Starting phenix.real_space_refine on Fri Aug 7 21:37:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjl_54946/08_2026/9sjl_54946.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjl_54946/08_2026/9sjl_54946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sjl_54946/08_2026/9sjl_54946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjl_54946/08_2026/9sjl_54946.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjl_54946/08_2026/9sjl_54946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjl_54946/08_2026/9sjl_54946.cif" } resolution = 3.93 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= 0.003 sd= 0.039 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 91 5.49 5 S 116 5.16 5 C 14645 2.51 5 N 3932 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23452 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2666 Classifications: {'peptide': 334} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 316} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 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: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1416 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain breaks: 1 Chain: "L" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 187 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2612 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "E" 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: "F" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2622 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 307} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2626 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 307} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2610 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "H" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2334 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 2 Chain: "K" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} 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': 19, 'rna2p_pyr': 11, 'rna3p_pur': 18, 'rna3p_pyr': 12} Link IDs: {'rna2p': 29, 'rna3p': 30} Time building chain proxies: 5.17, per 1000 atoms: 0.22 Number of scatterers: 23452 At special positions: 0 Unit cell: (120.35, 147.9, 155.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 91 15.00 O 4668 8.00 N 3932 7.00 C 14645 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: 1.44 Conformation dependent library (CDL) restraints added in 1.0 seconds 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5056 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 41 sheets defined 36.0% alpha, 9.6% beta 24 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.984A pdb=" N LEU A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 29 removed outlier: 3.589A pdb=" N ILE A 20 " --> pdb=" O GLU A 16 " (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 83 through 86 Processing helix chain 'A' and resid 87 through 93 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.665A pdb=" N GLN A 108 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 removed outlier: 4.634A pdb=" N MET A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.859A 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 180 Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.544A pdb=" N THR A 198 " --> pdb=" O ALA A 194 " (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 281 through 293 Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.769A pdb=" N PHE B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 36 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.657A pdb=" N GLU B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.869A pdb=" N LEU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.554A pdb=" N LEU B 240 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 21 removed outlier: 3.946A pdb=" N ILE I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 35 removed outlier: 3.747A pdb=" N HIS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 78 through 81 Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 128 through 140 Processing helix chain 'D' and resid 36 through 43 removed outlier: 3.560A pdb=" N ARG D 40 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HIS D 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.889A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.634A pdb=" N TYR D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 145 through 152 removed outlier: 6.935A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 202 Processing helix chain 'D' and resid 242 through 246 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 71 removed outlier: 4.148A pdb=" N LYS E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.747A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.519A pdb=" N ALA E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 137 " --> pdb=" O THR E 133 " (cutoff:3.500A) 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 removed outlier: 3.717A