Starting phenix.real_space_refine on Fri Aug 7 21:15:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjc_54943/08_2026/9sjc_54943.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjc_54943/08_2026/9sjc_54943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sjc_54943/08_2026/9sjc_54943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjc_54943/08_2026/9sjc_54943.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjc_54943/08_2026/9sjc_54943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjc_54943/08_2026/9sjc_54943.cif" } resolution = 1.92 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= 0.030 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 93 5.49 5 S 115 5.16 5 C 14669 2.51 5 N 3953 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23510 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2721 Classifications: {'peptide': 340} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 322} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 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: "L" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2621 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain: "E" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2639 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "F" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2628 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "G" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2500 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain breaks: 2 Chain: "H" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2347 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 11, 'TRANS': 275} Chain breaks: 2 Chain: "K" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} 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': 16, 'rna2p_pyr': 10, 'rna3p_pur': 21, 'rna3p_pyr': 13} Link IDs: {'rna2p': 25, 'rna3p': 34} Time building chain proxies: 5.63, per 1000 atoms: 0.24 Number of scatterers: 23510 At special positions: 0 Unit cell: (118.9, 150.075, 156.6, 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 115 16.00 P 93 15.00 O 4680 8.00 N 3953 7.00 C 14669 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: 1.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5058 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 32 sheets defined 33.6% alpha, 8.9% beta 27 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.860A pdb=" N LEU A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.972A pdb=" N LYS A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) 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 87 through 93 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.854A pdb=" N GLN A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 109' Processing helix chain 'A' and resid 111 through 122 removed outlier: 3.837A pdb=" N MET A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.531A pdb=" N ARG A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.568A pdb=" N THR A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 4.094A 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 255 through 267 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.719A pdb=" N PHE B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.878A 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 238 removed outlier: 3.646A pdb=" N SER B 238 " --> pdb=" O ASP B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 238' Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.252A pdb=" N ILE I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE I 24 " --> pdb=" O ILE I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 35 removed outlier: 3.868A pdb=" N SER I 30 " --> pdb=" O PRO I 26 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 71 removed outlier: 4.096A pdb=" N LEU I 68 " --> pdb=" O ASP I 64 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 107 through 119 Processing helix chain 'I' and resid 124 through 135 removed outlier: 4.305A pdb=" N HIS I 130 " --> pdb=" O PRO I 126 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE I 131 " --> pdb=" O LEU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 141 removed outlier: 3.883A pdb=" N CYS I 140 " --> pdb=" O GLN I 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 4.138A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) 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 removed outlier: 3.507A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) 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: 3.888A pdb=" N LYS E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) 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 63 through 71 removed outlier: 4.302A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (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 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 186 through 201 removed outlier: 3.531A pdb=" N GLN F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.527A 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 removed outlier: 3.554A pdb=" N TYR F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 63 through 71 removed outlier: 4.453A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 186 through 201 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 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 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 186 through 201 Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 267 through 272 removed outlier: 3.534A pdb=" N TYR G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 312 through 326 removed outlier: 3.776A pdb=" N TYR G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.518A pdb=" N ARG H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE H 142 " --> pdb=" O TYR H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.596A pdb=" N ALA H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) 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 removed outlier: 3.724A pdb=" N TYR H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) 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 154 removed outlier: 4.237A 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 157 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 147 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 147 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 301 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 59 through 61 removed outlier: 5.705A pdb=" N