Starting phenix.real_space_refine on Sat Jul 4 20:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjn_54948/07_2026/9sjn_54948.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjn_54948/07_2026/9sjn_54948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sjn_54948/07_2026/9sjn_54948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjn_54948/07_2026/9sjn_54948.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjn_54948/07_2026/9sjn_54948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjn_54948/07_2026/9sjn_54948.cif" } resolution = 3.03 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= 0.002 sd= 0.029 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: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 116 5.16 5 C 14311 2.51 5 N 3817 2.21 5 O 4476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s 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: 22779 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2684 Classifications: {'peptide': 336} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 318} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1986 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "I" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1438 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "D" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2521 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "E" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2603 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "F" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2610 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 306} Chain: "G" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2610 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "H" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2409 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1288 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 18, 'rna2p_pyr': 10, 'rna3p_pur': 19, 'rna3p_pyr': 13} Link IDs: {'rna2p': 28, 'rna3p': 31} Time building chain proxies: 4.53, per 1000 atoms: 0.20 Number of scatterers: 22779 At special positions: 0 Unit cell: (131.95, 146.45, 150.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 59 15.00 O 4476 8.00 N 3817 7.00 C 14311 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: 1.29 Conformation dependent library (CDL) restraints added in 861.8 milliseconds 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5054 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 35 sheets defined 34.8% alpha, 8.4% beta 6 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.867A pdb=" N GLN A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.099A pdb=" N ARG A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.656A pdb=" N GLY A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 264 removed outlier: 4.231A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.645A pdb=" N TYR A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 324 through 339 Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.609A pdb=" N PHE B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 4.058A pdb=" N GLU B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.674A pdb=" N LEU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.863A pdb=" N LEU B 240 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.566A pdb=" N ILE I 24 " --> pdb=" O ILE I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 35 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 72 through 77 removed outlier: 3.655A pdb=" N HIS I 76 " --> pdb=" O CYS I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 124 through 138 removed outlier: 3.608A pdb=" N GLU I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 272 Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 63 through 70 removed outlier: 3.949A pdb=" N LYS E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 186 through 201 Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 63 through 71 removed outlier: 4.736A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.885A pdb=" N MET F 106 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.553A pdb=" N ILE F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.544A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'C' and resid 63 through 71 removed outlier: 5.064A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.626A pdb=" N MET C 106 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 145 through 153 removed outlier: 6.313A pdb=" N ARG C 150 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'G' and resid 36 through 40 removed outlier: 3.665A pdb=" N ARG G 40 " --> pdb=" O PHE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 70 removed outlier: 3.855A pdb=" N GLU G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 186 through 202 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.508A pdb=" N ILE G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 Processing helix chain 'G' and resid 296 through 305 Processing helix chain 'G' and resid 312 through 326 Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 145 through 153 removed outlier: 6.162A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 250 through 259 Processing helix chain 'H' and resid 267 through 272 Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 312 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 152 removed outlier: 4.288A pdb=" N LYS A 148 " --> pdb=" O ILE A 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 159 through 163 current: chain 'B' and resid 101 through 112 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 101 through 112 current: chain 'B' and resid 137 through 141 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 141 current: chain 'B' and resid 214 through 229 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 214 through 229 current: chain 'B' and resid 249 through 253 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA7, first strand: chain 'I' and resid 39 through 42 removed outlier: 3.707A pdb=" N THR I 91 " --> pdb=" O SER I 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'I' and resid 142 through 143 Processing sheet with id=AB1, first strand: chain 'D' and resid 106 through 109 Processing sheet with id=AB2, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 172 through 173 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.219A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 57 Processing sheet with id=AB5, first strand: chain 'E' and resid 106 through 109 Processing sheet with id=AB6, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 46 current: chain 'E' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 172 through 173 current: chain 'E' and resid 246 through 249 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 50 through 57 removed outlier: 4.159A pdb=" N CYS E 82 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 227 through 228 removed outlier: 4.549A pdb=" N LYS E 239 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 282 through 283 removed outlier: 3.981A pdb=" N ALA E 283 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE E 288 " --> pdb=" O ALA E 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 46 current: chain 'F' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 167 through 168 current: chain 'F' and resid 246 through 249 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 54 through 57 removed outlier: 3.579A pdb=" N GLN F 77 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 82 through 83 removed outlier: 4.462A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 227 through 228 removed outlier: 4.578A pdb=" N LYS F 239 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 172 through 173 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 50 through 56 removed outlier: 4.233A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 106 through 109 Processing sheet with id=AC9, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 46 current: chain 'G' and resid 167 through 168 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 50 through 55 removed outlier: 4.135A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 227 through 228 removed outlier: 4.283A pdb=" N LYS G 239 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD4, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AD5, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.917A pdb=" N ALA G 283 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'H' and resid 106 through 108 removed outlier: 7.037A pdb=" N SER H 20 " --> pdb=" O TYR H 107 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 46 current: chain 'H' and resid 167 through 168 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 260 through 262 656 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6658 1.33 - 1.46: 4442 1.46 - 1.58: 11999 1.58 - 1.70: 118 1.70 - 1.82: 185 Bond restraints: 23402 Sorted by residual: bond pdb=" CA ALA G 22 " pdb=" CB ALA G 22 " ideal model delta sigma weight residual 1.532 1.478 0.053 1.59e-02 3.96e+03 1.13e+01 bond pdb=" CA LYS I 85 " pdb=" CB LYS I 85 " ideal model delta sigma weight residual 1.527 1.563 -0.036 1.27e-02 6.20e+03 8.03e+00 bond pdb=" C ILE A 14 " pdb=" N PRO A 15 " ideal model delta sigma weight residual 1.332 