pdb=" N GLU E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 192 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 63 through 71 removed outlier: 4.036A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU F 70 " --> pdb=" O LYS F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 4.135A pdb=" N MET F 106 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 145 Processing helix chain 'F' and resid 146 through 152 removed outlier: 6.488A pdb=" N ARG F 150 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 250 through 260 Processing helix chain 'F' and resid 267 through 272 Processing helix chain 'F' and resid 296 through 306 removed outlier: 4.251A pdb=" N ASP F 302 " --> pdb=" O TYR F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 326 removed outlier: 4.143A 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 70 removed outlier: 3.629A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.534A pdb=" N ARG C 137 " --> pdb=" O THR C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 removed outlier: 6.160A pdb=" N ARG C 150 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.792A pdb=" N GLN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) 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 305 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 63 through 68 removed outlier: 4.250A pdb=" N GLU G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 72 removed outlier: 4.372A pdb=" N MET G 72 " --> pdb=" O LYS G 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 69 through 72' Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.668A pdb=" N TYR G 119 " --> pdb=" O ARG G 115 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) 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 removed outlier: 3.519A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 267 through 272 Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 312 through 326 removed outlier: 3.946A pdb=" N TYR G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU G 323 " --> pdb=" O VAL G 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.566A pdb=" N TYR H 119 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.697A pdb=" N ILE H 142 " --> pdb=" O TYR H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 6.068A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 250 through 258 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: 3.577A 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 149 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 158 through 163 current: chain 'B' and resid 101 through 110 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 101 through 110 current: chain 'B' and resid 137 through 141 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 141 current: chain 'B' and resid 214 through 229 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 214 through 229 current: chain 'B' and resid 249 through 251 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 5 through 9 removed outlier: 3.855A pdb=" N TYR B 5 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA8, first strand: chain 'I' and resid 6 through 8 Processing sheet with id=AA9, first strand: chain 'I' and resid 41 through 42 Processing sheet with id=AB1, first strand: chain 'I' and resid 98 through 100 Processing sheet with id=AB2, first strand: chain 'D' and resid 106 through 109 removed outlier: 3.905A pdb=" N SER D 108 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.223A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 54 through 57 Processing sheet with id=AB6, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AB7, first strand: chain 'E' and resid 106 through 109 removed outlier: 3.705A pdb=" N SER E 108 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 46 current: chain 'E' and resid 172 through 173 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AC1, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AC2, first strand: chain 'E' and resid 242 through 243 Processing sheet with id=AC3, first strand: chain 'E' and resid 260 through 262 Processing sheet with id=AC4, first strand: chain 'E' and resid 282 through 283 removed outlier: 3.770A pdb=" N ALA E 283 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 288 " --> pdb=" O ALA E 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 46 current: chain 'F' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 167 through 168 current: chain 'F' and resid 246 through 249 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 50 through 57 Processing sheet with id=AC7, first strand: chain 'F' and resid 282 through 283 removed outlier: 4.432A pdb=" N ALA F 283 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE F 288 " --> pdb=" O ALA F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 20 through 21 removed outlier: 3.620A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 25 through 27 removed outlier: 4.237A pdb=" N VAL C 162 " --> pdb=" O TYR C 