Starting phenix.real_space_refine on Thu Mar 5 17:16:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjc_54943/03_2026/9sjc_54943.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjc_54943/03_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_54943/03_2026/9sjc_54943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjc_54943/03_2026/9sjc_54943.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjc_54943/03_2026/9sjc_54943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjc_54943/03_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-dev-5986/lib/python3.9/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: 5.40, per 1000 atoms: 0.23 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: 1.82 Conformation dependent library (CDL) restraints added in 878.7 milliseconds 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: 3.33 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: 3.78 Time building geometry restraints manager: 2.34 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 1.50e-02 4.44e+03 6.23e+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: 32504 2.27 - 4.54: 545 4.54 - 6.81: 60 6.81 - 9.08: 11 9.08 - 11.35: 5 Bond angle restraints: 33125 Sorted by residual: angle pdb=" O3' U J 34 " pdb=" P U J 35 " pdb=" O5' U J 35 " ideal model delta sigma weight residual 104.00 96.58 7.42 1.50e+00 4.44e-01 2.45e+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=" 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=" CA LYS F 13 " pdb=" CB LYS F 13 " pdb=" CG LYS F 13 " ideal model delta sigma weight residual 114.10 122.31 -8.21 2.00e+00 2.50e-01 1.68e+01 angle pdb=" N ARG A 142 " pdb=" CA ARG A 142 " pdb=" C ARG A 142 " ideal model delta sigma weight residual 108.23 113.86 -5.63 1.38e+00 5.25e-01 1.66e+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: 3571 0.107 - 0.214: 94 0.214 - 0.321: 5 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 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.30e+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: 6.880 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.010 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 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 : 0.003 0.118 24213 Z= 0.197 Angle : 0.699 11.352 33125 Z= 0.411 Chirality : 0.046 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 covalent geometry : bond 0.00339 (24213) covalent geometry : angle 0.69928 (33125) hydrogen bonds : bond 0.23645 ( 689) hydrogen bonds : angle 7.80208 ( 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 : 0.808 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: 0.7862 (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: 0.7079 (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: G 256 ASN cc_start: 0.6902 (t0) cc_final: 0.6283 (m-40) 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: 0.5875 time to fit residues: 449.4657 Evaluate side-chains 545 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 528 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 134 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN D 140 ASN D 141 ASN D 178 ASN D 195 GLN F 208 ASN C 140 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.191941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.160090 restraints weight = 36008.143| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 1.81 r_work: 0.4350 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4254 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24213 Z= 0.167 Angle : 0.637 10.191 33125 Z= 0.340 Chirality : 0.044 0.253 3675 Planarity : 0.005 0.067 3901 Dihedral : 17.846 162.816 4223 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.17 % Favored : 94.68 % Rotamer: Outliers : 5.41 % Allowed : 28.67 % Favored : 65.92 % 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: -0.59 (0.16), residues: 2631 helix: 0.57 (0.18), residues: 786 sheet: 0.14 (0.26), residues: 440 loop : -1.13 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 204 TYR 0.030 0.002 TYR G 125 PHE 0.025 0.002 PHE F 273 TRP 0.014 0.001 TRP H 33 HIS 0.007 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00367 (24213) covalent geometry : angle 0.63743 (33125) hydrogen bonds : bond 0.04965 ( 689) hydrogen bonds : angle 5.55619 ( 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 697 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 569 time to evaluate : 0.868 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: 0.8160 (t0) cc_final: 0.7714 (t0) REVERT: A 61 ASP cc_start: 0.3982 (m-30) cc_final: 0.3596 (m-30) REVERT: A 125 TYR cc_start: 0.7081 (t80) cc_final: 0.6843 (t80) REVERT: A 176 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7721 (mmt180) REVERT: A 180 SER cc_start: 0.7843 (t) cc_final: 0.7395 (m) REVERT: A 229 ASP cc_start: 0.8459 (t0) cc_final: 0.8121 (t0) REVERT: A 307 VAL cc_start: 0.8132 (t) cc_final: 0.7891 (p) REVERT: A 322 MET cc_start: 0.6373 (ttt) cc_final: 0.6157 (ttt) REVERT: B 176 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7500 (tt) REVERT: B 183 LEU cc_start: 0.7931 (mt) cc_final: 0.7704 (mt) REVERT: B 206 GLU cc_start: 0.7359 (tt0) cc_final: 0.6941 (tt0) REVERT: D 35 THR cc_start: 0.7511 (t) cc_final: 0.6939 (m) REVERT: D 72 MET cc_start: 0.6577 (mmm) cc_final: 0.5927 (mtt) REVERT: D 106 MET cc_start: 0.7987 (tpp) cc_final: 0.7623 (ttp) REVERT: D 229 MET cc_start: 0.7928 (tpp) cc_final: 0.7581 (tpp) REVERT: E 51 ASP cc_start: 0.7811 (p0) cc_final: 0.7581 (p0) REVERT: E 72 MET cc_start: 0.2301 (OUTLIER) cc_final: 0.2045 (mtt) REVERT: E 111 ASP cc_start: 0.6639 (t0) cc_final: 0.6398 (t0) REVERT: F 111 ASP cc_start: 0.7440 (t0) cc_final: 0.7177 (t0) REVERT: F 123 ASP cc_start: 0.7379 (m-30) cc_final: 0.7154 (m-30) REVERT: F 304 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7470 (tpt) REVERT: G 112 TYR cc_start: 0.6832 (t80) cc_final: 0.6586 (t80) REVERT: G 119 TYR cc_start: 0.8106 (m-80) cc_final: 0.7903 (m-80) REVERT: G 122 ILE cc_start: 0.8154 (mt) cc_final: 0.7925 (mp) REVERT: G 219 CYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5795 (m) REVERT: G 299 LYS cc_start: 0.8128 (mttt) cc_final: 0.7471 (mmtt) REVERT: H 150 ARG cc_start: 0.8000 (mmm160) cc_final: 0.7093 (mmm-85) REVERT: H 210 TYR cc_start: 0.6189 (m-80) cc_final: 0.5804 (m-80) REVERT: H 275 ILE cc_start: 0.7495 (pt) cc_final: 0.6973 (mp) REVERT: H 304 MET cc_start: 0.7230 (tpt) cc_final: 0.6645 (tpt) outliers start: 128 outliers final: 46 residues processed: 638 average time/residue: 0.5539 time to fit residues: 411.2481 Evaluate side-chains 598 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 548 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 31 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 176 LEU 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 123 LEU Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 226 SER 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 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 171 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 304 MET 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 124 GLU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 269 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 21 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 259 optimal weight: 0.0670 chunk 112 optimal weight: 0.4980 chunk 47 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 247 optimal weight: 0.5980 chunk 245 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 136 GLN D 140 ASN F 208 ASN F 308 ASN C 80 GLN C 140 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 ASN ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.184829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.152328 restraints weight = 36743.176| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.25 r_work: 0.4250 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24213 Z= 0.133 Angle : 0.587 8.912 33125 Z= 0.312 Chirality : 0.042 0.260 3675 Planarity : 0.005 0.061 3901 Dihedral : 17.623 163.002 4202 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Rotamer: Outliers : 3.72 % Allowed : 31.54 % Favored : 64.74 % 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: -0.55 (0.16), residues: 2631 helix: 0.68 (0.18), residues: 781 sheet: 0.22 (0.26), residues: 446 loop : -1.18 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 204 TYR 0.024 0.001 TYR F 224 PHE 0.036 0.002 PHE H 329 TRP 0.010 0.001 TRP H 33 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00299 (24213) covalent geometry : angle 0.58677 (33125) hydrogen bonds : bond 0.04418 ( 689) hydrogen bonds : angle 5.27970 ( 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 639 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 551 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8292 (t0) cc_final: 0.7782 (t0) REVERT: A 61 ASP cc_start: 0.4581 (m-30) cc_final: 0.4023 (m-30) REVERT: A 97 MET cc_start: 0.3813 (mmt) cc_final: 0.3596 (mmt) REVERT: A 125 TYR cc_start: 0.7014 (t80) cc_final: 0.6768 (t80) REVERT: A 180 SER cc_start: 0.7918 (t) cc_final: 0.7704 (p) REVERT: A 229 ASP cc_start: 0.8492 (t0) cc_final: 0.8163 (t0) REVERT: A 241 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6885 (pm20) REVERT: A 281 LYS cc_start: 0.5071 (OUTLIER) cc_final: 0.4692 (mttp) REVERT: A 322 MET cc_start: 0.6540 (ttt) cc_final: 0.6300 (ttt) REVERT: B 183 LEU cc_start: 0.7958 (mt) cc_final: 0.7724 (mt) REVERT: B 240 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8494 (mp) REVERT: I 43 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: I 56 ASN cc_start: 0.5418 (OUTLIER) cc_final: 0.4973 (t0) REVERT: I 141 HIS cc_start: 0.4252 (OUTLIER) cc_final: 0.4044 (t70) REVERT: D 35 THR cc_start: 0.7194 (t) cc_final: 0.6154 (m) REVERT: D 43 PHE cc_start: 0.7628 (t80) cc_final: 0.7424 (t80) REVERT: D 72 MET cc_start: 0.6574 (mmm) cc_final: 0.5832 (mmt) REVERT: E 51 ASP cc_start: 0.7912 (p0) cc_final: 0.7657 (p0) REVERT: F 111 ASP cc_start: 0.7490 (t0) cc_final: 0.7219 (t0) REVERT: F 123 ASP cc_start: 0.7395 (m-30) cc_final: 0.7181 (m-30) REVERT: F 238 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8325 (ttpt) REVERT: F 284 ARG cc_start: 0.7675 (ttm170) cc_final: 0.7081 (mtp85) REVERT: F 308 ASN cc_start: 0.8171 (t0) cc_final: 0.7879 (t0) REVERT: G 112 TYR cc_start: 0.6874 (t80) cc_final: 0.6658 (t80) REVERT: G 219 CYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5832 (m) REVERT: G 299 LYS cc_start: 0.8140 (mttt) cc_final: 0.7439 (mmtt) REVERT: H 131 PHE cc_start: 0.7485 (m-80) cc_final: 0.7256 (m-80) REVERT: H 210 TYR cc_start: 0.6211 (m-80) cc_final: 0.5798 (m-80) REVERT: H 275 ILE cc_start: 0.7442 (pt) cc_final: 0.6946 (mp) REVERT: H 304 MET cc_start: 0.7186 (tpt) cc_final: 0.6852 (tpt) outliers start: 88 outliers final: 34 residues processed: 599 average time/residue: 0.5579 time to fit residues: 388.5536 Evaluate side-chains 555 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 514 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 98 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 281 LYS 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 201 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 THR 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 129 MET Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 246 SER 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 54 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain G residue 219 CYS 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 269 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 130 