1.367 -0.035 1.30e-02 5.92e+03 7.31e+00 bond pdb=" CA TYR G 265 " pdb=" C TYR G 265 " ideal model delta sigma weight residual 1.522 1.488 0.033 1.29e-02 6.01e+03 6.73e+00 bond pdb=" CA TYR E 265 " pdb=" C TYR E 265 " ideal model delta sigma weight residual 1.528 1.498 0.030 1.18e-02 7.18e+03 6.45e+00 ... (remaining 23397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 31360 2.36 - 4.71: 474 4.71 - 7.07: 33 7.07 - 9.43: 19 9.43 - 11.78: 4 Bond angle restraints: 31890 Sorted by residual: angle pdb=" O3' A J 39 " pdb=" C3' A J 39 " pdb=" C2' A J 39 " ideal model delta sigma weight residual 109.50 121.28 -11.78 1.50e+00 4.44e-01 6.17e+01 angle pdb=" N ILE A 259 " pdb=" CA ILE A 259 " pdb=" C ILE A 259 " ideal model delta sigma weight residual 110.53 105.58 4.95 9.40e-01 1.13e+00 2.78e+01 angle pdb=" CA PHE G 21 " pdb=" CB PHE G 21 " pdb=" CG PHE G 21 " ideal model delta sigma weight residual 113.80 118.83 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" CA TYR E 265 " pdb=" CB TYR E 265 " pdb=" CG TYR E 265 " ideal model delta sigma weight residual 113.90 122.63 -8.73 1.80e+00 3.09e-01 2.35e+01 angle pdb=" C TRP H 149 " pdb=" CA TRP H 149 " pdb=" CB TRP H 149 " ideal model delta sigma weight residual 116.63 111.24 5.39 1.16e+00 7.43e-01 2.16e+01 ... (remaining 31885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 13278 31.38 - 62.76: 875 62.76 - 94.14: 105 94.14 - 125.53: 5 125.53 - 156.91: 1 Dihedral angle restraints: 14264 sinusoidal: 6437 harmonic: 7827 Sorted by residual: dihedral pdb=" C4' G J 59 " pdb=" C3' G J 59 " pdb=" C2' G J 59 " pdb=" C1' G J 59 " ideal model delta sinusoidal sigma weight residual -35.00 35.73 -70.73 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" C5' G J 59 " pdb=" C4' G J 59 " pdb=" C3' G J 59 " pdb=" O3' G J 59 " ideal model delta sinusoidal sigma weight residual 147.00 76.92 70.08 1 8.00e+00 1.56e-02 9.89e+01 dihedral pdb=" O4' G J 59 " pdb=" C4' G J 59 " pdb=" C3' G J 59 " pdb=" C2' G J 59 " ideal model delta sinusoidal sigma weight residual 24.00 -37.04 61.04 1 8.00e+00 1.56e-02 7.74e+01 ... (remaining 14261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3456 0.113 - 0.226: 73 0.226 - 0.338: 1 0.338 - 0.451: 1 0.451 - 0.564: 2 Chirality restraints: 3533 Sorted by residual: chirality pdb=" P A J 40 " pdb=" OP1 A J 40 " pdb=" OP2 A J 40 " pdb=" O5' A J 40 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.96e+00 chirality pdb=" P A J 39 " pdb=" OP1 A J 39 " pdb=" OP2 A J 39 " pdb=" O5' A J 39 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C3' G J 59 " pdb=" C4' G J 59 " pdb=" O3' G J 59 " pdb=" C2' G J 59 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 3530 not shown) Planarity restraints: 3870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 92 " -0.023 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE A 92 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 92 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 92 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 92 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 92 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 92 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 264 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C TRP E 264 " -0.042 2.00e-02 2.50e+03 pdb=" O TRP E 264 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR E 265 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 166 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ASP F 166 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP F 166 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS F 167 " -0.014 2.00e-02 2.50e+03 ... (remaining 3867 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2010 2.74 - 3.28: 23882 3.28 - 3.82: 41266 3.82 - 4.36: 51354 4.36 - 4.90: 82848 Nonbonded interactions: 201360 Sorted by model distance: nonbonded pdb=" OG1 THR A 81 " pdb=" O ASP A 83 " model vdw 2.196 3.040 nonbonded pdb=" O PRO A 298 " pdb=" NE2 GLN I 136 " model vdw 2.198 3.120 nonbonded pdb=" O LEU G 55 " pdb=" O2' A J 37 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR F 265 " pdb=" O PHE F 273 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR C 169 " pdb=" OE1 GLN C 195 " model vdw 2.213 3.040 ... (remaining 201355 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 'C' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'D' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'E' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'F' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'G' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'H' and resid 12 through 331) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.520 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.820 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.004 0.055 23402 Z= 0.205 Angle : 0.726 11.783 31890 Z= 0.433 Chirality : 0.045 0.564 3533 Planarity : 0.005 0.057 3870 Dihedral : 19.331 156.906 9210 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 0.42 % Allowed : 28.34 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2634 helix: 0.97 (0.19), residues: 749 sheet: -0.36 (0.25), residues: 445 loop : -1.34 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.027 0.001 TYR E 265 PHE 0.057 0.002 PHE A 92 TRP 0.022 0.001 TRP H 33 HIS 0.013 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.21 (23402) covalent geometry : angle 0.72611 / 0.43 (31890) hydrogen bonds : bond 0.15012 / 10.09 ( 673) hydrogen bonds : angle 6.67859 / 4.50 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 581 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.5469 (mtt) cc_final: 0.5221 (mtt) REVERT: A 118 MET cc_start: 0.1180 (tpt) cc_final: 0.0887 (tpt) REVERT: A 171 TYR cc_start: 0.6205 (t80) cc_final: 0.5760 (t80) REVERT: A 180 SER cc_start: 0.6997 (t) cc_final: 0.6748 (m) REVERT: A 311 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7120 (mm-40) REVERT: B 219 GLU cc_start: 0.7772 (pt0) cc_final: 0.7558 (pt0) REVERT: I 115 MET cc_start: 0.0148 (mmm) cc_final: -0.0059 (mmm) REVERT: D 23 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7447 (ptt-90) REVERT: D 89 ASP cc_start: 0.8187 (p0) cc_final: 0.7656 (p0) REVERT: D 227 GLN cc_start: 0.8363 (tt0) cc_final: 0.8084 (tt0) REVERT: D 228 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7147 (mm-30) REVERT: D 262 ASP cc_start: 0.8061 (t0) cc_final: 0.7670 (t0) REVERT: D 320 MET cc_start: 0.7907 (mmp) cc_final: 0.7452 (mmp) REVERT: E 45 LEU cc_start: 0.8143 (mt) cc_final: 0.7909 (mt) REVERT: E 123 ASP cc_start: 0.7556 (m-30) cc_final: 0.7351 (m-30) REVERT: E 244 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7606 (mt-10) REVERT: E 275 ILE cc_start: 0.8077 (pt) cc_final: 0.7715 (pt) REVERT: F 51 ASP cc_start: 0.7294 (m-30) cc_final: 0.7068 (m-30) REVERT: F 72 MET cc_start: -0.0237 (ptp) cc_final: -0.0554 (ptp) REVERT: F 119 TYR cc_start: 0.7929 (m-10) cc_final: 0.7497 (m-10) REVERT: F 123 ASP cc_start: 0.8209 (m-30) cc_final: 0.7942 (m-30) REVERT: F 125 TYR cc_start: 0.8325 (t80) cc_final: 0.8093 (t80) REVERT: F 224 TYR cc_start: 0.8077 (m-80) cc_final: 0.7560 (m-80) REVERT: F 278 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6412 (mt-10) REVERT: F 303 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7647 (mtp180) REVERT: C 72 MET cc_start: -0.1089 (ttm) cc_final: -0.1540 (ttm) REVERT: C 103 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7512 (mtpt) REVERT: C 104 GLU cc_start: 0.6865 (mp0) cc_final: 0.6524 (mp0) REVERT: C 121 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7006 (mmtt) REVERT: C 173 ASN cc_start: 0.8219 (t0) cc_final: 0.7780 (t0) REVERT: C 228 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7509 (mt-10) REVERT: C 262 ASP cc_start: 0.8482 (t0) cc_final: 0.8190 (t0) REVERT: C 304 MET cc_start: 0.7826 (ttm) cc_final: 0.7542 (ttm) REVERT: G 21 PHE cc_start: 0.7911 (m-80) cc_final: 0.7673 (m-10) REVERT: G 41 HIS cc_start: 0.7415 (m-70) cc_final: 0.7170 (m170) REVERT: G 165 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6866 (mm-30) REVERT: G 188 THR cc_start: 0.8159 (p) cc_final: 0.7804 (t) REVERT: G 198 ASP cc_start: 0.7025 (m-30) cc_final: 0.6633 (m-30) REVERT: G 288 ILE cc_start: 0.5257 (OUTLIER) cc_final: 0.5048 (mt) REVERT: G 300 LEU cc_start: 0.8044 (mm) cc_final: 0.7836 (mt) REVERT: H 121 LYS cc_start: 0.7448 (mmtp) cc_final: 0.7141 (mmtm) REVERT: H 132 LEU cc_start: 0.7609 (tp) cc_final: 0.7181 (pp) REVERT: H 149 TRP cc_start: 0.6903 (m100) cc_final: 0.6082 (m100) REVERT: H 167 LYS cc_start: 0.7174 (tttm) cc_final: 0.6964 (tttm) REVERT: H 186 ASN cc_start: 0.6562 (m-40) cc_final: 0.6239 (m-40) REVERT: H 206 TYR cc_start: 0.7918 (p90) cc_final: 0.7627 (p90) REVERT: H 208 ASN cc_start: 0.7997 (m-40) cc_final: 0.7555 (m-40) REVERT: H 241 PHE cc_start: 0.6699 (t80) cc_final: 0.5872 (t80) outliers start: 10 outliers final: 2 residues processed: 589 average time/residue: 0.1540 time to fit residues: 137.6438 Evaluate side-chains 507 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 504 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 288 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0060 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 overall best weight: 0.