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AD2, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AD3, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AD4, first strand: chain 'C' and resid 54 through 57 Processing sheet with id=AD5, first strand: chain 'C' and resid 260 through 262 Processing sheet with id=AD6, first strand: chain 'G' and resid 106 through 109 removed outlier: 3.518A pdb=" N SER G 108 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing sheet with id=AD7, 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=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 50 through 57 removed outlier: 4.104A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 227 through 228 removed outlier: 4.591A pdb=" N LYS G 239 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AE2, first strand: chain 'H' and resid 106 through 109 Processing sheet with id=AE3, first strand: chain 'H' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 26 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 207 through 216 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AE5, first strand: chain 'H' and resid 282 through 283 removed outlier: 3.994A pdb=" N ALA H 283 " --> pdb=" O ILE H 288 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6573 1.33 - 1.45: 4449 1.45 - 1.57: 12763 1.57 - 1.69: 181 1.69 - 1.81: 185 Bond restraints: 24151 Sorted by residual: bond pdb=" C THR C 163 " pdb=" N ILE C 164 " ideal model delta sigma weight residual 1.332 1.396 -0.064 1.36e-02 5.41e+03 2.21e+01 bond pdb=" C3' DT K 42 " pdb=" C2' DT K 42 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" P DA L 2 " pdb=" O5' DA L 2 " ideal model delta sigma weight residual 1.593 1.622 -0.029 1.00e-02 1.00e+04 8.56e+00 bond pdb=" N ILE C 164 " pdb=" CA ILE C 164 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.11e+00 bond pdb=" C3' DG L 8 " pdb=" C2' DG L 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.08e+00 ... (remaining 24146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 32116 2.11 - 4.22: 832 4.22 - 6.33: 70 6.33 - 8.43: 16 8.43 - 10.54: 2 Bond angle restraints: 33036 Sorted by residual: angle pdb=" O4' DC K 38 " pdb=" C4' DC K 38 " pdb=" C3' DC K 38 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" N ILE D 261 " pdb=" CA ILE D 261 " pdb=" C ILE D 261 " ideal model delta sigma weight residual 113.71 109.10 4.61 9.50e-01 1.11e+00 2.36e+01 angle pdb=" C1' C J 16 " pdb=" N1 C J 16 " pdb=" C2 C J 16 " ideal model delta sigma weight residual 118.80 113.69 5.11 1.10e+00 8.26e-01 2.15e+01 angle pdb=" O4' DT K 37 " pdb=" C4' DT K 37 " pdb=" C3' DT K 37 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT K 42 " pdb=" C4 DT K 42 " pdb=" O4 DT K 42 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 33031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.93: 12996 19.93 - 39.86: 1167 39.86 - 59.79: 346 59.79 - 79.73: 104 79.73 - 99.66: 15 Dihedral angle restraints: 14628 sinusoidal: 6801 harmonic: 7827 Sorted by residual: dihedral pdb=" O4' U J 54 " pdb=" C1' U J 54 " pdb=" N1 U J 54 " pdb=" C2 U J 54 " ideal model delta sinusoidal sigma weight residual -160.00 -82.17 -77.83 1 1.50e+01 4.44e-03 3.37e+01 dihedral pdb=" CA GLU A 231 " pdb=" C GLU A 231 " pdb=" N TYR A 232 " pdb=" CA TYR A 232 " ideal model delta harmonic sigma weight residual 180.00 153.68 26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PRO A 298 " pdb=" C PRO A 298 " pdb=" N VAL A 299 " pdb=" CA VAL A 299 " ideal model delta harmonic sigma weight residual -180.00 -155.71 -24.29 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 14625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3509 0.102 - 0.204: 150 0.204 - 0.306: 4 0.306 - 0.408: 1 0.408 - 0.510: 3 Chirality restraints: 3667 Sorted by residual: chirality pdb=" P DA L 2 " pdb=" OP1 DA L 2 " pdb=" OP2 DA L 2 " pdb=" O5' DA L 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" P U J 44 " pdb=" OP1 U J 44 " pdb=" OP2 U J 44 " pdb=" O5' U J 44 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" P G J 43 " pdb=" OP1 G J 43 " pdb=" OP2 G J 43 " pdb=" O5' G J 43 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.70e+00 ... (remaining 3664 not shown) Planarity restraints: 3897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 200 " -0.024 2.00e-02 2.50e+03 2.36e-02 9.77e+00 pdb=" CG PHE H 200 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE H 200 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE H 200 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE H 200 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE H 200 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 200 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 43 " -0.018 2.00e-02 2.50e+03 1.89e-02 6.24e+00 pdb=" CG PHE I 43 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE I 43 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE I 43 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE I 43 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE I 43 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE I 43 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 78 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C LYS C 78 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS C 78 " -0.015 2.00e-02 2.50e+03 pdb=" N SER C 79 " -0.012 2.00e-02 2.50e+03 ... (remaining 3894 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 791 2.66 - 3.22: 24681 3.22 - 3.78: 42164 3.78 - 4.34: 58782 4.34 - 4.90: 88278 Nonbonded interactions: 214696 Sorted by model distance: nonbonded pdb=" O2' A J 12 " pdb=" O4' A J 13 " model vdw 2.103 3.040 nonbonded pdb=" N LYS B 10 " pdb=" OG SER B 107 " model vdw 2.199 3.120 nonbonded pdb=" O CYS H 109 " pdb=" NH1 ARG H 115 " model vdw 2.201 3.120 nonbonded pdb=" O GLU E 278 " pdb=" OH TYR E 318 " model vdw 2.204 3.040 nonbonded pdb=" NH1 ARG H 137 " pdb=" OG1 THR H 263 " model vdw 2.206 3.120 ... (remaining 214691 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 50 or resid 80 through 230 or resid 237 through \ 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) or r \ esid 260 through 331)) selection = (chain 'D' and (resid 12 through 50 or resid 80 through 230 or resid 237 through \ 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) or r \ esid 260 through 331)) selection = (chain 'E' and (resid 12 through 50 or resid 80 through 230 or resid 237 through \ 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) or r \ esid 260 through 331)) selection = (chain 'F' and (resid 12 through 50 or resid 80 through 230 or resid 237 through \ 331)) selection = (chain 'G' and (resid 12 through 50 or resid 80 through 230 or resid 237 through \ 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) or r \ esid 260 through 331)) selection = (chain 'H' and (resid 12 through 258 or (resid 259 and (name N or name CA or nam \ e C or name O or name CB )) or resid 260 through 331)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.180 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24151 Z= 0.252 Angle : 0.767 10.542 33036 Z= 0.508 Chirality : 0.048 0.510 3667 Planarity : 0.005 0.050 3897 Dihedral : 17.208 99.656 9572 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.77 % Favored : 93.00 % Rotamer: Outliers : 0.30 % Allowed : 0.64 % Favored : 99.07 % 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: -1.33 (0.16), residues: 2629 helix: 0.20 (0.18), residues: 779 sheet: -1.04 (0.24), residues: 453 loop : -1.46 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 140 TYR 0.034 0.002 TYR I 155 PHE 0.055 0.002 PHE H 200 TRP 0.016 0.001 TRP G 264 HIS 0.011 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.25 (24151) covalent geometry : angle 0.76746 / 0.51 (33036) hydrogen bonds : bond 0.26679 / 17.82 ( 737) hydrogen bonds : angle 8.59645 / 6.02 ( 1941) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 950 time to evaluate : 0.758 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 24 ILE cc_start: 0.8193 (mm) cc_final: 0.7992 (mm) REVERT: A 42 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8477 (mmtm) REVERT: A 69 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 95 MET cc_start: 0.3702 (tmm) cc_final: 0.3496 (tmm) REVERT: A 118 MET cc_start: 0.7622 (tpt) cc_final: 0.7163 (tpt) REVERT: A 169 LEU cc_start: 0.9021 (mp) cc_final: 0.8760 (mp) REVERT: A 181 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7342 (mmtt) REVERT: A 205 LYS cc_start: 0.6850 (mmpt) cc_final: 0.6127 (mmpt) REVERT: A 208 TRP cc_start: 0.7744 (m-10) cc_final: 0.7391 (m-10) REVERT: A 217 PRO cc_start: 0.5869 (Cg_exo) cc_final: 0.5632 (Cg_endo) REVERT: A 232 TYR cc_start: 0.7751 (m-10) cc_final: 0.7439 (m-80) REVERT: A 264 LYS cc_start: 0.6122 (mtmt) cc_final: 0.5708 (mttm) REVERT: A 305 HIS cc_start: 0.6932 (m90) cc_final: 0.6240 (m90) REVERT: B 22 ILE cc_start: 0.8098 (mm) cc_final: 0.7687 (mm) REVERT: B 80 LEU cc_start: 0.8579 (tt) cc_final: 0.8074 (tt) REVERT: B 119 MET cc_start: 0.4284 (tpt) cc_final: 0.4076 (tpt) REVERT: B 146 ARG cc_start: 0.7645 (tpm170) cc_final: 0.7066 (tpm170) REVERT: B 175 MET cc_start: 0.7306 (mtp) cc_final: 0.6807 (mtp) REVERT: B 179 MET cc_start: 0.7923 (mmm) cc_final: 0.7091 (mmm) REVERT: B 224 LEU cc_start: 0.8498 (mm) cc_final: 0.8287 (mm) REVERT: I 57 ILE cc_start: 0.8446 (mp) cc_final: 0.8182 (mp) REVERT: I 92 PHE cc_start: 0.6873 (t80) cc_final: 0.6438 (t80) REVERT: I 115 MET cc_start: -0.2050 (mmp) cc_final: -0.3069 (ttm) REVERT: D 12 LEU cc_start: 0.7936 (tt) cc_final: 0.7592 (tt) REVERT: D 35 THR cc_start: 0.8067 (t) cc_final: 0.7819 (t) REVERT: D 45 LEU cc_start: 0.8491 (mt) cc_final: 0.8026 (mt) REVERT: D 120 GLN cc_start: 0.8462 (mp10) cc_final: 0.8068 (mp10) REVERT: D 125 TYR cc_start: 0.6839 (t80) cc_final: 0.6516 (t80) REVERT: D 138 TYR cc_start: 0.8260 (m-10) cc_final: 0.8013 (m-80) REVERT: D 178 ASN cc_start: 0.7627 (t0) cc_final: 0.7333 (t0) REVERT: D 204 ARG cc_start: 0.7548 (mmm160) cc_final: 