SER I 3 " --> pdb=" O GLU I 89 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU I 89 " --> pdb=" O SER I 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AA9, first strand: chain 'D' and resid 106 through 109 Processing sheet with id=AB1, 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 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 167 through 168 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.341A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 54 through 57 Processing sheet with id=AB4, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AB5, first strand: chain 'E' and resid 106 through 109 removed outlier: 3.567A pdb=" N SER E 108 " --> pdb=" O SER E 20 " (cutoff:3.500A) 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 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 168 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 53 through 57 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.335A pdb=" N CYS E 82 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 282 through 283 removed outlier: 3.787A pdb=" N ALA E 283 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 3.653A 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 30 through 35 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 Processing sheet with id=AC2, first strand: chain 'F' and resid 50 through 57 removed outlier: 4.343A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 227 through 228 removed outlier: 4.208A pdb=" N LYS F 239 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AC5, first strand: chain 'F' and resid 282 through 283 removed outlier: 4.291A pdb=" N ALA F 283 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE F 288 " --> pdb=" O ALA F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 106 through 109 removed outlier: 3.552A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AC7, 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 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 172 through 173 current: chain 'C' and resid 246 through 249 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 50 through 57 removed outlier: 4.131A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 106 through 109 Processing sheet with id=AD1, 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 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 167 through 168 current: chain 'G' and resid 246 through 249 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 50 through 54 removed outlier: 4.130A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AD4, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AD5, 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 169 No H-bonds generated for sheet with id=AD5 624 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6885 1.34 - 1.46: 4588 1.46 - 1.58: 12373 1.58 - 1.70: 184 1.70 - 1.82: 183 Bond restraints: 24213 Sorted by residual: bond pdb=" O3' DA L 1 " pdb=" P DA L 2 " ideal model delta sigma weight residual 1.607 1.489 0.118 1.20e-02 6.94e+03 9.73e+01 bond pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.332 1.386 -0.054 1.30e-02 5.92e+03 1.72e+01 bond pdb=" N TYR A 232 " pdb=" CA TYR A 232 " ideal model delta sigma weight residual 1.457 1.509 -0.051 1.29e-02 6.01e+03 1.59e+01 bond pdb=" N PHE I 25 " pdb=" CA PHE I 25 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.04e-02 9.25e+03 1.47e+01 bond pdb=" N VAL A 80 " pdb=" CA VAL A 80 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.18e-02 7.18e+03 1.11e+01 ... (remaining 24208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 32401 2.27 - 4.54: 648 4.54 - 6.81: 60 6.81 - 9.08: 11 9.08 - 11.35: 5 Bond angle restraints: 33125 Sorted by residual: angle pdb=" O4' DC K 38 " pdb=" C4' DC K 38 " pdb=" C3' DC K 38 " ideal model delta sigma weight residual 106.00 102.48 3.52 6.00e-01 2.78e+00 3.44e+01 angle pdb=" N ALA A 84 " pdb=" CA ALA A 84 " pdb=" C ALA A 84 " ideal model delta sigma weight residual 113.72 107.73 5.99 1.30e+00 5.92e-01 2.12e+01 angle pdb=" N3 DT K 42 " pdb=" C4 DT K 42 " pdb=" O4 DT K 42 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N TYR A 232 " pdb=" CA TYR A 232 " pdb=" CB TYR A 232 " ideal model delta sigma weight residual 110.49 118.14 -7.65 1.69e+00 3.50e-01 2.05e+01 angle pdb=" O4 DT K 42 " pdb=" C4 DT K 42 " pdb=" C5 DT K 42 " ideal model delta sigma weight residual 124.90 121.85 3.05 7.00e-01 2.04e+00 1.90e+01 ... (remaining 33120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.15: 13585 32.15 - 64.30: 992 64.30 - 96.46: 89 96.46 - 128.61: 0 128.61 - 160.76: 2 Dihedral angle restraints: 14668 sinusoidal: 6840 harmonic: 7828 Sorted by residual: dihedral pdb=" CA ASP G 310 " pdb=" C ASP G 310 " pdb=" N LEU G 311 " pdb=" CA LEU G 311 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" O4' U J 44 " pdb=" C1' U J 44 " pdb=" N1 U J 44 " pdb=" C2 U J 44 " ideal model delta sinusoidal sigma weight residual -128.00 -48.44 -79.56 1 1.70e+01 3.46e-03 2.72e+01 dihedral pdb=" O4' A J 45 " pdb=" C1' A J 45 " pdb=" N9 A J 45 " pdb=" C4 A J 45 " ideal model delta sinusoidal sigma weight residual 254.00 175.09 78.91 1 1.70e+01 3.46e-03 2.68e+01 ... (remaining 14665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3536 0.107 - 0.214: 128 0.214 - 0.321: 6 0.321 - 0.428: 1 0.428 - 0.535: 4 Chirality restraints: 3675 Sorted by residual: chirality pdb=" P U J 54 " pdb=" OP1 U J 54 " pdb=" OP2 U J 54 " pdb=" O5' U J 54 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" P DA L 2 " pdb=" OP1 DA L 2 " pdb=" OP2 DA L 2 " pdb=" O5' DA L 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" P G J 33 " pdb=" OP1 G J 33 " pdb=" OP2 G J 33 " pdb=" O5' G J 33 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 3672 not shown) Planarity restraints: 3901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 279 " -0.024 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" C GLU A 279 " 0.083 2.00e-02 2.50e+03 pdb=" O GLU A 279 " -0.031 2.00e-02 2.50e+03 pdb=" N ARG A 280 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 231 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU A 231 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU A 231 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR A 232 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 53 " -0.015 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ALA F 53 " 0.056 2.00e-02 2.50e+03 pdb=" O ALA F 53 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL F 54 " -0.019 2.00e-02 2.50e+03 ... (remaining 3898 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1008 2.70 - 3.25: 23791 3.25 - 3.80: 41229 3.80 - 4.35: 55932 4.35 - 4.90: 87482 Nonbonded interactions: 209442 Sorted by model distance: nonbonded pdb=" O2' A J 30 " pdb=" O4' C J 31 " model vdw 2.155 3.040 nonbonded pdb=" O2' G J 59 " pdb=" OP1 G J 60 " model vdw 2.162 3.040 nonbonded pdb=" OD2 ASP A 78 " pdb=" OG1 THR A 167 " model vdw 2.208 3.040 nonbonded pdb=" O LYS H 136 " pdb=" ND2 ASN H 140 " model vdw 2.214 3.120 nonbonded pdb=" O2' U J 18 " pdb=" O4' U J 19 " model vdw 2.217 3.040 ... (remaining 209437 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 81 through 230 or resid 239 through \ 333)) selection = (chain 'D' and (resid 12 through 52 or resid 81 through 230 or resid 239 through \ 333)) selection = (chain 'E' and (resid 12 through 52 or resid 81 through 230 or resid 239 through \ 333)) selection = (chain 'F' and (resid 12 through 52 or resid 81 through 230 or resid 239 through \ 333)) selection = (chain 'G' and (resid 12 through 52 or resid 81 through 230 or resid 239 through \ 333)) selection = (chain 'H' and resid 12 through 333) } 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: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.230 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 0.118 24213 Z= 0.245 Angle : 0.727 11.352 33125 Z= 0.480 Chirality : 0.048 0.535 3675 Planarity : 0.005 0.085 3901 Dihedral : 20.190 160.759 9610 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.06 % Favored : 94.60 % Rotamer: Outliers : 0.93 % Allowed : 26.26 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 2631 helix: 0.80 (0.19), residues: 750 sheet: 0.13 (0.26), residues: 454 loop : -0.98 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 146 TYR 0.024 0.001 TYR G 265 PHE 0.024 0.001 PHE I 32 TRP 0.026 0.001 TRP H 33 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.24 (24213) covalent geometry : angle 0.72673 / 0.48 (33125) hydrogen bonds : bond 0.23645 / 15.60 ( 689) hydrogen bonds : angle 7.80208 / 5.48 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 649 time to evaluate : 0.930 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: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.7862 (t0) cc_final: 0.7631 (t0) REVERT: A 104 MET cc_start: 0.4104 (mmp) cc_final: 0.3733 (mmt) REVERT: A 173 VAL cc_start: 0.7567 (t) cc_final: 0.7314 (p) REVERT: A 230 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7570 (mmmt) REVERT: A 282 GLU cc_start: 0.6124 (pm20) cc_final: 0.5913 (tp30) REVERT: A 307 VAL cc_start: 0.7775 (t) cc_final: 0.7495 (p) REVERT: A 309 LEU cc_start: 0.8219 (mt) cc_final: 0.7929 (mm) REVERT: B 44 ASN cc_start: 0.7592 (m-40) cc_final: 0.7098 (m-40) REVERT: B 183 LEU cc_start: 0.8123 (mt) cc_final: 0.7897 (mt) REVERT: B 240 LEU cc_start: 0.8687 (mp) cc_final: 0.8446 (mm) REVERT: I 140 CYS cc_start: 0.0782 (OUTLIER) cc_final: 0.0354 (t) REVERT: D 72 MET cc_start: 0.6483 (mmm) cc_final: 0.5746 (mtt) REVERT: D 106 MET cc_start: 0.7582 (tpp) cc_final: 0.6881 (ttp) REVERT: D 107 TYR cc_start: 0.7579 (t80) cc_final: 0.7080 (t80) REVERT: D 265 TYR cc_start: 0.7656 (p90) cc_final: 0.7110 (p90) REVERT: E 35 THR cc_start: 0.6954 (t) cc_final: 0.6741 (t) REVERT: E 51 ASP cc_start: 0.7404 (p0) cc_final: 0.7191 (p0) REVERT: E 302 ASP cc_start: 0.7216 (m-30) cc_final: 0.6984 (m-30) REVERT: F 111 ASP cc_start: 0.7336 (t0) cc_final: 0.7054 (t0) REVERT: F 114 TYR cc_start: 0.8171 (t80) cc_final: 0.7956 (t80) REVERT: F 228 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: C 269 THR cc_start: 0.7140 (p) cc_final: 0.6639 (m) REVERT: G 112 TYR cc_start: 0.6660 (t80) cc_final: 0.6435 (t80) REVERT: G 118 ILE cc_start: 0.7757 (mm) cc_final: 0.7443 (tp) REVERT: G 158 ILE cc_start: 0.7499 (mt) cc_final: 0.7203 (mt) REVERT: G 180 ASP cc_start: 0.6701 (m-30) cc_final: 0.6408 (m-30) REVERT: G 249 MET cc_start: 0.8223 (ttt) cc_final: 0.7994 (ttp) REVERT: H 150 ARG cc_start: 0.7766 (mmm160) cc_final: 0.6767 (mmm-85) REVERT: H 275 ILE cc_start: 0.7070 (pt) cc_final: 0.6866 (tp) REVERT: H 279 ASN cc_start: 0.6171 (OUTLIER) cc_final: 0.5833 (m-40) REVERT: H 304 MET cc_start: 0.7264 (tpt) cc_final: 0.6674 (tpt) REVERT: H 320 MET cc_start: 0.6581 (mmm) cc_final: 0.6061 (mtt) outliers start: 22 outliers final: 14 residues processed: 665 average time/residue: 0.5794 time to fit residues: 446.0433 Evaluate side-chains 548 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 531 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 279 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0270 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 HIS I 136 GLN I 137 GLN D 140 ASN D 141 ASN D 178 ASN D 195 GLN F 173 ASN F 208 ASN C 140 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 ASN ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.192490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.160557 restraints weight = 36176.932| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 1.83 r_work: 0.4354 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4258 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24213 Z= 0.180 Angle : 0.667 11.078 33125 Z= 0.360 Chirality : 0.046 0.312 3675 Planarity : 0.006 0.067 3901 Dihedral : 17.824 162.110 4223 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.98 % Favored : 94.87 % Rotamer: Outliers : 5.24 % Allowed : 28.46 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2631 helix: 0.49 (0.18), residues: 790 sheet: 0.22 (0.26), residues: 443 loop : -1.16 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 146 TYR 0.032 0.002 TYR F 224 PHE 0.023 0.002 PHE F 273 TRP 0.014 0.001 TRP H 33 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (24213) covalent geometry : angle 0.66669 / 0.36 (33125) hydrogen bonds : bond 0.05737 / 3.84 ( 689) hydrogen bonds : angle 5.81072 / 3.98 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 548 time to evaluate : 0.774 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: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8101 (t0) cc_final: 0.7654 (t0) REVERT: A 61 ASP cc_start: 0.3779 (m-30) cc_final: 0.3534 (m-30) REVERT: A 87 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7633 (ttmm) REVERT: A 180 SER cc_start: 0.7812 (t) cc_final: 0.7350 (m) REVERT: A 229 ASP cc_start: 0.8413 (t0) cc_final: 0.8068 (t0) REVERT: A 322 MET cc_start: 0.6391 (ttt) cc_final: 0.6182 (ttt) REVERT: B 183 LEU cc_start: 0.7979 (mt) cc_final: 0.7705 (mp) REVERT: B 206 GLU cc_start: 0.7403 (tt0) cc_final: 0.6988 (tt0) REVERT: D 35 THR cc_start: 0.7565 (t) cc_final: 0.6990 (m) REVERT: D 72 MET cc_start: 0.6477 (mmm) cc_final: 0.5293 (mmt) REVERT: D 106 MET cc_start: 0.8024 (tpp) cc_final: 0.7576 (ttp) REVERT: D 320 MET cc_start: 0.7529 (mpp) cc_final: 0.7257 (mpp) REVERT: E 51 ASP cc_start: 0.7857 (p0) cc_final: 0.7637 (p0) REVERT: E 111 ASP cc_start: 0.6643 (t0) cc_final: 0.6380 (t0) REVERT: F 90 THR cc_start: 0.7859 (m) cc_final: 0.7534 (p) REVERT: F 111 ASP cc_start: 0.7473 (t0) cc_final: 0.7245 (t0) REVERT: F 123 ASP cc_start: 0.7323 (m-30) cc_final: 0.7114 (m-30) REVERT: F 308 ASN cc_start: 0.8011 (t0) cc_final: 0.7767 (t0) REVERT: G 92 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7880 (ttp80) REVERT: G 112 TYR cc_start: 0.6848 (t80) cc_final: 0.6581 (t80) REVERT: G 249 MET cc_start: 0.8458 (ttt) cc_final: 0.8232 (ttp) REVERT: G 256 ASN cc_start: 0.7676 (t0) cc_final: 0.7472 (t160) REVERT: G 299 LYS cc_start: 0.8136 (mttp) cc_final: 0.7352 (mmpt) REVERT: H 150 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7093 (mmm-85) REVERT: H 275 ILE cc_start: 0.7507 (pt) cc_final: 0.7206 (tp) REVERT: H 288 ILE cc_start: 0.4990 (tp) cc_final: 0.4743 (tp) REVERT: H 304 MET cc_start: 0.7294 (tpt) cc_final: 0.7046 (tpt) outliers start: 124 outliers final: 48 residues processed: 617 average time/residue: 0.5396 time to fit residues: 388.0860 Evaluate side-chains 575 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 526 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 315 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 21 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 chunk 259 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 250 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN D 140 ASN C 80 GLN C 140 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN G 141 ASN ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 255 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.183217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.151058 restraints weight = 36806.295| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 1.89 r_work: 0.4249 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4150 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24213 Z= 0.178 Angle : 0.629 9.323 33125 Z= 0.340 Chirality : 0.045 0.323 3675 Planarity : 0.005 0.073 3901 Dihedral : 17.723 164.221 4206 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.28 % Favored : 94.56 % Rotamer: Outliers : 4.86 % Allowed : 29.60 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2631 helix: 0.45 (0.18), residues: 785 sheet: 0.10 (0.26), residues: 448 loop : -1.24 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 204 TYR 0.026 0.002 TYR F 224 PHE 0.044 0.002 PHE H 329 TRP 0.011 0.001 TRP E 33 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (24213) covalent geometry : angle 0.62908 / 0.34 (33125) hydrogen bonds : bond 0.05185 / 3.50 ( 689) hydrogen bonds : angle 5.55842 / 3.81 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 534 time to evaluate : 0.840 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: symmetry clash REVERT: A 56 ASP cc_start: 0.8224 (t0) cc_final: 0.7818 (t0) REVERT: A 61 ASP cc_start: 0.4605 (m-30) cc_final: 0.3987 (m-30) REVERT: A 117 GLU cc_start: 0.6793 (tp30) cc_final: 0.6585 (tp30) REVERT: A 180 SER cc_start: 0.7875 (t) cc_final: 0.7426 (m) REVERT: A 229 ASP cc_start: 0.8466 (t0) cc_final: 0.8111 (t0) REVERT: A 241 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: A 322 MET cc_start: 0.6460 (ttt) cc_final: 0.6210 (ttt) REVERT: B 183 LEU cc_start: 0.7979 (mt) cc_final: 0.7751 (mt) REVERT: B 249 LEU cc_start: 0.7880 (tp) cc_final: 0.7605 (tm) REVERT: I 43 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: I 56 ASN cc_start: 0.5473 (OUTLIER) cc_final: 0.5128 (t0) REVERT: D 35 THR cc_start: 0.7269 (t) cc_final: 0.6176 (m) REVERT: D 72 MET cc_start: 0.6531 (mmm) cc_final: 0.5006 (mmt) REVERT: D 229 MET cc_start: 0.7789 (tpp) cc_final: 0.7394 (tpp) REVERT: E 51 ASP cc_start: 0.7864 (p0) cc_final: 0.7628 (p0) REVERT: F 111 ASP cc_start: 0.7488 (t0) cc_final: 0.7254 (t0) REVERT: F 123 ASP cc_start: 0.7322 (m-30) cc_final: 0.7111 (m-30) REVERT: F 308 ASN cc_start: 0.8077 (t0) cc_final: 0.7870 (t0) REVERT: G 112 TYR cc_start: 0.6842 (t80) cc_final: 0.6625 (t80) REVERT: G 119 TYR cc_start: 0.8149 (m-80) cc_final: 0.7941 (m-80) REVERT: G 219 CYS cc_start: 0.5964 (OUTLIER) cc_final: 0.4773 (t) REVERT: G 299 LYS cc_start: 0.8147 (mttp) cc_final: 0.7319 (mmpt) REVERT: H 131 PHE cc_start: 0.7468 (m-80) cc_final: 0.7193 (m-80) REVERT: H 150 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7090 (mmm-85) REVERT: H 210 TYR cc_start: 0.6191 (m-80) cc_final: 0.5746 (m-80) REVERT: H 304 MET cc_start: 0.7072 (tpt) cc_final: 0.6835 (tpt) REVERT: H 320 MET cc_start: 0.6522 (mmt) cc_final: 0.6126 (mtt) outliers start: 115 outliers final: 46 residues processed: 598 average time/residue: 0.5226 time to fit residues: 364.8727 Evaluate side-chains 558 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 508 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 43 PHE Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 130 optimal weight: 0.3980 chunk 269 optimal weight: 40.0000 chunk 225 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 201 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 44 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4631 r_free = 0.4631 target = 0.181098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.149282 restraints weight = 36523.471| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 1.85 r_work: 0.4244 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4144 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24213 Z= 0.170 Angle : 0.611 9.276 33125 Z= 0.328 Chirality : 0.044 0.321 3675 Planarity : 0.005 0.072 3901 Dihedral : 17.635 164.133 4198 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.53 % Rotamer: Outliers : 5.07 % Allowed : 30.78 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2631 helix: 0.47 (0.18), residues: 772 sheet: 0.04 (0.26), residues: 433 loop : -1.21 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 204 TYR 0.028 0.001 TYR F 224 PHE 0.059 0.002 PHE H 329 TRP 0.011 0.001 TRP E 33 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (24213) covalent geometry : angle 0.61122 / 0.33 (33125) hydrogen bonds : bond 0.04662 / 3.17 ( 689) hydrogen bonds : angle 5.32411 / 3.63 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 527 time to evaluate : 0.804 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 56 ASP cc_start: 0.8218 (t0) cc_final: 0.7830 (t0) REVERT: A 61 ASP cc_start: 0.4910 (m-30) cc_final: 0.4075 (m-30) REVERT: A 125 TYR cc_start: 0.7074 (t80) cc_final: 0.6832 (t80) REVERT: A 180 SER cc_start: 0.7862 (t) cc_final: 0.7461 (m) REVERT: A 241 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: A 282 GLU cc_start: 0.5316 (tp30) cc_final: 0.5080 (tm-30) REVERT: A 310 SER cc_start: 0.7231 (OUTLIER) cc_final: 0.7022 (p) REVERT: A 322 MET cc_start: 0.6444 (ttt) cc_final: 0.6169 (ttt) REVERT: B 183 LEU cc_start: 0.8005 (mt) cc_final: 0.7790 (mt) REVERT: I 43 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: I 56 ASN cc_start: 0.5436 (OUTLIER) cc_final: 0.4995 (t0) REVERT: D 35 THR cc_start: 0.7203 (t) cc_final: 0.6204 (m) REVERT: D 43 PHE cc_start: 0.7580 (t80) cc_final: 0.7336 (t80) REVERT: D 72 MET cc_start: 0.6539 (mmm) cc_final: 0.6203 (mmt) REVERT: D 115 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7877 (ttm-80) REVERT: E 51 ASP cc_start: 0.7931 (p0) cc_final: 0.7706 (p0) REVERT: F 23 ARG cc_start: 0.8101 (ptp-170) cc_final: 0.7605 (ptt-90) REVERT: F 123 ASP cc_start: 0.7329 (m-30) cc_final: 0.7109 (m-30) REVERT: F 238 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8186 (ttpt) REVERT: F 284 ARG cc_start: 0.7713 (ttm170) cc_final: 0.7174 (mtp85) REVERT: F 308 ASN cc_start: 0.8130 (t0) cc_final: 0.7824 (t0) REVERT: C 66 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7308 (ttmt) REVERT: G 26 ASN cc_start: 0.7405 (t160) cc_final: 0.6942 (t0) REVERT: G 119 TYR cc_start: 0.8148 (m-80) cc_final: 0.7919 (m-80) REVERT: G 122 ILE cc_start: 0.8155 (mt) cc_final: 0.7769 (mp) REVERT: G 224 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7208 (m-80) REVERT: G 229 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.5456 (mtt) REVERT: G 299 LYS cc_start: 0.8155 (mttp) cc_final: 0.7361 (mmpt) REVERT: H 210 TYR cc_start: 0.6153 (m-80) cc_final: 0.5768 (m-80) REVERT: H 275 ILE cc_start: 0.7528 (pt) cc_final: 0.7257 (tp) REVERT: H 279 ASN cc_start: 0.6459 (OUTLIER) cc_final: 0.5976 (m-40) outliers start: 120 outliers final: 58 residues processed: 605 average time/residue: 0.5716 time to fit residues: 404.4328 Evaluate side-chains 578 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 511 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 43 PHE Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 279 ASN Chi-restraints excluded: chain H residue 305 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 141 optimal weight: 0.4980 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 HIS D 140 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.180397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.148711 restraints weight = 36096.442| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 1.83 r_work: 0.4236 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 24213 Z= 0.188 Angle : 0.629 10.494 33125 Z= 0.335 Chirality : 0.045 0.320 3675 Planarity : 0.005 0.075 3901 Dihedral : 17.576 164.075 4195 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 5.33 % Allowed : 30.40 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2631 helix: 0.50 (0.18), residues: 773 sheet: 0.01 (0.26), residues: 428 loop : -1.22 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 15 TYR 0.027 0.002 TYR G 112 PHE 0.033 0.002 PHE H 329 TRP 0.015 0.001 TRP A 208 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (24213) covalent geometry : angle 0.62940 / 0.34 (33125) hydrogen bonds : bond 0.04626 / 3.14 ( 689) hydrogen bonds : angle 5.20454 / 3.55 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 546 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8252 (t0) cc_final: 0.7764 (t0) REVERT: A 61 ASP cc_start: 0.5312 (m-30) cc_final: 0.4217 (m-30) REVERT: A 95 MET cc_start: 0.6774 (mpp) cc_final: 0.6320 (mtm) REVERT: A 117 GLU cc_start: 0.6777 (tp30) cc_final: 0.6383 (tp30) REVERT: A 121 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7208 (mm) REVERT: A 125 TYR cc_start: 0.7068 (t80) cc_final: 0.6786 (t80) REVERT: A 241 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: A 282 GLU cc_start: 0.5526 (tp30) cc_final: 0.5307 (mm-30) REVERT: A 322 MET cc_start: 0.6373 (ttt) cc_final: 0.6084 (ttt) REVERT: B 89 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6310 (pm20) REVERT: B 183 LEU cc_start: 0.8027 (mt) cc_final: 0.7818 (mt) REVERT: I 43 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: I 56 ASN cc_start: 0.5429 (OUTLIER) cc_final: 0.5031 (t0) REVERT: D 35 THR cc_start: 0.7277 (t) cc_final: 0.6360 (m) REVERT: D 72 MET cc_start: 0.6312 (mmm) cc_final: 0.5640 (mtt) REVERT: D 115 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7851 (ttm-80) REVERT: E 273 PHE cc_start: 0.7941 (p90) cc_final: 0.7645 (p90) REVERT: F 23 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7653 (ptt-90) REVERT: F 123 ASP cc_start: 0.7427 (m-30) cc_final: 0.7213 (m-30) REVERT: F 124 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: F 150 ARG cc_start: 0.7624 (ttt90) cc_final: 0.7043 (ttt90) REVERT: F 238 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8190 (ttpt) REVERT: F 284 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7218 (mtm180) REVERT: F 308 ASN cc_start: 0.8187 (t0) cc_final: 0.7833 (t0) REVERT: G 21 PHE cc_start: 0.8232 (m-80) cc_final: 0.7972 (m-80) REVERT: G 122 ILE cc_start: 0.8162 (mt) cc_final: 0.7769 (mp) REVERT: G 224 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: G 229 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5435 (mtt) REVERT: G 299 LYS cc_start: 0.8138 (mttp) cc_final: 0.7354 (mmpt) REVERT: H 175 LYS cc_start: 0.7831 (mmtp) cc_final: 0.7630 (mmtp) REVERT: H 210 TYR cc_start: 0.6171 (m-80) cc_final: 0.5694 (m-80) REVERT: H 275 ILE cc_start: 0.7501 (pt) cc_final: 0.7222 (tp) REVERT: H 279 ASN cc_start: 0.6487 (OUTLIER) cc_final: 0.5991 (m-40) outliers start: 126 outliers final: 59 residues processed: 623 average time/residue: 0.5816 time to fit residues: 422.3278 Evaluate side-chains 583 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 512 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 43 PHE Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 279 ASN Chi-restraints excluded: chain H