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 98 ASN D 178 ASN E 173 ASN E 279 ASN F 41 HIS F 190 ASN F 256 ASN C 26 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN G 279 ASN H 141 ASN H 252 GLN H 256 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.180785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141759 restraints weight = 34544.590| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.34 r_work: 0.3696 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23402 Z= 0.128 Angle : 0.595 16.338 31890 Z= 0.314 Chirality : 0.042 0.291 3533 Planarity : 0.005 0.053 3870 Dihedral : 14.915 152.461 3810 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 3.05 % Allowed : 26.69 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.68 (0.16), residues: 2634 helix: 1.04 (0.19), residues: 744 sheet: -0.34 (0.25), residues: 458 loop : -1.32 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 146 TYR 0.015 0.001 TYR H 125 PHE 0.042 0.001 PHE A 92 TRP 0.012 0.001 TRP E 149 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (23402) covalent geometry : angle 0.59508 / 0.31 (31890) hydrogen bonds : bond 0.04572 / 3.11 ( 673) hydrogen bonds : angle 5.75982 / 3.93 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 542 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.5532 (mtt) cc_final: 0.5286 (mtt) REVERT: A 118 MET cc_start: 0.1136 (tpt) cc_final: 0.0821 (tpt) REVERT: A 171 TYR cc_start: 0.6636 (t80) cc_final: 0.6126 (t80) REVERT: A 180 SER cc_start: 0.7331 (t) cc_final: 0.7078 (m) REVERT: A 233 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6755 (mm) REVERT: A 311 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7316 (mm-40) REVERT: B 126 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8120 (ttmm) REVERT: B 138 ILE cc_start: 0.8396 (mp) cc_final: 0.8143 (mp) REVERT: B 185 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: B 219 GLU cc_start: 0.8362 (pt0) cc_final: 0.8047 (pt0) REVERT: B 240 LEU cc_start: 0.8219 (mp) cc_final: 0.7956 (mp) REVERT: B 246 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5774 (mm-30) REVERT: D 89 ASP cc_start: 0.8587 (p0) cc_final: 0.8300 (p0) REVERT: D 262 ASP cc_start: 0.8364 (t0) cc_final: 0.8051 (t0) REVERT: E 45 LEU cc_start: 0.8499 (mt) cc_final: 0.8253 (mt) REVERT: E 128 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7166 (tm-30) REVERT: E 129 ASP cc_start: 0.7627 (t70) cc_final: 0.7261 (t0) REVERT: E 190 ASN cc_start: 0.8168 (m-40) cc_final: 0.7657 (m110) REVERT: E 244 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7878 (mt-10) REVERT: E 303 ARG cc_start: 0.8320 (mtp180) cc_final: 0.7918 (mtp85) REVERT: E 314 GLU cc_start: 0.8055 (mp0) cc_final: 0.7798 (mp0) REVERT: F 43 PHE cc_start: 0.8167 (t80) cc_final: 0.7947 (t80) REVERT: F 72 MET cc_start: 0.0015 (ptp) cc_final: -0.0435 (ptp) REVERT: F 103 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8291 (mtmm) REVERT: F 119 TYR cc_start: 0.8168 (m-10) cc_final: 0.7855 (m-10) REVERT: F 123 ASP cc_start: 0.8491 (m-30) cc_final: 0.8247 (m-30) REVERT: F 125 TYR cc_start: 0.8512 (t80) cc_final: 0.8149 (t80) REVERT: F 265 TYR cc_start: 0.8265 (p90) cc_final: 0.7711 (p90) REVERT: F 278 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7534 (mt-10) REVERT: F 298 TYR cc_start: 0.8415 (m-80) cc_final: 0.8089 (m-80) REVERT: C 103 LYS cc_start: 0.8466 (mtmm) cc_final: 0.7768 (mtpt) REVERT: C 104 GLU cc_start: 0.7538 (mp0) cc_final: 0.7148 (mp0) REVERT: C 121 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7442 (mmtt) REVERT: C 179 LEU cc_start: 0.8496 (mt) cc_final: 0.8282 (mt) REVERT: C 241 PHE cc_start: 0.8719 (t80) cc_final: 0.8176 (t80) REVERT: C 304 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7777 (ttp) REVERT: G 159 GLU cc_start: 0.8089 (tt0) cc_final: 0.7837 (tt0) REVERT: G 188 THR cc_start: 0.8342 (p) cc_final: 0.7542 (m) REVERT: G 198 ASP cc_start: 0.7861 (m-30) cc_final: 0.7553 (m-30) REVERT: G 300 LEU cc_start: 0.8503 (mm) cc_final: 0.8301 (mt) REVERT: H 39 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7721 (pttp) REVERT: H 113 ASN cc_start: 0.7380 (p0) cc_final: 0.7090 (p0) REVERT: H 121 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7588 (mmtm) REVERT: H 149 TRP cc_start: 0.6994 (m100) cc_final: 0.6247 (m100) REVERT: H 186 ASN cc_start: 0.7228 (m-40) cc_final: 0.6909 (m-40) REVERT: H 206 TYR cc_start: 0.7999 (p90) cc_final: 0.7696 (p90) REVERT: H 208 ASN cc_start: 0.8025 (m-40) cc_final: 0.7591 (m-40) REVERT: H 210 TYR cc_start: 0.7544 (m-80) cc_final: 0.7340 (m-80) REVERT: H 241 PHE cc_start: 0.6990 (t80) cc_final: 0.6447 (t80) REVERT: H 243 PHE cc_start: 0.7887 (t80) cc_final: 0.7669 (t80) REVERT: H 253 LYS cc_start: 0.8351 (tptt) cc_final: 0.8080 (tppt) REVERT: H 299 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7306 (mtmt) REVERT: H 303 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7828 (ttm170) outliers start: 72 outliers final: 34 residues processed: 589 average time/residue: 0.1444 time to fit residues: 130.0175 Evaluate side-chains 547 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 508 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 221 MET Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 171 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS B 21 ASN B 98 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN F 151 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 252 GLN G 308 ASN H 141 ASN H 256 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.173998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134437 restraints weight = 34153.127| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.32 r_work: 0.3583 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 23402 Z= 0.310 Angle : 0.680 15.820 31890 Z= 0.360 Chirality : 0.047 0.320 3533 Planarity : 0.006 0.068 3870 Dihedral : 14.839 159.484 3805 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 5.03 % Allowed : 25.42 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.06 (0.16), residues: 2634 helix: 0.53 (0.18), residues: 764 sheet: -0.45 (0.24), residues: 463 loop : -1.51 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 101 TYR 0.029 0.002 TYR H 125 PHE 0.031 0.003 PHE G 147 TRP 0.019 0.003 TRP C 33 HIS 0.009 0.002 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.31 (23402) covalent geometry : angle 0.67957 / 0.36 (31890) hydrogen bonds : bond 0.05068 / 3.46 ( 673) hydrogen bonds : angle 5.74970 / 3.93 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 562 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.5328 (tp) cc_final: 0.4975 (mt) REVERT: A 104 MET cc_start: 0.5970 (OUTLIER) cc_final: 0.5653 (mtt) REVERT: A 169 LEU cc_start: 0.6607 (tp) cc_final: 0.6309 (tp) REVERT: A 171 TYR cc_start: 0.6613 (t80) cc_final: 0.6163 (t80) REVERT: A 180 SER cc_start: 0.7474 (t) cc_final: 0.7221 (m) REVERT: A 233 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6888 (mm) REVERT: A 265 ARG cc_start: 0.7000 (mtm110) cc_final: 0.6732 (mtm110) REVERT: A 282 GLU cc_start: 0.7046 (pm20) cc_final: 0.6579 (pm20) REVERT: A 311 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7468 (mm-40) REVERT: A 326 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: B 126 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8141 (ttmm) REVERT: B 185 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6430 (pm20) REVERT: B 213 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7570 (mmtm) REVERT: B 240 LEU cc_start: 0.8478 (mp) cc_final: 0.8214 (mp) REVERT: I 90 ILE cc_start: 0.4480 (OUTLIER) cc_final: 0.4085 (mp) REVERT: D 89 ASP cc_start: 0.8775 (p0) cc_final: 0.8259 (p0) REVERT: D 104 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7472 (mt-10) REVERT: D 227 GLN cc_start: 0.8729 (tt0) cc_final: 0.8371 (tt0) REVERT: D 262 ASP cc_start: 0.8507 (t0) cc_final: 0.8084 (t0) REVERT: E 28 THR cc_start: 0.8643 (p) cc_final: 0.8394 (p) REVERT: E 228 GLU cc_start: 0.7665 (tp30) cc_final: 0.7394 (tp30) REVERT: E 314 GLU cc_start: 0.8070 (mp0) cc_final: 0.7830 (mp0) REVERT: F 72 MET cc_start: 0.0247 (ptp) cc_final: -0.0274 (ptp) REVERT: F 103 LYS cc_start: 0.8779 (mtmm) cc_final: 0.8468 (mtmm) REVERT: F 136 LYS cc_start: 0.8259 (mttp) cc_final: 0.8026 (mttt) REVERT: F 265 TYR cc_start: 0.8406 (p90) cc_final: 0.8041 (p90) REVERT: F 325 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8284 (ttt180) REVERT: C 121 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7412 (mmtt) REVERT: C 173 ASN cc_start: 0.8522 (t0) cc_final: 0.8251 (t0) REVERT: C 229 MET cc_start: 0.8049 (ptm) cc_final: 0.7800 (ptp) REVERT: C 290 PHE cc_start: 0.7942 (m-10) cc_final: 0.7725 (m-80) REVERT: C 304 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7831 (ttm) REVERT: C 320 MET cc_start: 0.8025 (mmm) cc_final: 0.7821 (mmt) REVERT: G 41 HIS cc_start: 0.8037 (m-70) cc_final: 0.7804 (m-70) REVERT: G 104 GLU cc_start: 0.8042 (mp0) cc_final: 0.7386 (mp0) REVERT: G 159 GLU cc_start: 0.7985 (tt0) cc_final: 0.7647 (tt0) REVERT: G 188 THR cc_start: 0.8410 (p) cc_final: 0.7565 (m) REVERT: G 198 ASP cc_start: 0.7911 (m-30) cc_final: 0.7593 (m-30) REVERT: G 278 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: G 300 LEU cc_start: 0.8563 (mm) cc_final: 0.8237 (mt) REVERT: H 113 ASN cc_start: 0.7533 (p0) cc_final: 0.7264 (p0) REVERT: H 121 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7743 (mmtm) REVERT: H 149 TRP cc_start: 0.7274 (m100) cc_final: 0.6684 (m100) REVERT: H 186 ASN cc_start: 0.7242 (m-40) cc_final: 0.6835 (m-40) REVERT: H 206 TYR cc_start: 0.8242 (p90) cc_final: 0.7967 (p90) REVERT: H 208 ASN cc_start: 0.8073 (m-40) cc_final: 0.7635 (m-40) REVERT: H 241 PHE cc_start: 0.7217 (t80) cc_final: 0.6569 (t80) REVERT: H 243 PHE cc_start: 0.7990 (t80) cc_final: 0.7566 (t80) REVERT: H 253 LYS cc_start: 0.8356 (tptt) cc_final: 0.8114 (tppt) REVERT: H 299 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7469 (mtmt) REVERT: H 303 ARG cc_start: 0.8282 (ttp-170) cc_final: 0.7742 (ttm170) REVERT: H 309 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6197 (tt0) outliers start: 119 outliers final: 67 residues processed: 638 average time/residue: 0.1542 time to fit residues: 149.6302 Evaluate side-chains 625 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 549 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 221 MET Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 309 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 96 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN E 279 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN H 256 ASN ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.176451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137556 restraints weight = 34339.898| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.30 r_work: 0.3621 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23402 Z= 0.159 Angle : 0.577 13.072 31890 Z= 0.305 Chirality : 0.042 0.319 3533 Planarity : 0.005 0.048 3870 Dihedral : 14.769 162.068 3805 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.88 % Favored : 94.08 % Rotamer: Outliers : 4.61 % Allowed : 26.40 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2634 helix: 0.75 (0.18), residues: 754 sheet: -0.45 (0.25), residues: 451 loop : -1.45 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 15 TYR 0.031 0.001 TYR H 125 PHE 0.021 0.001 PHE A 92 TRP 0.011 0.001 TRP E 149 HIS 0.006 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (23402) covalent geometry : angle 0.57675 / 0.31 (31890) hydrogen bonds : bond 0.04206 / 2.86 ( 673) hydrogen bonds : angle 5.52852 / 3.78 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 542 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.5285 (tp) cc_final: 0.4957 (mt) REVERT: A 47 ASN cc_start: 0.5846 (OUTLIER) cc_final: 0.5615 (t160) REVERT: A 104 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5595 (mtt) REVERT: A 171 TYR cc_start: 0.6641 (t80) cc_final: 0.6155 (t80) REVERT: A 180 SER cc_start: 0.7398 (t) cc_final: 0.7150 (m) REVERT: A 233 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6922 (mm) REVERT: A 265 ARG cc_start: 0.6902 (mtm110) cc_final: 0.6589 (ttm110) REVERT: A 282 GLU cc_start: 0.6979 (pm20) cc_final: 0.6531 (pm20) REVERT: A 311 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7405 (mm-40) REVERT: B 126 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8196 (ttmm) REVERT: B 185 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6423 (pm20) REVERT: B 213 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7399 (mmtm) REVERT: D 89 ASP cc_start: 0.8737 (p0) cc_final: 0.8148 (p0) REVERT: D 104 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7391 (mt-10) REVERT: D 210 TYR cc_start: 0.8274 (m-80) cc_final: 0.7972 (m-80) REVERT: D 227 GLN cc_start: 0.8704 (tt0) cc_final: 0.8334 (tt0) REVERT: D 238 LYS cc_start: 0.8207 (tttt) cc_final: 0.8003 (ttpp) REVERT: D 262 ASP cc_start: 0.8462 (t0) cc_final: 0.8070 (t0) REVERT: E 87 GLU cc_start: 0.8110 (mp0) cc_final: 0.7860 (mt-10) REVERT: E 228 GLU cc_start: 0.7559 (tp30) cc_final: 0.7331 (tp30) REVERT: F 72 MET cc_start: 0.0451 (ptp) cc_final: 0.0016 (ptp) REVERT: F 103 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8434 (mtmm) REVERT: F 125 TYR cc_start: 0.8518 (t80) cc_final: 0.8183 (t80) REVERT: F 136 LYS cc_start: 0.8232 (mttp) cc_final: 0.8006 (mttt) REVERT: F 190 ASN cc_start: 0.7626 (m-40) cc_final: 0.7153 (m-40) REVERT: F 265 TYR cc_start: 0.8360 (p90) cc_final: 0.7855 (p90) REVERT: F 325 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8322 (ttt180) REVERT: C 72 MET cc_start: -0.0164 (ttm) cc_final: -0.0793 (ttm) REVERT: C 104 GLU cc_start: 0.7588 (mp0) cc_final: 0.7245 (mp0) REVERT: C 121 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7438 (mmtt) REVERT: C 173 ASN cc_start: 0.8500 (t0) cc_final: 0.8261 (t0) REVERT: C 304 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7875 (ttp) REVERT: G 32 PHE cc_start: 0.8342 (m-10) cc_final: 0.8137 (m-10) REVERT: G 89 ASP cc_start: 0.7869 (t70) cc_final: 0.7621 (t0) REVERT: G 104 GLU cc_start: 0.7969 (mp0) cc_final: 0.7325 (mp0) REVERT: G 159 GLU cc_start: 0.7951 (tt0) cc_final: 0.7515 (tt0) REVERT: G 198 ASP cc_start: 0.7904 (m-30) cc_final: 0.7565 (m-30) REVERT: G 214 PHE cc_start: 0.8495 (m-80) cc_final: 0.8086 (m-80) REVERT: G 231 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.6132 (m-80) REVERT: G 244 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7871 (mt-10) REVERT: G 278 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: G 300 LEU cc_start: 0.8479 (mm) cc_final: 0.8174 (mt) REVERT: H 113 ASN cc_start: 0.7586 (p0) cc_final: 0.7323 (p0) REVERT: H 121 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7824 (mmtm) REVERT: H 149 TRP cc_start: 0.7187 (m100) cc_final: 0.6447 (m100) REVERT: H 186 ASN cc_start: 0.7074 (m-40) cc_final: 0.6845 (m-40) REVERT: H 206 TYR cc_start: 0.8201 (p90) cc_final: 0.7970 (p90) REVERT: H 208 ASN cc_start: 0.8041 (m-40) cc_final: 0.7633 (m-40) REVERT: H 241 PHE cc_start: 0.7186 (t80) cc_final: 0.6605 (t80) REVERT: H 243 PHE cc_start: 0.8003 (t80) cc_final: 0.7731 (t80) REVERT: H 253 LYS cc_start: 0.8378 (tptt) cc_final: 0.7984 (tppt) REVERT: H 260 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8088 (p) REVERT: H 291 ARG cc_start: 0.6298 (mtp85) cc_final: 0.6048 (mtp85) REVERT: H 293 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7028 (p0) REVERT: H 299 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7438 (mtmt) REVERT: H 303 ARG cc_start: 0.8244 (ttp-170) cc_final: 0.7728 (ttm170) REVERT: H 309 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6274 (tt0) outliers start: 109 outliers final: 64 residues processed: 614 average time/residue: 0.1623 time to fit residues: 151.7001 Evaluate side-chains 616 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 541 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 60 HIS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 221 MET Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 311 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 259 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 67 optimal weight: 9.9990 chunk 184 optimal weight: 0.6980 chunk 175 optimal weight: 0.0670 chunk 151 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN G 178 ASN G 308 ASN ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.177244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138290 restraints weight = 33860.231| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.28 r_work: 0.3644 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23402 Z= 0.127 Angle : 0.547 10.426 31890 Z= 0.290 Chirality : 0.041 0.322 3533 Planarity : 0.004 0.048 3870 Dihedral : 14.684 166.937 3805 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.34 % Rotamer: Outliers : 4.19 % Allowed : 27.45 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.78 (0.16), residues: 2634 helix: 0.87 (0.18), residues: 753 sheet: -0.24 (0.26), residues: 432 loop : -1.41 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 137 TYR 0.029 0.001 TYR H 125 PHE 0.018 0.001 PHE A 92 TRP 0.011 0.001 TRP E 149 HIS 0.007 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (23402) covalent geometry : angle 0.54666 / 0.29 (31890) hydrogen bonds : bond 0.03895 / 2.64 ( 673) hydrogen bonds : angle 5.34059 / 3.66 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 552 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.5767 (OUTLIER) cc_final: 0.5520 (t160) REVERT: A 104 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.5475 (mtt) REVERT: A 171 TYR cc_start: 0.6627 (t80) cc_final: 0.6133 (t80) REVERT: A 180 SER cc_start: 0.7391 (t) cc_final: 0.7165 (m) REVERT: A 233 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6874 (mm) REVERT: A 265 ARG cc_start: 0.6869 (mtm110) cc_final: 0.6569 (ttm110) REVERT: A 282 GLU cc_start: 0.6966 (pm20) cc_final: 0.6528 (pm20) REVERT: A 311 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7349 (mm-40) REVERT: B 143 LYS cc_start: 0.8774 (tttm) cc_final: 0.8562 (tttm) REVERT: B 185 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: B 221 ILE cc_start: 0.8643 (pt) cc_final: 0.8362 (mt) REVERT: B 236 ILE cc_start: 0.8104 (mt) cc_final: 0.7805 (mt) REVERT: B 240 LEU cc_start: 0.8503 (mp) cc_final: 0.8222 (mp) REVERT: B 246 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5870 (mm-30) REVERT: I 90 ILE cc_start: 0.4415 (OUTLIER) cc_final: 0.3957 (mp) REVERT: I 115 MET cc_start: -0.0329 (mmm) cc_final: -0.0915 (mmm) REVERT: D 89 ASP cc_start: 0.8753 (p0) cc_final: 