0.7004 (mmm-85) REVERT: D 300 LEU cc_start: 0.7972 (mt) cc_final: 0.7693 (mt) REVERT: E 97 ILE cc_start: 0.8207 (tp) cc_final: 0.7981 (tp) REVERT: E 98 LYS cc_start: 0.7610 (ttmm) cc_final: 0.7371 (mtmt) REVERT: E 134 LEU cc_start: 0.8524 (mm) cc_final: 0.8320 (mt) REVERT: E 194 GLN cc_start: 0.8173 (tp40) cc_final: 0.7911 (tp40) REVERT: E 206 TYR cc_start: 0.7084 (p90) cc_final: 0.6817 (p90) REVERT: E 229 MET cc_start: 0.4517 (tpt) cc_final: 0.3923 (tpt) REVERT: E 260 THR cc_start: 0.8146 (m) cc_final: 0.7692 (p) REVERT: E 291 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7589 (mmt90) REVERT: E 299 LYS cc_start: 0.8578 (mttt) cc_final: 0.8143 (mtmt) REVERT: F 34 GLN cc_start: 0.7202 (pt0) cc_final: 0.6713 (pt0) REVERT: F 85 SER cc_start: 0.6914 (p) cc_final: 0.5900 (m) REVERT: F 95 PHE cc_start: 0.7283 (p90) cc_final: 0.6809 (p90) REVERT: F 136 LYS cc_start: 0.7777 (mtpp) cc_final: 0.7468 (pttt) REVERT: F 164 ILE cc_start: 0.7725 (tt) cc_final: 0.7241 (tt) REVERT: F 206 TYR cc_start: 0.7340 (p90) cc_final: 0.7085 (p90) REVERT: F 207 LEU cc_start: 0.8385 (tp) cc_final: 0.7666 (mt) REVERT: F 230 THR cc_start: 0.8354 (m) cc_final: 0.8046 (t) REVERT: F 241 PHE cc_start: 0.7727 (t80) cc_final: 0.7505 (t80) REVERT: F 304 MET cc_start: 0.7653 (ttt) cc_final: 0.7325 (ttt) REVERT: C 93 ILE cc_start: 0.6820 (mm) cc_final: 0.5831 (mt) REVERT: C 119 TYR cc_start: 0.7465 (m-10) cc_final: 0.6986 (m-10) REVERT: C 136 LYS cc_start: 0.7525 (pptt) cc_final: 0.7153 (pptt) REVERT: C 153 LYS cc_start: 0.8112 (mptt) cc_final: 0.7415 (tptt) REVERT: C 156 GLU cc_start: 0.7819 (tt0) cc_final: 0.7596 (tt0) REVERT: C 164 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6882 (mt) REVERT: C 165 GLU cc_start: 0.8785 (pt0) cc_final: 0.8408 (pt0) REVERT: C 170 PRO cc_start: 0.8747 (Cg_exo) cc_final: 0.8478 (Cg_endo) REVERT: C 185 ASP cc_start: 0.7510 (p0) cc_final: 0.7205 (p0) REVERT: C 195 GLN cc_start: 0.7381 (pm20) cc_final: 0.7052 (pm20) REVERT: C 198 ASP cc_start: 0.6811 (m-30) cc_final: 0.6602 (m-30) REVERT: C 207 LEU cc_start: 0.8103 (tp) cc_final: 0.7820 (tp) REVERT: C 216 LYS cc_start: 0.7063 (tttp) cc_final: 0.6252 (tttt) REVERT: C 232 ASP cc_start: 0.7544 (t0) cc_final: 0.7326 (t0) REVERT: C 264 TRP cc_start: 0.7474 (m-90) cc_final: 0.7129 (m-10) REVERT: C 272 GLU cc_start: 0.7577 (mp0) cc_final: 0.7342 (mm-30) REVERT: C 310 ASP cc_start: 0.7361 (t70) cc_final: 0.7126 (t70) REVERT: G 51 ASP cc_start: 0.6327 (m-30) cc_final: 0.6112 (m-30) REVERT: G 80 GLN cc_start: 0.7459 (mt0) cc_final: 0.7231 (mt0) REVERT: G 82 CYS cc_start: 0.7891 (t) cc_final: 0.7629 (t) REVERT: G 113 ASN cc_start: 0.8278 (m-40) cc_final: 0.7905 (p0) REVERT: G 115 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7054 (ttm110) REVERT: G 133 THR cc_start: 0.8997 (m) cc_final: 0.8717 (t) REVERT: G 161 ILE cc_start: 0.8550 (mt) cc_final: 0.8319 (mp) REVERT: G 167 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8585 (ptmm) REVERT: G 180 ASP cc_start: 0.8897 (m-30) cc_final: 0.8674 (m-30) REVERT: G 182 PHE cc_start: 0.6584 (m-80) cc_final: 0.6229 (m-10) REVERT: G 194 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7460 (tm-30) REVERT: G 195 GLN cc_start: 0.8189 (mp-120) cc_final: 0.7452 (mp-120) REVERT: G 198 ASP cc_start: 0.7333 (m-30) cc_final: 0.6999 (m-30) REVERT: G 212 THR cc_start: 0.6198 (m) cc_final: 0.5938 (m) REVERT: G 214 PHE cc_start: 0.6954 (m-80) cc_final: 0.6668 (m-80) REVERT: G 217 ILE cc_start: 0.8534 (mp) cc_final: 0.8123 (mp) REVERT: G 224 TYR cc_start: 0.8588 (m-80) cc_final: 0.8143 (m-80) REVERT: G 241 PHE cc_start: 0.8015 (t80) cc_final: 0.7609 (t80) REVERT: G 284 ARG cc_start: 0.7958 (ppt170) cc_final: 0.7565 (ttp-110) REVERT: G 300 LEU cc_start: 0.8065 (mt) cc_final: 0.7833 (mt) REVERT: G 322 ILE cc_start: 0.8444 (mm) cc_final: 0.7976 (mm) REVERT: G 329 PHE cc_start: 0.8349 (m-80) cc_final: 0.8091 (m-80) REVERT: H 29 GLU cc_start: 0.7165 (mp0) cc_final: 0.6296 (mp0) REVERT: H 98 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7262 (ttmm) REVERT: H 141 ASN cc_start: 0.8432 (m110) cc_final: 0.8227 (m110) REVERT: H 164 ILE cc_start: 0.7974 (mp) cc_final: 0.7449 (mp) REVERT: H 168 GLU cc_start: 0.7333 (pp20) cc_final: 0.7102 (tm-30) REVERT: H 173 ASN cc_start: 0.9058 (t0) cc_final: 0.8644 (t0) REVERT: H 186 ASN cc_start: 0.7946 (t0) cc_final: 0.7277 (t0) REVERT: H 188 THR cc_start: 0.8618 (m) cc_final: 0.8409 (p) REVERT: H 189 ILE cc_start: 0.8867 (mt) cc_final: 0.8628 (mt) REVERT: H 208 ASN cc_start: 0.7389 (m-40) cc_final: 0.5813 (m-40) REVERT: H 265 TYR cc_start: 0.5979 (p90) cc_final: 0.5222 (p90) REVERT: H 273 PHE cc_start: 0.6740 (p90) cc_final: 0.6320 (p90) REVERT: H 290 PHE cc_start: 0.7570 (m-10) cc_final: 0.7298 (m-10) REVERT: H 291 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7436 (mtt-85) REVERT: H 320 MET cc_start: 0.7712 (mmp) cc_final: 0.7512 (mmp) outliers start: 7 outliers final: 1 residues processed: 952 average time/residue: 0.1611 time to fit residues: 234.6287 Evaluate side-chains 772 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 768 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain C residue 164 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 69 ASN I 137 GLN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN E 140 ASN E 255 ASN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN F 186 ASN ** F 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 ASN G 195 GLN H 26 ASN H 41 HIS ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 ASN H 255 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.166249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.141582 restraints weight = 54767.