optimal weight: 0.8980 chunk 269 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 178 optimal weight: 0.0670 chunk 14 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 51 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 44 ASN B 168 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN D 140 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN D 256 ASN F 173 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** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.182830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.150728 restraints weight = 36673.139| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 2.19 r_work: 0.4248 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24213 Z= 0.134 Angle : 0.587 10.878 33125 Z= 0.312 Chirality : 0.042 0.260 3675 Planarity : 0.005 0.063 3901 Dihedral : 17.510 163.339 4196 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 4.78 % Allowed : 31.29 % Favored : 63.93 % 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: -0.52 (0.16), residues: 2631 helix: 0.69 (0.18), residues: 792 sheet: 0.10 (0.25), residues: 453 loop : -1.12 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 142 TYR 0.025 0.001 TYR F 114 PHE 0.048 0.002 PHE H 329 TRP 0.009 0.001 TRP F 33 HIS 0.009 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00302 (24213) covalent geometry : angle 0.58746 (33125) hydrogen bonds : bond 0.04055 ( 689) hydrogen bonds : angle 5.05683 ( 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 632 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 519 time to evaluate : 0.583 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: 0.7200 (OUTLIER) cc_final: 0.6863 (ppt170) REVERT: A 56 ASP cc_start: 0.8282 (t0) cc_final: 0.7825 (t0) REVERT: A 61 ASP cc_start: 0.4912 (m-30) cc_final: 0.3844 (m-30) REVERT: A 104 MET cc_start: 0.5624 (tpp) cc_final: 0.5401 (tpt) REVERT: A 125 TYR cc_start: 0.6956 (t80) cc_final: 0.6643 (t80) REVERT: A 241 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: A 272 ARG cc_start: 0.6393 (ttt180) cc_final: 0.6136 (mtt-85) REVERT: A 310 SER cc_start: 0.7249 (OUTLIER) cc_final: 0.7038 (p) REVERT: A 322 MET cc_start: 0.6464 (ttt) cc_final: 0.6200 (ttt) REVERT: B 183 LEU cc_start: 0.7983 (mt) cc_final: 0.7766 (mt) REVERT: I 43 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: I 56 ASN cc_start: 0.5385 (OUTLIER) cc_final: 0.4990 (t0) REVERT: I 141 HIS cc_start: 0.4236 (OUTLIER) cc_final: 0.4022 (t70) REVERT: D 35 THR cc_start: 0.7128 (t) cc_final: 0.6131 (m) REVERT: D 115 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7816 (ttm-80) REVERT: D 320 MET cc_start: 0.7776 (mmm) cc_final: 0.7482 (mpp) REVERT: E 51 ASP cc_start: 0.7927 (p0) cc_final: 0.7682 (p0) REVERT: E 104 GLU cc_start: 0.7730 (mp0) cc_final: 0.7526 (mp0) REVERT: F 123 ASP cc_start: 0.7393 (m-30) cc_final: 0.7172 (m-30) REVERT: F 238 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8215 (ttpt) REVERT: F 284 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7201 (mtp85) REVERT: G 112 TYR cc_start: 0.6751 (t80) cc_final: 0.6497 (t80) REVERT: G 122 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7729 (mp) REVERT: G 299 LYS cc_start: 0.8110 (mttt) cc_final: 0.7435 (mmtt) REVERT: H 175 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7610 (mmtp) REVERT: H 210 TYR cc_start: 0.6167 (m-80) cc_final: 0.5700 (m-80) REVERT: H 275 ILE cc_start: 0.7471 (pt) cc_final: 0.7205 (tp) REVERT: H 279 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.6081 (m110) REVERT: H 304 MET cc_start: 0.7023 (tpt) cc_final: 0.6823 (tpt) outliers start: 113 outliers final: 49 residues processed: 587 average time/residue: 0.5758 time to fit residues: 391.4225 Evaluate side-chains 559 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 500 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 166 SER 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 310 SER 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 B residue 245 THR Chi-restraints excluded: chain I residue 18 ILE 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 120 HIS Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 129 MET 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 141 HIS Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 181 THR 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 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 144 ASN 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 234 ASP Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain C residue 70 GLU 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 161 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 269 THR Chi-restraints excluded: chain H residue 279 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 141 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 51 ASN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS A 328 HIS ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 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** H 255 ASN ** H 279 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 = 0.4623 r_free = 0.4623 target = 0.182398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.149852 restraints weight = 36032.982| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.27 r_work: 0.4215 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24213 Z= 0.189 Angle : 0.617 10.504 33125 Z= 0.325 Chirality : 0.043 0.261 3675 Planarity : 0.005 0.068 3901 Dihedral : 17.480 163.323 4192 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 5.12 % Allowed : 31.25 % Favored : 63.64 % 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: -0.58 (0.16), residues: 2631 helix: 0.65 (0.18), residues: 787 sheet: 0.13 (0.26), residues: 421 loop : -1.15 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 