residue 305 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 206 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 205 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 231 optimal weight: 0.0050 chunk 59 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 HIS ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN E 195 GLN C 18 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4626 r_free = 0.4626 target = 0.180982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.149262 restraints weight = 36344.143| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 1.85 r_work: 0.4242 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4144 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24213 Z= 0.150 Angle : 0.620 11.132 33125 Z= 0.329 Chirality : 0.044 0.318 3675 Planarity : 0.005 0.076 3901 Dihedral : 17.541 164.231 4191 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 5.37 % Allowed : 31.42 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.16), residues: 2631 helix: 0.54 (0.18), residues: 774 sheet: -0.01 (0.26), residues: 433 loop : -1.21 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 204 TYR 0.035 0.001 TYR F 224 PHE 0.034 0.002 PHE E 95 TRP 0.015 0.001 TRP A 208 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (24213) covalent geometry : angle 0.61993 / 0.33 (33125) hydrogen bonds : bond 0.04432 / 3.02 ( 689) hydrogen bonds : angle 5.12411 / 3.51 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 513 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.7004 (ppt170) REVERT: A 56 ASP cc_start: 0.8242 (t0) cc_final: 0.7738 (t0) REVERT: A 61 ASP cc_start: 0.5268 (m-30) cc_final: 0.4117 (m-30) REVERT: A 180 SER cc_start: 0.7801 (t) cc_final: 0.7498 (m) REVERT: A 241 GLU cc_start: 0.7219 (pm20) cc_final: 0.7013 (pm20) REVERT: A 282 GLU cc_start: 0.5531 (tp30) cc_final: 0.5300 (mm-30) REVERT: A 322 MET cc_start: 0.6356 (ttt) cc_final: 0.6059 (ttt) REVERT: B 183 LEU cc_start: 0.7977 (mt) cc_final: 0.7760 (mt) REVERT: I 43 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: I 56 ASN cc_start: 0.5261 (OUTLIER) cc_final: 0.4932 (t0) REVERT: D 35 THR cc_start: 0.7218 (t) cc_final: 0.6320 (m) REVERT: D 62 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7411 (mtp) REVERT: D 72 MET cc_start: 0.6342 (mmm) cc_final: 0.5829 (mtt) REVERT: D 107 TYR cc_start: 0.7632 (t80) cc_final: 0.7219 (t80) REVERT: D 115 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7806 (ttm-80) REVERT: E 15 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.8074 (ttp-170) REVERT: F 23 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7636 (ptt-90) REVERT: F 123 ASP cc_start: 0.7412 (m-30) cc_final: 0.7193 (m-30) REVERT: F 244 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: F 284 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7228 (mtp85) REVERT: F 308 ASN cc_start: 0.8210 (t0) cc_final: 0.7868 (t0) REVERT: C 169 TYR cc_start: 0.8496 (m-80) cc_final: 0.8295 (m-80) REVERT: G 122 ILE cc_start: 0.8174 (mt) cc_final: 0.7866 (mp) REVERT: G 224 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: G 229 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.5324 (mtt) REVERT: G 299 LYS cc_start: 0.8117 (mttp) cc_final: 0.7366 (mmpt) REVERT: H 175 LYS cc_start: 0.7855 (mmtp) cc_final: 0.7638 (mmtp) REVERT: H 210 TYR cc_start: 0.6142 (m-80) cc_final: 0.5661 (m-80) REVERT: H 275 ILE cc_start: 0.7509 (pt) cc_final: 0.7100 (mp) REVERT: H 279 ASN cc_start: 0.6486 (OUTLIER) cc_final: 0.6015 (m-40) outliers start: 127 outliers final: 61 residues processed: 597 average time/residue: 0.5446 time to fit residues: 379.0695 Evaluate side-chains 582 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 510 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 43 PHE Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 279 ASN Chi-restraints excluded: chain H residue 305 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 180 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 259 optimal weight: 1.9990 chunk 104 optimal weight: 0.0470 chunk 185 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 60 HIS ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.180634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.148390 restraints weight = 36431.472| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.24 r_work: 0.4213 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4107 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24213 Z= 0.177 Angle : 0.636 11.947 33125 Z= 0.336 Chirality : 0.044 0.316 3675 Planarity : 0.005 0.079 3901 Dihedral : 17.507 164.511 4191 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 4.69 % Allowed : 32.18 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.16), residues: 2631 helix: 0.53 (0.18), residues: 773 sheet: 0.06 (0.27), residues: 424 loop : -1.22 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 146 TYR 0.044 0.002 TYR F 224 PHE 0.031 0.002 PHE E 95 TRP 0.013 0.001 TRP F 33 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (24213) covalent geometry : angle 0.63555 / 0.34 (33125) hydrogen bonds : bond 0.04478 / 3.06 ( 689) hydrogen bonds : angle 5.06715 / 3.48 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 511 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7080 (ppt170) REVERT: A 56 ASP cc_start: 0.8298 (t0) cc_final: 0.7791 (t0) REVERT: A 61 ASP cc_start: 0.5398 (m-30) cc_final: 0.4214 (m-30) REVERT: A 121 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7255 (mm) REVERT: A 125 TYR cc_start: 0.7168 (t80) cc_final: 0.6939 (t80) REVERT: A 180 SER cc_start: 0.7975 (t) cc_final: 0.7624 (m) REVERT: A 181 LYS cc_start: 0.7864 (mtmt) cc_final: 0.7634 (mtmt) REVERT: A 241 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.7021 (pm20) REVERT: A 272 ARG cc_start: 0.6611 (ttt180) cc_final: 0.6320 (mtt-85) REVERT: A 282 GLU cc_start: 0.5684 (tp30) cc_final: 0.5450 (mm-30) REVERT: A 322 MET cc_start: 0.6374 (ttt) cc_final: 0.6071 (ttt) REVERT: B 183 LEU cc_start: 0.8025 (mt) cc_final: 0.7815 (mt) REVERT: I 43 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7189 (m-80) REVERT: I 56 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4774 (t0) REVERT: I 143 TYR cc_start: 0.3469 (OUTLIER) cc_final: 0.3126 (p90) REVERT: D 35 THR cc_start: 0.7299 (t) cc_final: 0.6389 (m) REVERT: D 62 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7697 (mtp) REVERT: D 72 MET cc_start: 0.6414 (mmm) cc_final: 0.5937 (mtt) REVERT: D 115 