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.146180 restraints weight = 28914.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.149241 restraints weight = 17748.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.151231 restraints weight = 12120.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.152662 restraints weight = 9037.081| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24151 Z= 0.207 Angle : 0.763 14.419 33036 Z= 0.410 Chirality : 0.048 0.323 3667 Planarity : 0.006 0.061 3897 Dihedral : 18.259 100.042 4171 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.31 % Rotamer: Outliers : 2.88 % Allowed : 13.29 % Favored : 83.83 % 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: -1.60 (0.16), residues: 2629 helix: -0.24 (0.17), residues: 810 sheet: -1.14 (0.24), residues: 452 loop : -1.53 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 92 TYR 0.037 0.003 TYR E 268 PHE 0.039 0.003 PHE H 200 TRP 0.037 0.002 TRP F 264 HIS 0.008 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (24151) covalent geometry : angle 0.76333 / 0.41 (33036) hydrogen bonds : bond 0.06792 / 4.60 ( 737) hydrogen bonds : angle 6.65662 / 4.65 ( 1941) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 823 time to evaluate : 0.888 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.7751 (mm) cc_final: 0.7517 (mm) REVERT: A 61 ASP cc_start: 0.6875 (m-30) cc_final: 0.6389 (m-30) REVERT: A 69 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 95 MET cc_start: 0.3424 (tmm) cc_final: 0.3065 (tmm) REVERT: A 104 MET cc_start: 0.5111 (mmm) cc_final: 0.4590 (mmp) REVERT: A 118 MET cc_start: 0.7968 (tpt) cc_final: 0.7405 (tpt) REVERT: A 124 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6606 (tmtt) REVERT: A 169 LEU cc_start: 0.8805 (mp) cc_final: 0.8598 (mp) REVERT: A 175 ASP cc_start: 0.8543 (t0) cc_final: 0.8324 (t0) REVERT: A 181 LYS cc_start: 0.7591 (mmtt) cc_final: 0.7242 (mmtt) REVERT: A 217 PRO cc_start: 0.5827 (Cg_exo) cc_final: 0.5496 (Cg_endo) REVERT: A 230 LYS cc_start: 0.7563 (tptt) cc_final: 0.7295 (tptt) REVERT: A 232 TYR cc_start: 0.7763 (m-10) cc_final: 0.7273 (m-80) REVERT: B 80 LEU cc_start: 0.8529 (tt) cc_final: 0.8240 (tt) REVERT: B 98 ASN cc_start: 0.8133 (p0) cc_final: 0.7455 (p0) REVERT: B 130 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7346 (mp0) REVERT: B 144 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7797 (mmmt) REVERT: B 146 ARG cc_start: 0.7083 (tpm170) cc_final: 0.6657 (tpm170) REVERT: B 175 MET cc_start: 0.6845 (mtp) cc_final: 0.6026 (mtp) REVERT: B 176 LEU cc_start: 0.8969 (tp) cc_final: 0.8641 (tp) REVERT: B 179 MET cc_start: 0.7772 (mmm) cc_final: 0.6899 (mmm) REVERT: B 192 ILE cc_start: 0.8072 (mp) cc_final: 0.7799 (pt) REVERT: I 73 LEU cc_start: 0.8120 (mt) cc_final: 0.7895 (mt) REVERT: I 92 PHE cc_start: 0.6777 (t80) cc_final: 0.6434 (t80) REVERT: D 35 THR cc_start: 0.7892 (t) cc_final: 0.7641 (t) REVERT: D 45 LEU cc_start: 0.8488 (mt) cc_final: 0.8039 (mt) REVERT: D 100 LEU cc_start: 0.8394 (mp) cc_final: 0.8178 (mp) REVERT: D 125 TYR cc_start: 0.7392 (t80) cc_final: 0.7108 (t80) REVERT: D 153 LYS cc_start: 0.7666 (tppt) cc_final: 0.7401 (tppt) REVERT: D 194 GLN cc_start: 0.8028 (tp40) cc_final: 0.7670 (tp40) REVERT: D 204 ARG cc_start: 0.7641 (mmm160) cc_final: 0.7063 (mmm-85) REVERT: D 214 PHE cc_start: 0.5675 (m-80) cc_final: 0.5452 (m-80) REVERT: D 221 MET cc_start: 0.7720 (mpp) cc_final: 0.7415 (mpp) REVERT: D 273 PHE cc_start: 0.7674 (p90) cc_final: 0.7230 (p90) REVERT: E 21 PHE cc_start: 0.7601 (m-80) cc_final: 0.7271 (m-80) REVERT: E 34 GLN cc_start: 0.7033 (pm20) cc_final: 0.6490 (pm20) REVERT: E 43 PHE cc_start: 0.7542 (t80) cc_final: 0.7304 (t80) REVERT: E 44 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7646 (pttt) REVERT: E 138 TYR cc_start: 0.7998 (m-80) cc_final: 0.7735 (m-80) REVERT: E 194 GLN cc_start: 0.8309 (tp40) cc_final: 0.8036 (tp40) REVERT: E 216 LYS cc_start: 0.7721 (ptmm) cc_final: 0.7420 (ptmm) REVERT: E 229 MET cc_start: 0.4434 (tpt) cc_final: 0.3856 (tpt) REVERT: E 260 THR cc_start: 0.7972 (m) cc_final: 0.7673 (p) REVERT: E 268 TYR cc_start: 0.8190 (t80) cc_final: 0.7859 (t80) REVERT: E 291 ARG cc_start: 0.7591 (mtt-85) cc_final: 0.7261 (mmt90) REVERT: F 32 PHE