0.8146 (p0) REVERT: D 104 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7375 (mt-10) REVERT: D 227 GLN cc_start: 0.8691 (tt0) cc_final: 0.8306 (tt0) REVERT: D 229 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.4865 (ttp) REVERT: D 262 ASP cc_start: 0.8441 (t0) cc_final: 0.8150 (t0) REVERT: E 87 GLU cc_start: 0.8117 (mp0) cc_final: 0.7885 (mt-10) REVERT: E 111 ASP cc_start: 0.7260 (t0) cc_final: 0.7017 (m-30) REVERT: E 228 GLU cc_start: 0.7519 (tp30) cc_final: 0.7303 (tp30) REVERT: E 314 GLU cc_start: 0.8032 (mp0) cc_final: 0.7816 (mp0) REVERT: F 103 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8428 (mtmm) REVERT: F 125 TYR cc_start: 0.8515 (t80) cc_final: 0.8188 (t80) REVERT: F 136 LYS cc_start: 0.8234 (mttp) cc_final: 0.7963 (mttt) REVERT: F 265 TYR cc_start: 0.8326 (p90) cc_final: 0.7860 (p90) REVERT: C 72 MET cc_start: -0.0137 (ttm) cc_final: -0.0793 (ttm) REVERT: C 103 LYS cc_start: 0.8485 (mtmm) cc_final: 0.7871 (mtpt) REVERT: C 104 GLU cc_start: 0.7576 (mp0) cc_final: 0.7240 (mp0) REVERT: C 121 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7438 (mmtt) REVERT: C 137 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7595 (mmt-90) REVERT: C 173 ASN cc_start: 0.8486 (t0) cc_final: 0.8249 (t0) REVERT: C 195 GLN cc_start: 0.8405 (mt0) cc_final: 0.8200 (mt0) REVERT: C 291 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6599 (mtt180) REVERT: C 304 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7850 (ttp) REVERT: C 320 MET cc_start: 0.7793 (mmm) cc_final: 0.7576 (mmp) REVERT: G 48 LEU cc_start: 0.8531 (mp) cc_final: 0.8298 (mt) REVERT: G 104 GLU cc_start: 0.7982 (mp0) cc_final: 0.7332 (mp0) REVERT: G 157 ILE cc_start: 0.8906 (mt) cc_final: 0.8503 (tt) REVERT: G 159 GLU cc_start: 0.7871 (tt0) cc_final: 0.7439 (tt0) REVERT: G 188 THR cc_start: 0.8235 (p) cc_final: 0.7758 (t) REVERT: G 198 ASP cc_start: 0.7929 (m-30) cc_final: 0.7593 (m-30) REVERT: G 203 LYS cc_start: 0.8710 (mppt) cc_final: 0.8351 (mppt) REVERT: G 214 PHE cc_start: 0.8464 (m-80) cc_final: 0.8199 (m-80) REVERT: G 231 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6176 (m-80) REVERT: G 244 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7841 (mt-10) REVERT: G 278 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: G 300 LEU cc_start: 0.8464 (mm) cc_final: 0.8261 (mt) REVERT: H 113 ASN cc_start: 0.7661 (p0) cc_final: 0.7396 (p0) REVERT: H 121 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7788 (mmtm) REVERT: H 149 TRP cc_start: 0.7194 (m100) cc_final: 0.6337 (m100) REVERT: H 177 PHE cc_start: 0.8305 (m-80) cc_final: 0.8031 (m-80) REVERT: H 208 ASN cc_start: 0.8047 (m-40) cc_final: 0.7613 (m-40) REVERT: H 241 PHE cc_start: 0.7153 (t80) cc_final: 0.6632 (t80) REVERT: H 243 PHE cc_start: 0.8015 (t80) cc_final: 0.7753 (t80) REVERT: H 253 LYS cc_start: 0.8341 (tptt) cc_final: 0.7871 (tppt) REVERT: H 260 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8073 (p) REVERT: H 291 ARG cc_start: 0.6217 (mtp85) cc_final: 0.5929 (mtp85) REVERT: H 299 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7420 (mtmt) REVERT: H 303 ARG cc_start: 0.8213 (ttp-170) cc_final: 0.7916 (ttm170) outliers start: 99 outliers final: 62 residues processed: 614 average time/residue: 0.1626 time to fit residues: 151.6643 Evaluate side-chains 625 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 552 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 60 HIS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 311 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 266 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 267 optimal weight: 40.0000 chunk 146 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN F 178 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN H 317 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.176112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137076 restraints weight = 34207.977| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.30 r_work: 0.3623 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23402 Z= 0.168 Angle : 0.557 9.831 31890 Z= 0.296 Chirality : 0.042 0.317 3533 Planarity : 0.004 0.050 3870 Dihedral : 14.627 171.148 3805 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.69 % Favored : 94.27 % Rotamer: Outliers : 4.44 % Allowed : 27.33 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.78 (0.16), residues: 2634 helix: 0.82 (0.18), residues: 754 sheet: -0.21 (0.26), residues: 448 loop : -1.39 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 15 TYR 0.031 0.001 TYR H 125 PHE 0.018 0.001 PHE G 147 TRP 0.010 0.001 TRP F 33 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (23402) covalent geometry : angle 0.55663 / 0.30 (31890) hydrogen bonds : bond 0.03994 / 2.71 ( 673) hydrogen bonds : angle 5.29571 / 3.63 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 550 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.5841 (OUTLIER) cc_final: 0.5583 (t160) REVERT: A 67 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8472 (tp) REVERT: A 104 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5648 (mtt) REVERT: A 118 MET cc_start: 0.1784 (tpt) cc_final: 0.1519 (tpt) REVERT: A 171 TYR cc_start: 0.6645 (t80) cc_final: 0.6159 (t80) REVERT: A 180 SER cc_start: 0.7418 (t) cc_final: 0.7191 (m) REVERT: A 233 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6872 (mm) REVERT: A 265 ARG cc_start: 0.6870 (mtm180) cc_final: 0.6539 (ttm110) REVERT: A 282 GLU cc_start: 0.7003 (pm20) cc_final: 0.6574 (pm20) REVERT: A 311 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7383 (mm-40) REVERT: B 126 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8172 (ttmm) REVERT: B 144 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7427 (mtpp) REVERT: B 185 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6374 (pm20) REVERT: B 213 LYS cc_start: 0.7713 (mmtp) cc_final: 0.7435 (mmtm) REVERT: B 240 LEU cc_start: 0.8502 (mp) cc_final: 0.8224 (mp) REVERT: I 22 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.4821 (tm-30) REVERT: I 90 ILE cc_start: 0.4351 (OUTLIER) cc_final: 0.3898 (mp) REVERT: I 115 MET cc_start: -0.0321 (mmm) cc_final: -0.0971 (mmm) REVERT: D 89 ASP cc_start: 0.8746 (p0) cc_final: 0.8130 (p0) REVERT: D 104 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7389 (mt-10) REVERT: D 227 GLN cc_start: 0.8691 (tt0) cc_final: 0.8304 (tt0) REVERT: D 228 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7827 (mm-30) REVERT: D 229 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.4994 (ttp) REVERT: D 262 ASP cc_start: 0.8452 (t0) cc_final: 0.8172 (t0) REVERT: E 87 GLU cc_start: 0.8136 (mp0) cc_final: 0.7901 (mt-10) REVERT: E 314 GLU cc_start: 0.8035 (mp0) cc_final: 0.7817 (mp0) REVERT: F 103 LYS cc_start: 0.8779 (mtmm) cc_final: 0.8445 (mtmm) REVERT: F 125 TYR cc_start: 0.8528 (t80) cc_final: 0.8204 (t80) REVERT: F 136 LYS cc_start: 0.8266 (mttp) cc_final: 0.7987 (mttt) REVERT: F 190 ASN cc_start: 0.7612 (m-40) cc_final: 0.6960 (m110) REVERT: F 265 TYR cc_start: 0.8331 (p90) cc_final: 0.7657 (p90) REVERT: F 325 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8329 (ttt180) REVERT: C 72 MET cc_start: 0.0407 (ttm) cc_final: -0.0209 (ttm) REVERT: C 84 LEU cc_start: 0.8490 (mt) cc_final: 0.8245 (mt) REVERT: C 103 LYS cc_start: 0.8457 (mtmm) cc_final: 0.7713 (mtpt) REVERT: C 104 GLU cc_start: 0.7616 (mp0) cc_final: 0.7306 (mp0) REVERT: C 121 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7481 (mmtt) REVERT: C 137 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7589 (mmt-90) REVERT: C 173 ASN cc_start: 0.8477 (t0) cc_final: 0.8244 (t0) REVERT: C 228 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: C 291 ARG cc_start: 0.7181 (mtt180) cc_final: 0.6642 (mtt180) REVERT: C 304 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7902 (ttp) REVERT: C 320 MET cc_start: 0.7869 (mmm) cc_final: 0.7626 (mmt) REVERT: C 329 PHE cc_start: 0.6985 (m-10) cc_final: 0.6738 (m-10) REVERT: G 48 LEU cc_start: 0.8554 (mp) cc_final: 0.8320 (mt) REVERT: G 104 GLU cc_start: 0.8001 (mp0) cc_final: 0.7342 (mp0) REVERT: G 157 ILE cc_start: 0.8929 (mt) cc_final: 0.8493 (tt) REVERT: G 188 THR cc_start: 0.8251 (p) cc_final: 0.7748 (t) REVERT: G 198 ASP cc_start: 0.7944 (m-30) cc_final: 0.7587 (m-30) REVERT: G 231 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.6170 (m-80) REVERT: G 244 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7634 (mt-10) REVERT: G 278 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: G 300 LEU cc_start: 0.8481 (mm) cc_final: 0.8178 (mt) REVERT: H 113 ASN cc_start: 0.7668 (p0) cc_final: 0.7422 (p0) REVERT: H 121 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7689 (mmtt) REVERT: H 146 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7455 (ttp-170) REVERT: H 149 TRP cc_start: 0.7247 (m100) cc_final: 0.6375 (m100) REVERT: H 177 PHE cc_start: 0.8368 (m-80) cc_final: 0.8053 (m-80) REVERT: H 208 ASN cc_start: 0.8097 (m-40) cc_final: 0.7717 (m-40) REVERT: H 241 PHE cc_start: 0.7198 (t80) cc_final: 0.6712 (t80) REVERT: H 243 PHE cc_start: 0.8021 (t80) cc_final: 0.7704 (t80) REVERT: H 253 LYS cc_start: 0.8333 (tptt) cc_final: 0.7860 (tppt) REVERT: H 260 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7770 (p) REVERT: H 278 