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7854 (ttm-80) REVERT: E 309 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7532 (tt0) REVERT: F 23 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7598 (ptp-170) REVERT: F 123 ASP cc_start: 0.7541 (m-30) cc_final: 0.7304 (m-30) REVERT: F 244 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: F 284 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7325 (mtp85) REVERT: F 308 ASN cc_start: 0.8240 (t0) cc_final: 0.7872 (t0) REVERT: G 119 TYR cc_start: 0.8153 (m-80) cc_final: 0.7855 (m-80) REVERT: G 219 CYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5839 (t) REVERT: G 224 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: G 229 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5404 (mtt) REVERT: G 299 LYS cc_start: 0.8158 (mttp) cc_final: 0.7359 (mmpt) REVERT: H 175 LYS cc_start: 0.7887 (mmtp) cc_final: 0.7675 (mmtp) REVERT: H 275 ILE cc_start: 0.7534 (pt) cc_final: 0.7150 (mp) REVERT: H 279 ASN cc_start: 0.6524 (OUTLIER) cc_final: 0.6071 (m-40) outliers start: 111 outliers final: 63 residues processed: 584 average time/residue: 0.5512 time to fit residues: 375.0461 Evaluate side-chains 583 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 505 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 43 PHE Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 279 ASN Chi-restraints excluded: chain H residue 305 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 95 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN H 18 ASN ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** 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 = 0.4685 r_free = 0.4685 target = 0.186593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.154963 restraints weight = 35227.317| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 1.80 r_work: 0.4307 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4207 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24213 Z= 0.172 Angle : 0.643 12.005 33125 Z= 0.338 Chirality : 0.044 0.311 3675 Planarity : 0.005 0.075 3901 Dihedral : 17.478 164.546 4191 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 4.31 % Allowed : 33.15 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.16), residues: 2631 helix: 0.51 (0.18), residues: 780 sheet: -0.06 (0.26), residues: 432 loop : -1.25 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 265 TYR 0.030 0.002 TYR F 224 PHE 0.032 0.002 PHE E 95 TRP 0.014 0.001 TRP F 33 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (24213) covalent geometry : angle 0.64288 / 0.34 (33125) hydrogen bonds : bond 0.04394 / 3.01 ( 689) hydrogen bonds : angle 5.01362 / 3.43 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 524 time to evaluate : 0.843 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 3 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6751 (ppt170) REVERT: A 56 ASP cc_start: 0.8171 (t0) cc_final: 0.7759 (t0) REVERT: A 121 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7215 (mm) REVERT: A 125 TYR cc_start: 0.7155 (t80) cc_final: 0.6797 (t80) REVERT: A 282 GLU cc_start: 0.5866 (tp30) cc_final: 0.5599 (mm-30) REVERT: A 322 MET cc_start: 0.6211 (ttt) cc_final: 0.5905 (ttt) REVERT: B 89 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: I 56 ASN cc_start: 0.4934 (OUTLIER) cc_final: 0.4668 (t0) REVERT: I 143 TYR cc_start: 0.3467 (OUTLIER) cc_final: 0.3184 (p90) REVERT: D 35 THR cc_start: 0.7161 (t) cc_final: 0.6401 (m) REVERT: D 62 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7682 (mtp) REVERT: D 72 MET cc_start: 0.6379 (mmm) cc_final: 0.5932 (mtt) REVERT: D 115 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7731 (ttm-80) REVERT: F 23 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7541 (ptt-90) REVERT: F 123 ASP cc_start: 0.7355 (m-30) cc_final: 0.7129 (m-30) REVERT: F 244 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: F 284 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7320 (mtm180) REVERT: F 308 ASN cc_start: 0.8226 (t0) cc_final: 0.7872 (t0) REVERT: C 328 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7050 (mmt) REVERT: G 119 TYR cc_start: 0.8153 (m-80) cc_final: 0.7847 (m-80) REVERT: G 126 ILE cc_start: 0.7648 (mp) cc_final: 0.7446 (mt) REVERT: G 219 CYS cc_start: 0.6209 (OUTLIER) cc_final: 0.5882 (t) REVERT: G 224 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: G 299 LYS cc_start: 0.8110 (mttp) cc_final: 0.7376 (mmpt) REVERT: H 275 ILE cc_start: 0.7577 (pt) cc_final: 0.7228 (mp) outliers start: 102 outliers final: 57 residues processed: 585 average time/residue: 0.5844 time to fit residues: 397.6242 Evaluate side-chains 577 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 507 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 305 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 221 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN C 18 ASN C 75 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN H 34 GLN ** H 144 ASN ** 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 = 0.4689 r_free = 0.4689 target = 0.187001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.155238 restraints weight = 35408.248| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.82 r_work: 0.4312 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4213 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24213 Z= 0.159 Angle : 0.647 13.536 33125 Z= 0.339 Chirality : 0.044 0.305 3675 Planarity : 0.005 0.088 3901 Dihedral : 17.434 164.755 4191 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 3.76 % Allowed : 34.21 % Favored : 62.