265 TYR 0.026 0.001 TYR F 224 PHE 0.031 0.002 PHE H 329 TRP 0.014 0.001 TRP A 208 HIS 0.010 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00430 (24213) covalent geometry : angle 0.61651 (33125) hydrogen bonds : bond 0.04217 ( 689) hydrogen bonds : angle 5.00582 ( 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 651 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 530 time to evaluate : 0.885 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: 0.7320 (OUTLIER) cc_final: 0.7097 (ppt170) REVERT: A 51 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.6675 (p0) REVERT: A 56 ASP cc_start: 0.8331 (t0) cc_final: 0.7844 (t0) REVERT: A 61 ASP cc_start: 0.5338 (m-30) cc_final: 0.4255 (m-30) REVERT: A 95 MET cc_start: 0.6896 (mpp) cc_final: 0.6435 (pmm) REVERT: A 96 GLU cc_start: 0.4584 (OUTLIER) cc_final: 0.4159 (tp30) REVERT: A 125 TYR cc_start: 0.7007 (t80) cc_final: 0.6805 (t80) REVERT: A 173 VAL cc_start: 0.7767 (t) cc_final: 0.7539 (p) REVERT: A 241 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: A 272 ARG cc_start: 0.6565 (ttt180) cc_final: 0.6278 (mtt-85) REVERT: A 322 MET cc_start: 0.6516 (ttt) cc_final: 0.6218 (ttt) REVERT: B 89 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6515 (pm20) REVERT: B 176 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7358 (tt) REVERT: B 183 LEU cc_start: 0.8045 (mt) cc_final: 0.7837 (mt) REVERT: I 43 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: I 56 ASN cc_start: 0.5232 (OUTLIER) cc_final: 0.4892 (t0) REVERT: I 141 HIS cc_start: 0.4283 (OUTLIER) cc_final: 0.3972 (t70) REVERT: I 143 TYR cc_start: 0.3446 (OUTLIER) cc_final: 0.3159 (p90) REVERT: D 35 THR cc_start: 0.7247 (t) cc_final: 0.6358 (m) REVERT: D 107 TYR cc_start: 0.7675 (t80) cc_final: 0.7290 (t80) REVERT: D 115 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7828 (ttm-80) REVERT: D 320 MET cc_start: 0.7797 (mmm) cc_final: 0.7506 (mpp) REVERT: E 104 GLU cc_start: 0.7804 (mp0) cc_final: 0.7585 (mp0) REVERT: E 270 THR cc_start: 0.8478 (m) cc_final: 0.8276 (t) REVERT: F 123 ASP cc_start: 0.7604 (m-30) cc_final: 0.7382 (m-30) REVERT: F 124 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: F 224 TYR cc_start: 0.7732 (m-10) cc_final: 0.7512 (m-10) REVERT: F 304 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7707 (ttt) REVERT: C 328 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7243 (mmt) REVERT: G 112 TYR cc_start: 0.6837 (t80) cc_final: 0.6574 (t80) REVERT: G 119 TYR cc_start: 0.8135 (m-80) cc_final: 0.7865 (m-80) REVERT: G 122 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7836 (mp) REVERT: G 219 CYS cc_start: 0.6436 (OUTLIER) cc_final: 0.5872 (t) REVERT: G 229 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5538 (mtt) REVERT: G 299 LYS cc_start: 0.8159 (mttt) cc_final: 0.7465 (mmtt) REVERT: H 175 LYS cc_start: 0.7877 (mmtp) cc_final: 0.7674 (mmtp) REVERT: H 210 TYR cc_start: 0.6234 (m-80) cc_final: 0.5766 (m-80) REVERT: H 275 ILE cc_start: 0.7518 (pt) cc_final: 0.7290 (tp) REVERT: H 304 MET cc_start: 0.6962 (tpt) cc_final: 0.6694 (tpt) outliers start: 121 outliers final: 56 residues processed: 604 average time/residue: 0.5651 time to fit residues: 394.5406 Evaluate side-chains 593 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 520 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 134 ASN 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 276 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 176 LEU 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 220 SER 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 127 LEU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain E residue 12 LEU 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 F residue 20 SER 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 144 ASN 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 234 ASP Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 322 ILE 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 161 ILE Chi-restraints excluded: chain C residue 184 GLU 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 54 VAL Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 219 CYS 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 H residue 86 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 269 THR 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: 0.6980 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 231 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 154 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN D 140 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 75 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.185102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.153560 restraints weight = 35601.360| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 1.73 r_work: 0.4312 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4226 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24213 Z= 0.146 Angle : 0.603 12.115 33125 Z= 0.317 Chirality : 0.042 0.262 3675 Planarity : 0.005 0.069 3901 Dihedral : 17.434 163.457 4191 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 4.90 % Allowed : 32.60 % Favored : 62.49 % 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: -0.51 (0.16), residues: 2631 helix: 0.75 (0.18), residues: 776 sheet: 0.13 (0.27), residues: 428 loop : -1.11 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 15 TYR 0.029 0.001 TYR C 265 PHE 0.032 0.002 PHE E 95 TRP 0.011 0.001 TRP F 33 HIS 0.005 0.001 HIS G 317 Details of bonding type rmsd covalent geometry : bond 0.00336 (24213) covalent geometry : angle 0.60263 (33125) hydrogen bonds : bond 0.04032 ( 689) hydrogen bonds : angle 4.92696 ( 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: 116 poor density : 524 