVERT: e 149 HIS cc_start: 0.9240 (m90) cc_final: 0.8908 (m-70) REVERT: e 166 PHE cc_start: 0.8275 (m-80) cc_final: 0.8046 (m-80) REVERT: e 177 TRP cc_start: 0.7932 (t-100) cc_final: 0.7034 (t-100) REVERT: e 178 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6315 (pm20) REVERT: e 245 MET cc_start: 0.7552 (tmm) cc_final: 0.6989 (tmm) REVERT: f 252 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8222 (mtp85) REVERT: f 253 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7935 (mtp85) outliers start: 20 outliers final: 18 residues processed: 132 average time/residue: 0.1517 time to fit residues: 28.2345 Evaluate side-chains 134 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 GLU Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 221 ASN Chi-restraints excluded: chain b residue 261 VAL Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 23 ARG Chi-restraints excluded: chain e residue 98 ILE Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 178 GLU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 182 MET Chi-restraints excluded: chain f residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 128 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** d 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.135808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092652 restraints weight = 27997.529| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.35 r_work: 0.3173 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14000 Z= 0.151 Angle : 0.529 8.546 19039 Z= 0.278 Chirality : 0.045 0.353 2073 Planarity : 0.004 0.072 2357 Dihedral : 12.757 178.043 2036 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 1.39 % Allowed : 11.65 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1642 helix: 1.53 (0.19), residues: 764 sheet: 0.34 (0.38), residues: 195 loop : -0.21 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 97 TYR 0.016 0.001 TYR d 83 PHE 0.012 0.001 PHE c 248 TRP 0.045 0.001 TRP e 176 HIS 0.017 0.001 HIS e 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (14000) covalent geometry : angle 0.52853 / 0.28 (19039) hydrogen bonds : bond 0.03347 / 3.22 ( 564) hydrogen bonds : angle 4.10795 / 3.79 ( 1635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3352.47 seconds wall clock time: 58 minutes 19.91 seconds (3499.91 seconds total)