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2631 helix: 0.55 (0.18), residues: 784 sheet: -0.07 (0.27), residues: 426 loop : -1.22 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 146 TYR 0.030 0.001 TYR A 171 PHE 0.031 0.002 PHE E 329 TRP 0.012 0.001 TRP F 33 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (24213) covalent geometry : angle 0.64652 / 0.34 (33125) hydrogen bonds : bond 0.04334 / 2.98 ( 689) hydrogen bonds : angle 4.97126 / 3.40 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 517 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6787 (ppt170) REVERT: A 56 ASP cc_start: 0.8161 (t0) cc_final: 0.7733 (t0) REVERT: A 61 ASP cc_start: 0.5397 (m-30) cc_final: 0.4156 (m-30) REVERT: A 125 TYR cc_start: 0.7168 (t80) cc_final: 0.6782 (t80) REVERT: A 272 ARG cc_start: 0.6704 (ttt180) cc_final: 0.6436 (mtt-85) REVERT: A 282 GLU cc_start: 0.5909 (tp30) cc_final: 0.5660 (mm-30) REVERT: A 322 MET cc_start: 0.6160 (ttt) cc_final: 0.5874 (ttt) REVERT: B 89 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6472 (pm20) REVERT: I 143 TYR cc_start: 0.3393 (OUTLIER) cc_final: 0.3156 (p90) REVERT: D 35 THR cc_start: 0.7167 (t) cc_final: 0.6395 (m) REVERT: D 62 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7801 (mtp) REVERT: D 72 MET cc_start: 0.6362 (mmm) cc_final: 0.5987 (mtt) REVERT: D 115 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7720 (ttm-80) REVERT: F 23 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7576 (ptt-90) REVERT: F 123 ASP cc_start: 0.7409 (m-30) cc_final: 0.7207 (m-30) REVERT: F 244 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: F 284 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7336 (mtm180) REVERT: F 308 ASN cc_start: 0.8191 (t0) cc_final: 0.7951 (t0) REVERT: G 119 TYR cc_start: 0.8195 (m-80) cc_final: 0.7882 (m-80) REVERT: G 219 CYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5845 (t) REVERT: G 224 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: G 229 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.5098 (mtt) REVERT: G 298 TYR cc_start: 0.7060 (m-10) cc_final: 0.6833 (m-10) REVERT: G 299 LYS cc_start: 0.8101 (mttp) cc_final: 0.7365 (mmpt) REVERT: H 275 ILE cc_start: 0.7606 (pt) cc_final: 0.7261 (mp) outliers start: 89 outliers final: 57 residues processed: 567 average time/residue: 0.5570 time to fit residues: 367.2754 Evaluate side-chains 563 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 495 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 313 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 chunk 104 optimal weight: 0.0170 chunk 67 optimal weight: 0.0170 chunk 193 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 21 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 HIS I 56 ASN I 76 HIS ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN C 18 ASN C 75 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN H 144 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.181042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.149560 restraints weight = 36290.248| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 1.87 r_work: 0.4248 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24213 Z= 0.132 Angle : 0.650 15.300 33125 Z= 0.341 Chirality : 0.043 0.301 3675 Planarity : 0.005 0.088 3901 Dihedral : 17.368 164.817 4191 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 3.34 % Allowed : 34.93 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2631 helix: 0.60 (0.18), residues: 780 sheet: -0.11 (0.26), residues: 455 loop : -1.20 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 146 TYR 0.033 0.001 TYR F 224 PHE 0.026 0.002 PHE E 95 TRP 0.010 0.001 TRP F 33 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (24213) covalent geometry : angle 0.65020 / 0.34 (33125) hydrogen bonds : bond 0.04198 / 2.88 ( 689) hydrogen bonds : angle 4.93907 / 3.39 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 497 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6839 (ppt170) REVERT: A 121 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7060 (mm) REVERT: A 272 ARG cc_start: 0.6734 (ttt180) cc_final: 0.6465 (mtt-85) REVERT: A 282 GLU cc_start: 0.5897 (tp30) cc_final: 0.5646 (mm-30) REVERT: A 322 MET cc_start: 0.6264 (ttt) cc_final: 0.5947 (ttt) REVERT: I 43 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: I 143 TYR cc_start: 0.3454 (OUTLIER) cc_final: 0.3158 (p90) REVERT: D 35 THR cc_start: 0.7087 (t) cc_final: 0.6212 (m) REVERT: D 43 PHE cc_start: 0.7286 (t80) cc_final: 0.7075 (t80) REVERT: D 115 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7711 (ttm-80) REVERT: F 23 ARG cc_start: 0.8134 (ptp-170) cc_final: 0.7612 (ptt-90) REVERT: F 123 ASP cc_start: 0.7517 (m-30) cc_final: 0.7274 (m-30) REVERT: F 284 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7321 (mtp85) REVERT: F 308 ASN cc_start: 0.8234 (t0) cc_final: 0.7964 (t0) REVERT: C 328 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6536 (mmm) REVERT: G 26 ASN cc_start: 0.7469 (t160) cc_final: 0.7120 (t0) REVERT: G 119 TYR cc_start: 0.8168 (m-80) cc_final: 0.7904 (m-80) REVERT: G 219 CYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5810 (t) REVERT: G 224 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: G 229 MET cc_start: 0.5731 (OUTLIER) cc_final: 0.5305 (mtt) REVERT: G 298 TYR cc_start: 0.7114 (m-10) cc_final: 0.6884 (m-10) REVERT: G 299 LYS cc_start: 0.8148 (mttp) cc_final: 0.7368 (mmpt) REVERT: H 275 ILE cc_start: 0.7555 (pt) cc_final: 0.7219 (mp) outliers start: 79 outliers final: 51 residues processed: 544 average time/residue: 0.5508 time to fit residues: 350.2461 Evaluate side-chains 543 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 482 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 43 PHE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 313 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 0.0060 chunk 236 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 259 optimal weight: 0.0870 chunk 31 optimal weight: 7.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN C 18 ASN C 77 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN H 308 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.180750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.149339 restraints weight = 36192.604| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 1.85 r_work: 0.4246 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4149 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24213 Z= 0.147 Angle : 0.662 14.807 33125 Z= 0.346 Chirality : 0.043 0.278 3675 Planarity : 0.005 0.079 3901 Dihedral : 17.314 165.100 4191 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.02 % Rotamer: Outliers : 3.21 % Allowed : 34.80 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2631 helix: 0.63 (0.18), residues: 775 sheet: -0.12 (0.26), residues: 454 loop : -1.23 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 146 TYR 0.053 0.001 TYR G 112 PHE 0.031 0.002 PHE E 329 TRP 0.014 0.001 TRP F 33 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (24213) covalent geometry : angle 0.66240 / 0.35 (33125) hydrogen bonds : bond 0.04178 / 2.88 ( 689) hydrogen bonds : angle 4.98749 / 3.44 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19245.21 seconds wall clock time: 325 minutes 34.32 seconds (19534.32 seconds total)