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6820 (ppt170) REVERT: A 95 MET cc_start: 0.6980 (mpp) cc_final: 0.6690 (pmm) REVERT: A 104 MET cc_start: 0.5553 (OUTLIER) cc_final: 0.5139 (tpp) REVERT: A 125 TYR cc_start: 0.7051 (t80) cc_final: 0.6688 (t80) REVERT: A 229 ASP cc_start: 0.8231 (t0) cc_final: 0.7902 (t0) REVERT: A 241 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7086 (pm20) REVERT: A 322 MET cc_start: 0.6242 (ttt) cc_final: 0.5951 (ttt) REVERT: B 176 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7205 (tt) REVERT: I 43 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: I 56 ASN cc_start: 0.4892 (OUTLIER) cc_final: 0.4663 (t0) REVERT: I 141 HIS cc_start: 0.4208 (OUTLIER) cc_final: 0.3891 (t70) REVERT: I 143 TYR cc_start: 0.3323 (OUTLIER) cc_final: 0.3084 (p90) REVERT: D 35 THR cc_start: 0.6847 (t) cc_final: 0.6143 (m) REVERT: D 62 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7650 (mtp) REVERT: D 115 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7652 (ttm-80) REVERT: D 320 MET cc_start: 0.7488 (mmm) cc_final: 0.7251 (mpp) REVERT: F 124 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: F 284 ARG cc_start: 0.7734 (ttm170) cc_final: 0.7368 (mtp85) REVERT: F 304 MET cc_start: 0.7945 (tpp) cc_final: 0.7510 (ttt) REVERT: G 112 TYR cc_start: 0.6830 (t80) cc_final: 0.6612 (t80) REVERT: G 219 CYS cc_start: 0.6507 (OUTLIER) cc_final: 0.5974 (t) REVERT: G 229 MET cc_start: 0.5745 (OUTLIER) cc_final: 0.5282 (mtt) REVERT: G 299 LYS cc_start: 0.8026 (mttt) cc_final: 0.7502 (mmtt) REVERT: H 210 TYR cc_start: 0.6211 (m-80) cc_final: 0.5756 (m-80) REVERT: H 275 ILE cc_start: 0.7627 (pt) cc_final: 0.7258 (mp) REVERT: H 279 ASN cc_start: 0.6531 (OUTLIER) cc_final: 0.6167 (m110) REVERT: H 304 MET cc_start: 0.6957 (tpt) cc_final: 0.6725 (tpt) outliers start: 116 outliers final: 50 residues processed: 600 average time/residue: 0.5695 time to fit residues: 396.1414 Evaluate side-chains 563 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 499 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 241 GLU 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 147 LEU Chi-restraints excluded: chain B residue 176 LEU 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 220 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 ILE 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 129 MET 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 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 144 ASN 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 C residue 72 MET 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 23 ARG Chi-restraints excluded: chain G residue 36 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 229 MET Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 269 THR Chi-restraints excluded: chain H residue 279 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 180 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 259 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 51 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN D 18 ASN D 140 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN C 18 ASN C 75 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN H 34 GLN ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.179391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.147725 restraints weight = 36191.970| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 1.85 r_work: 0.4229 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24213 Z= 0.173 Angle : 0.625 11.987 33125 Z= 0.327 Chirality : 0.043 0.263 3675 Planarity : 0.005 0.082 3901 Dihedral : 17.391 163.742 4191 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.64 % Favored : 95.25 % Rotamer: Outliers : 4.99 % Allowed : 32.39 % Favored : 62.62 % 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: -0.60 (0.16), residues: 2631 helix: 0.64 (0.18), residues: 785 sheet: 0.04 (0.26), residues: 431 loop : -1.14 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 146 TYR 0.030 0.001 TYR F 224 PHE 0.033 0.002 PHE E 95 TRP 0.014 0.001 TRP F 33 HIS 0.005 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00397 (24213) covalent geometry : angle 0.62512 (33125) hydrogen bonds : bond 0.04166 ( 689) hydrogen bonds : angle 4.91701 ( 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 633 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 515 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6828 (ppt170) REVERT: A 95 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6872 (pmm) REVERT: A 96 GLU cc_start: 0.4811 (OUTLIER) cc_final: 0.4569 (tp30) REVERT: A 104 MET cc_start: 0.5381 (OUTLIER) cc_final: 0.4890 (tpp) REVERT: A 125 TYR cc_start: 0.6985 (t80) cc_final: 0.6636 (t80) REVERT: A 241 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: A 272 ARG cc_start: 0.6651 (ttt180) cc_final: 0.6375 (mtt-85) REVERT: A 282 GLU cc_start: 0.5777 (tp30) cc_final: 0.5568 (mm-30) REVERT: A 322 MET cc_start: 0.6276 (ttt) cc_final: 0.5966 (ttt) REVERT: B 89 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6399 (pm20) REVERT: I 43 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: I 56 ASN cc_start: 0.4946 (OUTLIER) cc_final: 0.4725 (t0) REVERT: I 141 HIS cc_start: 0.4185 (OUTLIER) cc_final: 0.3886 (t70) REVERT: I 143 TYR cc_start: 0.3378 (OUTLIER) cc_final: 0.3097 (p90) REVERT: D 35 THR cc_start: 0.7109 (t) cc_final: 0.6322 (m) REVERT: D 62 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7957 (mtp) REVERT: D 115 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7804 (ttm-80) REVERT: F 123 ASP cc_start: 0.7285 (m-30) cc_final: 0.7078 (m-30) REVERT: F 124 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: F 284 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7390 (mtp85) REVERT: F 304 