cc_start: 0.8248 (m-80) cc_final: 0.8026 (m-80) REVERT: F 34 GLN cc_start: 0.7296 (pt0) cc_final: 0.7093 (pt0) REVERT: F 61 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.5222 (tt0) REVERT: F 85 SER cc_start: 0.6767 (p) cc_final: 0.6461 (m) REVERT: F 95 PHE cc_start: 0.7455 (p90) cc_final: 0.7134 (p90) REVERT: F 111 ASP cc_start: 0.6867 (t0) cc_final: 0.6525 (t0) REVERT: F 112 TYR cc_start: 0.7657 (t80) cc_final: 0.7377 (t80) REVERT: F 115 ARG cc_start: 0.8171 (ptp-110) cc_final: 0.7011 (ptp-110) REVERT: F 207 LEU cc_start: 0.8546 (tp) cc_final: 0.7825 (mt) REVERT: F 229 MET cc_start: 0.5933 (ttt) cc_final: 0.5526 (ttt) REVERT: F 230 THR cc_start: 0.8387 (m) cc_final: 0.8143 (t) REVERT: F 263 THR cc_start: 0.7492 (p) cc_final: 0.6968 (t) REVERT: F 268 TYR cc_start: 0.7440 (t80) cc_final: 0.6418 (t80) REVERT: F 314 GLU cc_start: 0.7646 (tp30) cc_final: 0.7424 (tp30) REVERT: C 34 GLN cc_start: 0.6838 (pt0) cc_final: 0.6535 (pt0) REVERT: C 44 LYS cc_start: 0.7680 (pttm) cc_final: 0.7456 (pttm) REVERT: C 93 ILE cc_start: 0.7045 (mm) cc_final: 0.6014 (mt) REVERT: C 120 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 141 ASN cc_start: 0.8382 (m110) cc_final: 0.7816 (m110) REVERT: C 170 PRO cc_start: 0.8887 (Cg_exo) cc_final: 0.8661 (Cg_endo) REVERT: C 185 ASP cc_start: 0.7221 (p0) cc_final: 0.6945 (p0) REVERT: C 191 GLU cc_start: 0.7158 (tp30) cc_final: 0.5999 (tp30) REVERT: C 216 LYS cc_start: 0.7079 (tttp) cc_final: 0.6505 (tttp) REVERT: C 232 ASP cc_start: 0.7696 (t0) cc_final: 0.7304 (t0) REVERT: C 243 PHE cc_start: 0.8078 (t80) cc_final: 0.7775 (t80) REVERT: C 244 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7464 (mt-10) REVERT: C 264 TRP cc_start: 0.7539 (m-90) cc_final: 0.7251 (m-10) REVERT: C 272 GLU cc_start: 0.7497 (mp0) cc_final: 0.6779 (mp0) REVERT: G 51 ASP cc_start: 0.6924 (m-30) cc_final: 0.6622 (m-30) REVERT: G 113 ASN cc_start: 0.8531 (m-40) cc_final: 0.8311 (p0) REVERT: G 114 TYR cc_start: 0.8171 (t80) cc_final: 0.7944 (t80) REVERT: G 129 ASP cc_start: 0.7341 (t70) cc_final: 0.7041 (t70) REVERT: G 161 ILE cc_start: 0.8726 (mt) cc_final: 0.8501 (mp) REVERT: G 167 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8614 (ptmm) REVERT: G 169 TYR cc_start: 0.7567 (m-80) cc_final: 0.6851 (m-80) REVERT: G 182 PHE cc_start: 0.6779 (m-80) cc_final: 0.6540 (m-10) REVERT: G 191 GLU cc_start: 0.7876 (tp30) cc_final: 0.7376 (tp30) REVERT: G 198 ASP cc_start: 0.7512 (m-30) cc_final: 0.7072 (m-30) REVERT: G 208 ASN cc_start: 0.8096 (t0) cc_final: 0.7800 (t0) REVERT: G 209 ILE cc_start: 0.8877 (mm) cc_final: 0.8457 (tp) REVERT: G 214 PHE cc_start: 0.7107 (m-80) cc_final: 0.6677 (m-80) REVERT: G 217 ILE cc_start: 0.8273 (mp) cc_final: 0.8039 (mp) REVERT: G 224 TYR cc_start: 0.8542 (m-80) cc_final: 0.8164 (m-10) REVERT: G 229 MET cc_start: 0.6696 (ttm) cc_final: 0.6487 (mtm) REVERT: G 249 MET cc_start: 0.7134 (ttt) cc_final: 0.6840 (ttt) REVERT: G 256 ASN cc_start: 0.7656 (t0) cc_final: 0.7287 (t0) REVERT: G 284 ARG cc_start: 0.7952 (ppt170) cc_final: 0.7480 (ttp-110) REVERT: G 300 LEU cc_start: 0.8084 (mt) cc_final: 0.7826 (mt) REVERT: G 309 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6417 (tm-30) REVERT: G 329 PHE cc_start: 0.8493 (m-80) cc_final: 0.8234 (m-10) REVERT: H 29 GLU cc_start: 0.6951 (mp0) cc_final: 0.6302 (mp0) REVERT: H 98 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7332 (ttmm) REVERT: H 119 TYR cc_start: 0.8781 (m-10) cc_final: 0.8450 (m-80) REVERT: H 139 VAL cc_start: 0.8919 (m) cc_final: 0.8712 (m) REVERT: H 164 ILE cc_start: 0.7788 (mp) cc_final: 0.7561 (mp) REVERT: H 168 GLU cc_start: 0.7393 (pp20) cc_final: 0.7149 (tm-30) REVERT: H 173 ASN cc_start: 0.9056 (t0) cc_final: 0.8733 (t0) REVERT: H 180 ASP cc_start: 0.8137 (p0) cc_final: 0.6109 (m-30) REVERT: H 189 ILE cc_start: 0.8774 (mt) cc_final: 0.8547 (mt) REVERT: H 265 TYR cc_start: 0.6272 (p90) cc_final: 0.5484 (p90) REVERT: H 290 PHE cc_start: 0.7577 (m-10) cc_final: 0.7245 (m-10) REVERT: H 291 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7170 (mtt90) REVERT: H 304 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6973 (mmp) REVERT: H 311 LEU cc_start: 0.7982 (mt) cc_final: 0.6807 (mt) REVERT: H 316 LYS cc_start: 0.9116 (tttp) cc_final: 0.8649 (tppt) outliers start: 68 outliers final: 36 residues processed: 847 average time/residue: 0.1693 time to fit residues: 221.0985 Evaluate side-chains 803 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 762 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 44 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 304 MET Chi-restraints excluded: chain H residue 310 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 16 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.159386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.135826 restraints weight = 55573.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.140250 restraints weight = 29930.