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6802 (tm-30) REVERT: H 291 ARG cc_start: 0.6308 (mtp85) cc_final: 0.6054 (mtp85) REVERT: H 293 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7020 (p0) REVERT: H 299 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7422 (mtmt) REVERT: H 303 ARG cc_start: 0.8228 (ttp-170) cc_final: 0.7918 (ttm170) REVERT: H 320 MET cc_start: 0.7792 (mmm) cc_final: 0.7551 (mmm) outliers start: 105 outliers final: 72 residues processed: 615 average time/residue: 0.1608 time to fit residues: 150.7025 Evaluate side-chains 632 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 543 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 60 HIS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 208 ASN Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 221 MET Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 311 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 209 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 155 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 194 optimal weight: 0.2980 chunk 106 optimal weight: 5.9990 chunk 193 optimal weight: 0.5980 chunk 90 optimal weight: 0.0040 chunk 13 optimal weight: 0.0570 chunk 219 optimal weight: 0.9980 overall best weight: 0.2510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 213 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 98 ASN D 140 ASN D 173 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.177931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139118 restraints weight = 34065.400| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.30 r_work: 0.3656 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23402 Z= 0.108 Angle : 0.527 9.869 31890 Z= 0.280 Chirality : 0.041 0.316 3533 Planarity : 0.004 0.059 3870 Dihedral : 14.601 173.554 3805 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.65 % Rotamer: Outliers : 4.15 % Allowed : 28.21 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.63 (0.16), residues: 2634 helix: 0.97 (0.18), residues: 758 sheet: -0.18 (0.26), residues: 452 loop : -1.29 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 303 TYR 0.028 0.001 TYR H 125 PHE 0.013 0.001 PHE A 339 TRP 0.010 0.001 TRP E 149 HIS 0.006 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (23402) covalent geometry : angle 0.52705 / 0.28 (31890) hydrogen bonds : bond 0.03647 / 2.46 ( 673) hydrogen bonds : angle 5.13598 / 3.52 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 539 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.5804 (OUTLIER) cc_final: 0.5521 (t160) REVERT: A 104 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5646 (mtt) REVERT: A 115 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.5597 (mpt180) REVERT: A 118 MET cc_start: 0.1872 (tpt) cc_final: 0.1630 (tpt) REVERT: A 171 TYR cc_start: 0.6610 (t80) cc_final: 0.6127 (t80) REVERT: A 180 SER cc_start: 0.7419 (t) cc_final: 0.7189 (m) REVERT: A 233 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6846 (mm) REVERT: A 265 ARG cc_start: 0.6837 (mtm180) cc_final: 0.6496 (ttm110) REVERT: A 282 GLU cc_start: 0.6966 (pm20) cc_final: 0.6548 (pm20) REVERT: A 311 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7321 (mm-40) REVERT: B 126 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8191 (ttmm) REVERT: B 144 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7436 (mtpp) REVERT: B 185 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6301 (pm20) REVERT: B 213 LYS cc_start: 0.7570 (mmtp) cc_final: 0.7173 (mttp) REVERT: B 240 LEU cc_start: 0.8488 (mp) cc_final: 0.8188 (mp) REVERT: B 246 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5775 (mm-30) REVERT: I 22 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.4767 (tm-30) REVERT: I 90 ILE cc_start: 0.4205 (OUTLIER) cc_final: 0.3747 (mp) REVERT: I 115 MET cc_start: -0.0471 (mmm) cc_final: -0.1253 (mmm) REVERT: D 89 ASP cc_start: 0.8747 (p0) cc_final: 0.8121 (p0) REVERT: D 104 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7401 (mt-10) REVERT: D 227 GLN cc_start: 0.8674 (tt0) cc_final: 0.8406 (tt0) REVERT: D 229 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.4893 (ttp) REVERT: D 238 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8156 (ttmm) REVERT: D 262 ASP cc_start: 0.8422 (t0) cc_final: 0.8154 (t0) REVERT: E 87 GLU cc_start: 0.8110 (mp0) cc_final: 0.7872 (mt-10) REVERT: E 171 SER cc_start: 0.8641 (p) cc_final: 0.8402 (m) REVERT: E 190 ASN cc_start: 0.8232 (m-40) cc_final: 0.7907 (m110) REVERT: F 103 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8420 (mtmm) REVERT: F 125 TYR cc_start: 0.8490 (t80) cc_final: 0.8176 (t80) REVERT: F 136 LYS cc_start: 0.8238 (mttp) cc_final: 0.7968 (mttt) REVERT: F 190 ASN cc_start: 0.7491 (m-40) cc_final: 0.6801 (m110) REVERT: C 72 MET cc_start: 0.0338 (ttm) cc_final: -0.0266 (ttm) REVERT: C 103 LYS cc_start: 0.8436 (mtmm) cc_final: 0.7735 (mtpt) REVERT: C 104 GLU cc_start: 0.7568 (mp0) cc_final: 0.7239 (mp0) REVERT: C 121 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7486 (mmtt) REVERT: C 137 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7616 (mmt-90) REVERT: C 173 ASN cc_start: 0.8461 (t0) cc_final: 0.8226 (t0) REVERT: C 291 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6359 (mtt180) REVERT: C 304 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7819 (ttp) REVERT: G 104 GLU cc_start: 0.7958 (mp0) cc_final: 0.7302 (mp0) REVERT: G 124 GLU cc_start: 0.7841 (tt0) cc_final: 0.7598 (tt0) REVERT: G 157 ILE cc_start: 0.8880 (mt) cc_final: 0.8523 (tt) REVERT: G 159 GLU cc_start: 0.7880 (tt0) cc_final: 0.7456 (tt0) REVERT: G 188 THR cc_start: 0.8146 (p) cc_final: 0.7626 (t) REVERT: G 198 ASP cc_start: 0.7902 (m-30) cc_final: 0.7553 (m-30) REVERT: G 231 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.6142 (m-80) REVERT: G 244 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7781 (mt-10) REVERT: G 278 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: G 300 LEU cc_start: 0.8427 (mm) cc_final: 0.8117 (mt) REVERT: H 113 ASN cc_start: 0.7645 (p0) cc_final: 0.7409 (p0) REVERT: H 121 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7835 (mmtm) REVERT: H 146 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7437 (ttp-170) REVERT: H 149 TRP cc_start: 0.7190 (m100) cc_final: 0.6352 (m100) REVERT: H 177 PHE cc_start: 0.8352 (m-80) cc_final: 0.8022 (m-80) REVERT: H 192 ILE cc_start: 0.8626 (mm) cc_final: 0.8261 (tt) REVERT: H 208 ASN cc_start: 0.8083 (m-40) cc_final: 0.7665 (m-40) REVERT: H 241 PHE cc_start: 0.7112 (t80) cc_final: 0.6696 (t80) REVERT: H 243 PHE cc_start: 0.8090 (t80) cc_final: 0.7712 (t80) REVERT: H 253 LYS cc_start: 0.8298 (tptt) cc_final: 0.7844 (tppt) REVERT: H 260 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7767 (p) REVERT: H 291 ARG cc_start: 0.6274 (mtp85) cc_final: 0.6008 (mtp85) REVERT: H 293 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.6922 (p0) REVERT: H 299 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7448 (mtmt) REVERT: H 303 ARG cc_start: 0.8176 (ttp-170) cc_final: 0.7954 (ttm170) outliers start: 98 outliers final: 57 residues processed: 603 average time/residue: 0.1739 time to fit residues: 160.1848 Evaluate side-chains 604 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 531 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 60 HIS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 208 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 221 MET Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 311 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 120 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 216 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN B 21 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.176485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137229 restraints weight = 33474.574| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.30 r_work: 0.3625 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23402 Z= 0.161 Angle : 0.549 9.759 31890 Z= 0.292 Chirality : 0.042 0.310 3533 Planarity : 0.005 0.056 3870 Dihedral : 14.556 175.710 3805 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 3.98 % Allowed : 28.21 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.65 (0.16), residues: 2634 helix: 0.93 (0.18), residues: 758 sheet: -0.17 (0.26), residues: 453 loop : -1.31 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 284 TYR 0.030 0.001 TYR H 125 PHE 0.019 0.002 PHE G 214 TRP 0.012 0.001 TRP G 149 HIS 0.006 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (23402) covalent geometry : angle 0.54901 / 0.29 (31890) hydrogen bonds : bond 0.03847 / 2.61 ( 673) hydrogen bonds : angle 5.14101 / 3.52 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 541 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.5856 (OUTLIER) cc_final: 0.5548 (t160) REVERT: A 67 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8444 (tp) REVERT: A 104 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.5650 (mtt) REVERT: A 115 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5617 (mpt180) REVERT: A 118 MET cc_start: 0.1966 (tpt) cc_final: 0.1713 (tpt) REVERT: A 171 TYR cc_start: 0.6614 (t80) cc_final: 0.6108 (t80) REVERT: A 180 SER cc_start: 0.7409 (t) cc_final: 0.7193 (m) REVERT: A 233 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6845 (mm) REVERT: A 265 ARG cc_start: 0.6793 (mtm180) cc_final: 0.6459 (ttm110) REVERT: A 282 GLU cc_start: 0.7021 (pm20) cc_final: 0.6606 (pm20) REVERT: A 311 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7381 (mm-40) REVERT: B 144 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7486 (mtpp) REVERT: B 185 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6318 (pm20) REVERT: B 213 LYS cc_start: 0.7625 (mmtp) cc_final: 0.7252 (mttp) REVERT: B 240 LEU cc_start: 0.8494 (mp) cc_final: 0.8191 (mp) REVERT: B 246 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5860 (mm-30) REVERT: I 22 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.4767 (tm-30) REVERT: I 90 ILE cc_start: 0.4160 (OUTLIER) cc_final: 0.3701 (mp) REVERT: I 115 MET cc_start: -0.0508 (mmm) cc_final: -0.1865 (mmm) REVERT: D 89 ASP cc_start: 0.8766 (p0) cc_final: 0.8130 (p0) REVERT: D 104 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7435 (mt-10) REVERT: D 227 GLN cc_start: 0.8675 (tt0) cc_final: 0.8432 (tt0) REVERT: D 229 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.5106 (ttp) REVERT: D 262 ASP cc_start: 0.8448 (t0) cc_final: 0.8177 (t0) REVERT: E 87 GLU cc_start: 0.8126 (mp0) cc_final: 0.7880 (mt-10) REVERT: E 171 SER cc_start: 0.8651 (p) cc_final: 0.8410 (m) REVERT: E 206 TYR cc_start: 0.8406 (p90) cc_final: 0.8013 (p90) REVERT: F 103 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8426 (mtmm) REVERT: F 125 TYR cc_start: 0.8497 (t80) cc_final: 0.8233 (t80) REVERT: F 136 LYS cc_start: 0.8270 (mttp) cc_final: 0.7990 (mtpt) REVERT: F 190 ASN cc_start: 0.7632 (m-40) cc_final: 0.6975 (m110) REVERT: F 265 TYR cc_start: 0.8320 (p90) cc_final: 0.7592 (p90) REVERT: F 298 TYR cc_start: 0.8391 (m-80) cc_final: 0.8168 (m-80) REVERT: C 72 MET cc_start: 0.0627 (ttm) cc_final: 0.0093 (ttm) REVERT: C 103 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7732 (mtpt) REVERT: C 104 GLU cc_start: 0.7597 (mp0) cc_final: 0.7300 (mp0) REVERT: C 121 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7484 (mmtt) REVERT: C 137 ARG cc_start: 0.8086 (mmt90) cc_final: 0.7636 (mmt-90) REVERT: C 173 ASN cc_start: 0.8489 (t0) cc_final: 0.8227 (t0) REVERT: C 291 ARG cc_start: 0.7154 (mtt180) cc_final: 0.6444 (mtt180) REVERT: C 304 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7883 (ttp) REVERT: C 320 MET cc_start: 0.7840 (mmm) cc_final: 0.7613 (mmt) REVERT: C 329 PHE cc_start: 0.6994 (m-10) cc_final: 0.6718 (m-10) REVERT: G 104 GLU cc_start: 0.8044 (mp0) cc_final: 0.7370 (mp0) REVERT: G 119 TYR cc_start: 0.8292 (m-80) cc_final: 0.8079 (m-80) REVERT: G 124 GLU cc_start: 0.7864 (tt0) cc_final: 0.7620 (tt0) REVERT: G 157 ILE cc_start: 0.8909 (mt) cc_final: 0.8481 (tt) REVERT: G 159 GLU cc_start: 0.7863 (tt0) cc_final: 0.7395 (tt0) REVERT: G 188 THR cc_start: 0.8177 (p) cc_final: 0.7644 (t) REVERT: G 198 ASP cc_start: 0.7940 (m-30) cc_final: 0.7568 (m-30) REVERT: G 214 PHE cc_start: 0.8490 (m-80) cc_final: 0.8074 (m-80) REVERT: G 244 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7824 (mt-10) REVERT: G 278 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: G 300 LEU cc_start: 0.8458 (mm) cc_final: 0.8165 (mt) REVERT: H 113 ASN cc_start: 0.7686 (p0) cc_final: 0.7449 (p0) REVERT: H 146 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7399 (ttp-170) REVERT: H 149 TRP cc_start: 0.7260 (m100) cc_final: 0.6578 (m100) REVERT: H 177 PHE cc_start: 0.8396 (m-80) cc_final: 0.8056 (m-80) REVERT: H 192 ILE cc_start: 0.8609 (mm) cc_final: 0.8268 (tt) REVERT: H 208 ASN cc_start: 0.8089 (m-40) cc_final: 0.7678 (m-40) REVERT: H 241 PHE cc_start: 0.7162 (t80) cc_final: 0.6706 (t80) REVERT: H 243 PHE cc_start: 0.8055 (t80) cc_final: 0.7640 (t80) REVERT: H 260 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.7754 (p) REVERT: H 280 TYR cc_start: 0.7693 (m-10) cc_final: 0.7449 (m-10) REVERT: H 291 ARG cc_start: 0.6409 (mtp85) cc_final: 0.6140 (mtp85) REVERT: H 293 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7012 (p0) REVERT: H 299 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7421 (mtmt) REVERT: H 303 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.7896 (ttm170) outliers start: 94 outliers final: 65 residues processed: 604 average time/residue: 0.1760 time to fit residues: 162.2102 Evaluate side-chains 617 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 536 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 208 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 221 MET Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 311 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 247 optimal weight: 0.8980 chunk 266 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 246 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 133 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 153 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN D 140 ASN E 279 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN G 227 GLN G 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.177111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137971 restraints weight = 33961.593| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.28 r_work: 0.3643 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23402 Z= 0.135 Angle : 0.536 9.780 31890 Z= 0.285 Chirality : 0.042 0.310 3533 Planarity : 0.004 0.057 3870 Dihedral : 14.550 177.402 3805 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 3.51 % Allowed : 28.93 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.59 (0.16), residues: 2634 helix: 0.97 (0.18), residues: 756 sheet: -0.08 (0.26), residues: 448 loop : -1.28 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 15 TYR 0.030 0.001 TYR H 125 PHE 0.014 0.001 PHE H 290 TRP 0.010 0.001 TRP E 149 HIS 0.007 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (23402) covalent geometry : angle 0.53629 / 0.29 (31890) hydrogen bonds : bond 0.03718 / 2.52 ( 673) hydrogen bonds : angle 5.10766 / 3.50 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 527 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.5795 (OUTLIER) cc_final: 0.5465 (t160) REVERT: A 67 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (tp) REVERT: A 104 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5772 (mtt) REVERT: A 115 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.5600 (mpt180) REVERT: A 118 MET cc_start: 0.1933 (tpt) cc_final: 0.1716 (tpt) REVERT: A 171 TYR cc_start: 0.6615 (t80) cc_final: 0.6118 (t80) REVERT: A 180 SER cc_start: 0.7430 (t) cc_final: 0.7221 (m) REVERT: A 233 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6820 (mm) REVERT: A 265 ARG cc_start: 0.6737 (mtm180) cc_final: 0.6434 (ttm110) REVERT: A 311 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7377 (mm-40) REVERT: B 144 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7510 (mtpp) REVERT: B 185 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6244 (pm20) REVERT: B 213 LYS cc_start: 0.7531 (mmtp) cc_final: 0.7206 (mttp) REVERT: B 240 LEU cc_start: 0.8506 (mp) cc_final: 0.8198 (mp) REVERT: B 246 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5856 (mm-30) REVERT: I 22 GLU cc_start: 0.5680 (OUTLIER) cc_final: 0.4747 (tm-30) REVERT: I 90 ILE cc_start: 0.4100 (OUTLIER) cc_final: 0.3666 (mp) REVERT: I 115 MET cc_start: -0.0489 (mmm) cc_final: -0.1891 (mmm) REVERT: D 89 ASP cc_start: 0.8747 (p0) cc_final: 0.8120 (p0) REVERT: D 104 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7394 (mt-10) REVERT: D 227 GLN cc_start: 0.8627 (tt0) cc_final: 0.8369 (tt0) REVERT: D 262 ASP cc_start: 0.8440 (t0) cc_final: 0.8168 (t0) REVERT: D 298 TYR cc_start: 0.7393 (m-80) cc_final: 0.6724 (m-80) REVERT: E 87 GLU cc_start: 0.8111 (mp0) cc_final: 0.7866 (mt-10) REVERT: E 171 SER cc_start: 0.8634 (p) cc_final: 0.8408 (m) REVERT: E 190 ASN cc_start: 0.8172 (m-40) cc_final: 0.7763 (m110) REVERT: F 103 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8413 (mtmm) REVERT: F 125 TYR cc_start: 0.8486 (t80) cc_final: 0.8177 (t80) REVERT: F 136 LYS cc_start: 0.8263 (mttp) cc_final: 0.8000 (mtpt) REVERT: F 190 ASN cc_start: 0.7562 (m-40) cc_final: 0.6913 (m110) REVERT: F 265 TYR cc_start: 0.8309 (p90) cc_final: 0.7554 (p90) REVERT: C 21 PHE cc_start: 0.8293 (m-80) cc_final: 0.7982 (m-80) REVERT: C 72 MET cc_start: 0.0819 (ttm) cc_final: 0.0241 (ttm) REVERT: C 103 LYS cc_start: 0.8437 (mtmm) cc_final: 0.7736 (mtpt) REVERT: C 104 GLU cc_start: 0.7563 (mp0) cc_final: 0.7284 (mp0) REVERT: C 121 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7522 (mmtt) REVERT: C 137 ARG cc_start: 0.8052 (mmt90) cc_final: 0.7627 (mmt-90) REVERT: C 173 ASN cc_start: 0.8437 (t0) cc_final: 0.8205 (t0) REVERT: C 262 ASP cc_start: 0.8559 (t0) cc_final: 0.8105 (t0) REVERT: C 291 ARG cc_start: 0.7160 (mtt180) cc_final: 0.6483 (mtt180) REVERT: C 304 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7864 (ttp) REVERT: C 329 PHE cc_start: 0.6987 (m-10) cc_final: 0.6721 (m-10) REVERT: G 104 GLU cc_start: 0.7991 (mp0) cc_final: 0.7331 (mp0) REVERT: G 119 TYR cc_start: 0.8274 (m-80) cc_final: 0.8067 (m-80) REVERT: G 124 GLU cc_start: 0.7814 (tt0) cc_final: 0.7553 (tt0) REVERT: G 157 ILE cc_start: 0.8897 (mt) cc_final: 0.8501 (tt) REVERT: G 159 GLU cc_start: 0.7873 (tt0) cc_final: 0.7373 (tt0) REVERT: G 188 THR cc_start: 0.8137 (p) cc_final: 0.7607 (t) REVERT: G 198 ASP cc_start: 0.7934 (m-30) cc_final: 0.7552 (m-30) REVERT: G 244 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7792 (mt-10) REVERT: G 278 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: G 300 LEU cc_start: 0.8438 (mm) cc_final: 0.8160 (mt) REVERT: H 113 ASN cc_start: 0.7658 (p0) cc_final: 0.7430 (p0) REVERT: H 121 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7693 (mttm) REVERT: H 146 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7434 (ttp-170) REVERT: H 149 TRP cc_start: 0.7231 (m100) cc_final: 0.6572 (m100) REVERT: H 177 PHE cc_start: 0.8352 (m-80) cc_final: 0.8027 (m-80) REVERT: H 192 ILE cc_start: 0.8612 (mm) cc_final: 0.8290 (tt) REVERT: H 208 ASN cc_start: 0.8080 (m-40) cc_final: 0.7667 (m-40) REVERT: H 241 PHE cc_start: 0.7141 (t80) cc_final: 0.6746 (t80) REVERT: H 243 PHE cc_start: 0.8111 (t80) cc_final: 0.7697 (t80) REVERT: H 260 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7752 (p) REVERT: H 291 ARG cc_start: 0.6435 (mtp85) cc_final: 0.6173 (mtp85) REVERT: H 293 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.6942 (p0) REVERT: H 299 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7412 (mtmt) REVERT: H 303 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7662 (ttm170) REVERT: H 309 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6346 (tt0) outliers start: 83 outliers final: 61 residues processed: 581 average time/residue: 0.1725 time to fit residues: 153.8265 Evaluate side-chains 607 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 530 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 208 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 221 MET Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 311 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 58 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 105 optimal weight: 0.0980 chunk 160 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.176838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137476 restraints weight = 33859.346| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.32 r_work: 0.3634 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23402 Z= 0.144 Angle : 0.543 9.735 31890 Z= 0.288 Chirality : 0.042 0.303 3533 Planarity : 0.004 0.059 3870 Dihedral : 14.509 178.188 3805 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 3.89 % Allowed : 28.89 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.61 (0.16), residues: 2634 helix: 0.91 (0.18), residues: 758 sheet: -0.11 (0.26), residues: 455 loop : -1.25 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 15 TYR 0.035 0.001 TYR C 125 PHE 0.016 0.001 PHE G 147 TRP 0.011 0.001 TRP G 33 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (23402) covalent geometry : angle 0.54271 / 0.29 (31890) hydrogen bonds : bond 0.03766 / 2.55 ( 673) hydrogen bonds : angle 5.10566 / 3.50 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 535 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.5761 (OUTLIER) cc_final: 0.5435 (t160) REVERT: A 67 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8395 (tp) REVERT: A 104 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5708 (mtt) REVERT: A 115 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5579 (mpt180) REVERT: A 118 MET cc_start: 0.2005 (tpt) cc_final: 0.1788 (tpt) REVERT: A 171 TYR cc_start: 0.6618 (t80) cc_final: 0.6095 (t80) REVERT: A 180 SER cc_start: 0.7379 (t) cc_final: 0.7169 (m) REVERT: A 233 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6832 (mm) REVERT: A 265 ARG cc_start: 0.6759 (mtm180) cc_final: 0.6474 (ttm110) REVERT: A 311 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7393 (mm-40) REVERT: B 144 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7523 (mtpp) REVERT: B 185 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6241 (pm20) REVERT: B 213 LYS cc_start: 0.7527 (mmtp) cc_final: 0.7311 (mttp) REVERT: B 246 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5905 (mm-30) REVERT: I 22 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.4786 (tm-30) REVERT: I 90 ILE cc_start: 0.4120 (OUTLIER) cc_final: 0.3657 (mp) REVERT: I 115 MET cc_start: -0.0600 (mmm) cc_final: -0.1972 (mmm) REVERT: D 89 ASP cc_start: 0.8760 (p0) cc_final: 0.8135 (p0) REVERT: D 104 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7437 (mt-10) REVERT: D 227 GLN cc_start: 0.8637 (tt0) cc_final: 0.8374 (tt0) REVERT: D 262 ASP cc_start: 0.8447 (t0) cc_final: 0.8171 (t0) REVERT: D 298 TYR cc_start: 0.7359 (m-80) cc_final: 0.6723 (m-80) REVERT: E 72 MET cc_start: 0.1092 (mmp) cc_final: -0.1133 (mmp) REVERT: E 87 GLU cc_start: 0.8109 (mp0) cc_final: 0.7857 (mt-10) REVERT: E 171 SER cc_start: 0.8641 (p) cc_final: 0.8413 (m) REVERT: E 190 ASN cc_start: 0.8233 (m-40) cc_final: 0.7856 (m110) REVERT: F 103 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8424 (mtmm) REVERT: F 125 TYR cc_start: 0.8487 (t80) cc_final: 0.8169 (t80) REVERT: F 136 LYS cc_start: 0.8267 (mttp) cc_final: 0.7997 (mtpt) REVERT: F 190 ASN cc_start: 0.7583 (m-40) cc_final: 0.6919 (m110) REVERT: F 265 TYR cc_start: 0.8307 (p90) cc_final: 0.7543 (p90) REVERT: C 21 PHE cc_start: 0.8302 (m-80) cc_final: 0.8067 (m-80) REVERT: C 72 MET cc_start: 0.0910 (ttm) cc_final: 0.0349 (ttm) REVERT: C 103 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7743 (mtpt) REVERT: C 104 GLU cc_start: 0.7586 (mp0) cc_final: 0.7304 (mp0) REVERT: C 121 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7537 (mmtt) REVERT: C 137 ARG cc_start: 0.8060 (mmt90) cc_final: 0.7627 (mmt-90) REVERT: C 173 ASN cc_start: 0.8429 (t0) cc_final: 0.8192 (t0) REVERT: C 262 ASP cc_start: 0.8574 (t0) cc_final: 0.8111 (t0) REVERT: C 291 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6520 (mtt180) REVERT: C 304 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7874 (ttp) REVERT: C 320 MET cc_start: 0.7875 (mmm) cc_final: 0.7486 (mmm) REVERT: C 329 PHE cc_start: 0.6979 (m-10) cc_final: 0.6738 (m-10) REVERT: G 104 GLU cc_start: 0.8028 (mp0) cc_final: 0.7349 (mp0) REVERT: G 119 TYR cc_start: 0.8281 (m-80) cc_final: 0.8067 (m-80) REVERT: G 124 GLU cc_start: 0.7827 (tt0) cc_final: 0.7572 (tt0) REVERT: G 157 ILE cc_start: 0.8906 (mt) cc_final: 0.8460 (tt) REVERT: G 159 GLU cc_start: 0.7889 (tt0) cc_final: 0.7416 (tt0) REVERT: G 188 THR cc_start: 0.8117 (p) cc_final: 0.7573 (t) REVERT: G 198 ASP cc_start: 0.7941 (m-30) cc_final: 0.7559 (m-30) REVERT: G 228 GLU cc_start: 0.8309 (tp30) cc_final: 0.8059 (tp30) REVERT: G 244 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7797 (mt-10) REVERT: G 278 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: G 300 LEU cc_start: 0.8426 (mm) cc_final: 0.8161 (mt) REVERT: H 113 ASN cc_start: 0.7700 (p0) cc_final: 0.7473 (p0) REVERT: H 146 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7382 (ttp-170) REVERT: H 149 TRP cc_start: 0.7248 (m100) cc_final: 0.6569 (m100) REVERT: H 177 PHE cc_start: 0.8332 (m-80) cc_final: 0.8013 (m-80) REVERT: H 192 ILE cc_start: 0.8598 (mm) cc_final: 0.8280 (tt) REVERT: H 208 ASN cc_start: 0.8090 (m-40) cc_final: 0.7685 (m-40) REVERT: H 241 PHE cc_start: 0.7167 (t80) cc_final: 0.6759 (t80) REVERT: H 243 PHE cc_start: 0.8086 (t80) cc_final: 0.7647 (t80) REVERT: H 260 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7780 (p) REVERT: H 291 ARG cc_start: 0.6525 (mtp85) cc_final: 0.6261 (mtp85) REVERT: H 293 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7114 (p0) REVERT: H 299 LYS cc_start: 0.7738 (mtpt) cc_final: 0.7330 (mtmt) REVERT: H 303 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7829 (ttp80) outliers start: 92 outliers final: 67 residues processed: 592 average time/residue: 0.1697 time to fit residues: 155.3577 Evaluate side-chains 605 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 523 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 208 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 221 MET Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 181 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN G 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.174132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134506 restraints weight = 33326.517| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.31 r_work: 0.3575 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23402 Z= 0.187 Angle : 0.569 10.594 31890 Z= 0.301 Chirality : 0.043 0.284 3533 Planarity : 0.005 0.058 3870 Dihedral : 14.470 175.121 3805 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 3.81 % Allowed : 28.85 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.65 (0.16), residues: 2634 helix: 0.84 (0.18), residues: 758 sheet: -0.10 (0.26), residues: 466 loop : -1.28 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 15 TYR 0.028 0.001 TYR C 125 PHE 0.019 0.002 PHE G 214 TRP 0.014 0.002 TRP G 149 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (23402) covalent geometry : angle 0.56936 / 0.30 (31890) hydrogen bonds : bond 0.03976 / 2.70 ( 673) hydrogen bonds : angle 5.17193 / 3.54 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7822.19 seconds wall clock time: 134 minutes 34.28 seconds (8074.28 seconds total)