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7808 (ttt) REVERT: C 328 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.6693 (mmm) REVERT: G 112 TYR cc_start: 0.6822 (t80) cc_final: 0.6568 (t80) REVERT: G 122 ILE cc_start: 0.8131 (mp) cc_final: 0.7930 (mp) REVERT: G 219 CYS cc_start: 0.6528 (OUTLIER) cc_final: 0.5881 (t) REVERT: G 229 MET cc_start: 0.5668 (OUTLIER) cc_final: 0.5225 (mtt) REVERT: G 299 LYS cc_start: 0.8129 (mttt) cc_final: 0.7527 (mmtt) REVERT: H 210 TYR cc_start: 0.6221 (m-80) cc_final: 0.5734 (m-80) REVERT: H 275 ILE cc_start: 0.7531 (pt) cc_final: 0.7209 (mp) REVERT: H 279 ASN cc_start: 0.6588 (OUTLIER) cc_final: 0.6231 (m110) outliers start: 118 outliers final: 57 residues processed: 589 average time/residue: 0.5690 time to fit residues: 389.7488 Evaluate side-chains 571 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 495 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 134 ASN 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 260 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 83 SER 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 147 LEU 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 220 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 ILE 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 129 MET Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 115 ARG 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 183 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 144 ASN 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 284 ARG Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 72 MET 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 C residue 328 MET Chi-restraints excluded: chain G residue 36 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 229 MET Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 269 THR Chi-restraints excluded: chain H residue 279 ASN Chi-restraints excluded: chain H residue 313 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 95 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 210 optimal weight: 3.9990 chunk 178 optimal weight: 0.0870 chunk 160 optimal weight: 0.0010 chunk 16 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 10 optimal weight: 0.0000 chunk 122 optimal weight: 1.9990 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS I 76 HIS ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 75 ASN C 140 ASN H 279 ASN H 308 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.181809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.150180 restraints weight = 36052.438| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 1.87 r_work: 0.4254 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4159 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24213 Z= 0.126 Angle : 0.613 15.015 33125 Z= 0.321 Chirality : 0.042 0.262 3675 Planarity : 0.005 0.071 3901 Dihedral : 17.337 163.924 4191 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 3.85 % Allowed : 33.78 % Favored : 62.37 % 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: -0.53 (0.16), residues: 2631 helix: 0.73 (0.18), residues: 780 sheet: 0.01 (0.26), residues: 441 loop : -1.09 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 146 TYR 0.034 0.001 TYR F 224 PHE 0.032 0.002 PHE F 273 TRP 0.008 0.001 TRP G 33 HIS 0.004 0.001 HIS G 317 Details of bonding type rmsd covalent geometry : bond 0.00287 (24213) covalent geometry : angle 0.61331 (33125) hydrogen bonds : bond 0.03885 ( 689) hydrogen bonds : angle 4.82021 ( 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 600 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 509 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6765 (ppt170) REVERT: A 95 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6895 (pmm) REVERT: A 104 MET cc_start: 0.5387 (OUTLIER) cc_final: 0.4940 (tpp) REVERT: A 241 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: A 264 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7534 (mtmt) REVERT: A 272 ARG cc_start: 0.6605 (ttt180) cc_final: 0.6347 (mtt-85) REVERT: A 282 GLU cc_start: 0.5872 (tp30) cc_final: 0.5637 (mm-30) REVERT: A 322 MET cc_start: 0.6216 (ttt) cc_final: 0.5891 (ttt) REVERT: B 119 MET cc_start: 0.5489 (mmp) cc_final: 0.5227 (mmp) REVERT: I 43 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7071 (m-80) REVERT: I 141 HIS cc_start: 0.4281 (OUTLIER) cc_final: 0.3954 (t70) REVERT: I 143 TYR cc_start: 0.3340 (OUTLIER) cc_final: 0.3100 (p90) REVERT: D 62 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7927 (mtp) REVERT: F 123 ASP cc_start: 0.7283 (m-30) cc_final: 0.7058 (m-30) REVERT: F 124 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: F 204 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7413 (ttp80) REVERT: F 284 ARG cc_start: 0.7812 (ttm170) cc_final: 0.7450 (mtp85) REVERT: F 304 MET cc_start: 0.8033 (tpp) cc_final: 0.7650 (ttt) REVERT: C 328 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.6593 (mmm) REVERT: G 112 TYR cc_start: 0.6759 (t80) cc_final: 0.6496 (t80) REVERT: G 229 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.5318 (mtt) REVERT: G 278 GLU cc_start: 0.6860 (mp0) cc_final: 0.6613 (mp0) REVERT: G 299 LYS cc_start: 0.8152 (mttt) cc_final: 0.7523 (mmtt) REVERT: G 303 ARG cc_start: 0.6770 (ttp-170) cc_final: 0.6557 (ttp80) REVERT: G 320 MET cc_start: 0.7314 (mmp) cc_final: 0.7032 (mmp) REVERT: H 139 VAL cc_start: 0.6746 (m) cc_final: 0.6544 (p) REVERT: H 253 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6812 (tttp) outliers start: 91 outliers final: 46 residues processed: 561 average time/residue: 0.5423 time to fit residues: 356.1725 Evaluate side-chains 554 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 496 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 95 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 134 ASN 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 278 ASP 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 I residue 1 MET 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 103 ARG Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 144 ASN 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 322 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 124 GLU 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 200 PHE Chi-restraints excluded: chain G residue 203 LYS 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 86 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 269 THR Chi-restraints excluded: chain H residue 313 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 221 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 185 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 HIS D 18 ASN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 77 GLN C 140 ASN C 186 ASN ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.179394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.148221 restraints weight = 36071.001| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 1.83 r_work: 0.4233 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 24213 Z= 0.180 Angle : 0.646 13.269 33125 Z= 0.336 Chirality : 0.043 0.262 3675 Planarity : 0.005 0.075 3901 Dihedral : 17.310 164.259 4191 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Rotamer: Outliers : 3.34 % Allowed : 34.38 % Favored : 62.28 % 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: -0.64 (0.16), residues: 2631 helix: 0.55 (0.18), residues: 788 sheet: 0.06 (0.26), residues: 423 loop : -1.15 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 146 TYR 0.031 0.001 TYR F 224 PHE 0.034 0.002 PHE F 273 TRP 0.015 0.001 TRP F 33 HIS 0.005 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00419 (24213) covalent geometry : angle 0.64588 (33125) hydrogen bonds : bond 0.04168 ( 689) hydrogen bonds : angle 4.88057 ( 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 599 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 520 time to evaluate : 0.852 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: 0.6968 (OUTLIER) cc_final: 0.6648 (ppt170) REVERT: A 52 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7707 (pt) REVERT: A 95 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6858 (pmm) REVERT: A 241 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: A 260 ILE cc_start: 0.7772 (pt) cc_final: 0.7285 (OUTLIER) REVERT: A 264 LYS cc_start: 0.7780 (mtmt) cc_final: 0.7547 (mtmt) REVERT: A 272 ARG cc_start: 0.6714 (ttt180) cc_final: 0.6445 (mtt-85) REVERT: A 282 GLU cc_start: 0.6032 (tp30) cc_final: 0.5764 (mm-30) REVERT: A 322 MET cc_start: 0.6241 (ttt) cc_final: 0.5921 (ttt) REVERT: B 89 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6393 (pm20) REVERT: B 237 ASN cc_start: 0.8058 (m-40) cc_final: 0.7702 (t0) REVERT: I 1 MET cc_start: -0.1553 (OUTLIER) cc_final: -0.3579 (mtt) REVERT: I 43 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: I 141 HIS cc_start: 0.4278 (OUTLIER) cc_final: 0.3966 (t70) REVERT: I 143 TYR cc_start: 0.3362 (OUTLIER) cc_final: 0.3112 (p90) REVERT: D 35 THR cc_start: 0.7100 (t) cc_final: 0.6342 (m) REVERT: D 62 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8067 (mtp) REVERT: F 123 ASP cc_start: 0.7277 (m-30) cc_final: 0.7056 (m-30) REVERT: F 124 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: F 284 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7504 (mtp85) REVERT: F 304 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7862 (ttt) REVERT: C 13 LYS cc_start: 0.7790 (tppt) cc_final: 0.7575 (tppt) REVERT: C 328 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7231 (mtp) REVERT: G 37 PHE cc_start: 0.6544 (t80) cc_final: 0.6325 (t80) REVERT: G 112 TYR cc_start: 0.6798 (t80) cc_final: 0.6529 (t80) REVERT: G 146 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.7082 (ttm-80) REVERT: G 216 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8332 (mtpp) REVERT: G 229 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5298 (mtt) REVERT: G 299 LYS cc_start: 0.8187 (mttt) cc_final: 0.7482 (mmpt) REVERT: G 320 MET cc_start: 0.7296 (mmp) cc_final: 0.7051 (mmp) REVERT: H 125 TYR cc_start: 0.7726 (t80) cc_final: 0.7458 (t80) REVERT: H 253 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6888 (tttp) outliers start: 79 outliers final: 43 residues processed: 569 average time/residue: 0.5598 time to fit residues: 371.1552 Evaluate side-chains 570 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 512 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 95 MET Chi-restraints excluded: chain A residue 134 ASN 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 278 ASP Chi-restraints excluded: chain B residue 83 SER 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 I residue 1 MET Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 43 PHE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 144 ASN 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 284 ARG Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 205 GLU 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 G residue 313 ILE Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 269 THR 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: 1.9990 chunk 152 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 193 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 HIS D 140 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 140 ASN C 186 ASN H 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.180081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.148881 restraints weight = 36168.317| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 1.83 r_work: 0.4240 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24213 Z= 0.161 Angle : 0.648 16.012 33125 Z= 0.337 Chirality : 0.042 0.260 3675 Planarity : 0.005 0.070 3901 Dihedral : 17.296 164.335 4191 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.06 % Favored : 94.83 % Rotamer: Outliers : 3.38 % Allowed : 34.63 % 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: -0.65 (0.16), residues: 2631 helix: 0.57 (0.18), residues: 787 sheet: 0.24 (0.27), residues: 398 loop : -1.21 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 265 TYR 0.033 0.001 TYR F 224 PHE 0.035 0.002 PHE F 273 TRP 0.012 0.001 TRP A 208 HIS 0.005 0.001 HIS G 317 Details of bonding type rmsd covalent geometry : bond 0.00375 (24213) covalent geometry : angle 0.64799 (33125) hydrogen bonds : bond 0.04081 ( 689) hydrogen bonds : angle 4.86677 ( 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 607 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 527 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6589 (ppt170) REVERT: A 52 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7740 (pt) REVERT: A 56 ASP cc_start: 0.8180 (t0) cc_final: 0.7767 (t0) REVERT: A 71 ASN cc_start: 0.8339 (t0) cc_final: 0.8133 (t0) REVERT: A 95 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6890 (pmm) REVERT: A 241 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: A 260 ILE cc_start: 0.7757 (pt) cc_final: 0.7246 (OUTLIER) REVERT: A 264 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7545 (mtmt) REVERT: A 272 ARG cc_start: 0.6730 (ttt180) cc_final: 0.6449 (mtt-85) REVERT: A 282 GLU cc_start: 0.6095 (tp30) cc_final: 0.5776 (mm-30) REVERT: A 322 MET cc_start: 0.6268 (ttt) cc_final: 0.5948 (ttt) REVERT: B 44 ASN cc_start: 0.7747 (m-40) cc_final: 0.7462 (m110) REVERT: B 89 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: B 119 MET cc_start: 0.5506 (mmp) cc_final: 0.5182 (mmp) REVERT: B 237 ASN cc_start: 0.8030 (m-40) cc_final: 0.7768 (t0) REVERT: I 1 MET cc_start: -0.1552 (OUTLIER) cc_final: -0.3586 (mtt) REVERT: I 43 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.7066 (m-80) REVERT: I 141 HIS cc_start: 0.4350 (OUTLIER) cc_final: 0.4027 (t70) REVERT: I 143 TYR cc_start: 0.3429 (OUTLIER) cc_final: 0.3192 (p90) REVERT: D 35 THR cc_start: 0.7045 (t) cc_final: 0.6304 (m) REVERT: D 43 PHE cc_start: 0.7286 (t80) cc_final: 0.7053 (t80) REVERT: D 62 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8079 (mtp) REVERT: E 43 PHE cc_start: 0.7638 (t80) cc_final: 0.7425 (t80) REVERT: F 123 ASP cc_start: 0.7227 (m-30) cc_final: 0.7015 (m-30) REVERT: F 124 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: F 284 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7504 (mtp85) REVERT: F 304 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7751 (ttt) REVERT: C 13 LYS cc_start: 0.7809 (tppt) cc_final: 0.7593 (tppt) REVERT: C 328 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7209 (mtp) REVERT: G 112 TYR cc_start: 0.6804 (t80) cc_final: 0.6536 (t80) REVERT: G 216 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8329 (mtpp) REVERT: G 229 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.5230 (mtt) REVERT: G 299 LYS cc_start: 0.8153 (mttt) cc_final: 0.7486 (mmtt) REVERT: H 125 TYR cc_start: 0.7735 (t80) cc_final: 0.7398 (t80) REVERT: H 253 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6919 (tttp) outliers start: 80 outliers final: 44 residues processed: 567 average time/residue: 0.5335 time to fit residues: 352.3535 Evaluate side-chains 568 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 510 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 95 MET Chi-restraints excluded: chain A residue 134 ASN 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 278 ASP Chi-restraints excluded: chain B residue 83 SER 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 176 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain I residue 1 MET 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 103 ARG Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 296 SER 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 44 LYS Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 144 ASN 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 304 MET Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 205 GLU 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 86 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 269 THR Chi-restraints excluded: chain H residue 286 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: 0.9980 chunk 10 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 259 optimal weight: 0.0670 chunk 31 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.180747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.149212 restraints weight = 36140.879| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 1.85 r_work: 0.4244 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24213 Z= 0.151 Angle : 0.653 16.864 33125 Z= 0.338 Chirality : 0.042 0.257 3675 Planarity : 0.005 0.066 3901 Dihedral : 17.266 164.585 4189 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 3.04 % Allowed : 35.39 % Favored : 61.56 % 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: -0.68 (0.16), residues: 2631 helix: 0.54 (0.18), residues: 793 sheet: 0.02 (0.26), residues: 446 loop : -1.20 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 265 TYR 0.029 0.001 TYR F 224 PHE 0.038 0.002 PHE E 241 TRP 0.011 0.001 TRP A 208 HIS 0.011 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00353 (24213) covalent geometry : angle 0.65291 (33125) hydrogen bonds : bond 0.04052 ( 689) hydrogen bonds : angle 4.87238 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19725.62 seconds wall clock time: 333 minutes 22.71 seconds (20002.71 seconds total)