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.143133 restraints weight = 18497.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.145043 restraints weight = 12710.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.146344 restraints weight = 9578.554| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24151 Z= 0.172 Angle : 0.710 13.559 33036 Z= 0.378 Chirality : 0.047 0.271 3667 Planarity : 0.005 0.051 3897 Dihedral : 18.191 100.341 4165 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.95 % Rotamer: Outliers : 2.88 % Allowed : 17.78 % Favored : 79.34 % 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: -1.49 (0.16), residues: 2629 helix: -0.17 (0.17), residues: 801 sheet: -1.03 (0.25), residues: 418 loop : -1.45 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 92 TYR 0.022 0.002 TYR I 155 PHE 0.034 0.002 PHE G 243 TRP 0.060 0.002 TRP F 264 HIS 0.008 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (24151) covalent geometry : angle 0.71036 / 0.38 (33036) hydrogen bonds : bond 0.05947 / 4.05 ( 737) hydrogen bonds : angle 6.20050 / 4.33 ( 1941) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 810 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 24 ILE cc_start: 0.7731 (mm) cc_final: 0.7500 (mm) REVERT: A 61 ASP cc_start: 0.6928 (m-30) cc_final: 0.6438 (m-30) REVERT: A 69 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7933 (p) REVERT: A 95 MET cc_start: 0.3416 (tmm) cc_final: 0.3100 (tmm) REVERT: A 104 MET cc_start: 0.5124 (mmm) cc_final: 0.4671 (mmp) REVERT: A 118 MET cc_start: 0.7921 (tpt) cc_final: 0.7406 (tpt) REVERT: A 181 LYS cc_start: 0.7453 (mmtt) cc_final: 0.7040 (mmtt) REVERT: A 186 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7408 (tpp80) REVERT: A 230 LYS cc_start: 0.7784 (tptt) cc_final: 0.7375 (tptt) REVERT: A 232 TYR cc_start: 0.7765 (m-10) cc_final: 0.7199 (m-10) REVERT: B 80 LEU cc_start: 0.8538 (tt) cc_final: 0.8320 (tt) REVERT: B 98 ASN cc_start: 0.8010 (p0) cc_final: 0.7683 (p0) REVERT: B 130 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 144 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7701 (mmpt) REVERT: B 175 MET cc_start: 0.6683 (mtp) cc_final: 0.5955 (mtp) REVERT: B 179 MET cc_start: 0.7569 (mmm) cc_final: 0.6771 (mmm) REVERT: B 192 ILE cc_start: 0.8083 (mp) cc_final: 0.7836 (pt) REVERT: I 20 ILE cc_start: 0.8446 (tp) cc_final: 0.7077 (tp) REVERT: I 25 PHE cc_start: 0.6612 (m-10) cc_final: 0.6352 (m-80) REVERT: I 63 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8034 (mm-30) REVERT: I 73 LEU cc_start: 0.8018 (mt) cc_final: 0.7786 (mt) REVERT: I 92 PHE cc_start: 0.6723 (t80) cc_final: 0.6388 (t80) REVERT: I 165 LYS cc_start: 0.6964 (mmpt) cc_final: 0.6696 (mmtt) REVERT: D 45 LEU cc_start: 0.8512 (mt) cc_final: 0.8046 (mt) REVERT: D 92 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7782 (ttt90) REVERT: D 121 LYS cc_start: 0.7822 (mmpt) cc_final: 0.7478 (mmpt) REVERT: D 125 TYR cc_start: 0.7419 (t80) cc_final: 0.7085 (t80) REVERT: D 194 GLN cc_start: 0.8039 (tp40) cc_final: 0.7698 (tp40) REVERT: D 204 ARG cc_start: 0.7561 (mmm160) cc_final: 0.7019 (mmm-85) REVERT: D 273 PHE cc_start: 0.7683 (p90) cc_final: 0.7227 (p90) REVERT: D 320 MET cc_start: 0.7794 (mmt) cc_final: 0.7152 (mmt) REVERT: E 43 PHE cc_start: 0.7513 (t80) cc_final: 0.7247 (t80) REVERT: E 44 LYS cc_start: 0.8283 (ptmt) cc_final: 0.7804 (ptpp) REVERT: E 85 SER cc_start: 0.7901 (t) cc_final: 0.7664 (m) REVERT: E 165 GLU cc_start: 0.7300 (tm-30) cc_final: 0.7049 (tm-30) REVERT: E 169 TYR cc_start: 0.8534 (m-80) cc_final: 0.8297 (m-10) REVERT: E 194 GLN cc_start: 0.8112 (tp40) cc_final: 0.7775 (tp40) REVERT: E 260 THR cc_start: 0.7917 (m) cc_final: 0.7626 (p) REVERT: E 268 TYR cc_start: 0.8068 (t80) cc_final: 0.7775 (t80) REVERT: E 291 ARG cc_start: 0.7424 (mtt-85) cc_final: 0.7146 (mmt90) REVERT: F 20 SER cc_start: 0.7571 (t) cc_final: 0.7369 (p) REVERT: F 34 GLN cc_start: 0.7353 (pt0) cc_final: 0.7067 (pt0) REVERT: F 85 SER cc_start: 0.7118 (p) cc_final: 0.6663 (m) REVERT: F 89 ASP cc_start: 0.7010 (p0) cc_final: 0.6541 (p0) REVERT: F 95 PHE cc_start: 0.7454 (p90) cc_final: 0.6995 (p90) REVERT: F 111 ASP cc_start: 0.6832 (t0) cc_final: 0.6077 (t0) REVERT: F 112 TYR cc_start: 0.7630 (t80) cc_final: 0.7162 (t80) REVERT: F 115 ARG cc_start: 0.8035 (ptp-110) cc_final: 0.7187 (ptp-110) REVERT: F 204 ARG cc_start: 0.7819 (mmm160) cc_final: 0.7018 (mmm160) REVERT: F 207 LEU cc_start: 0.8636 (tp) cc_final: 0.7915 (mt) REVERT: F 224 TYR cc_start: 0.6849 (m-10) cc_final: 0.6618 (m-10) REVERT: F 229 MET cc_start: 0.6059 (ttt) cc_final: 0.5856 (ttt) REVERT: F 230 THR cc_start: 0.8411 (m) cc_final: 0.8054 (t) REVERT: F 267 ASP cc_start: 0.7636 (m-30) cc_final: 0.7369 (m-30) REVERT: F 314 GLU cc_start: 0.7703 (tp30) cc_final: 0.7425 (tp30) REVERT: C 34 GLN cc_start: 0.6670 (pt0) cc_final: 0.6416 (pt0) REVERT: C 93 ILE cc_start: 0.6990 (mm) cc_final: 0.6022 (mt) REVERT: C 120 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7743 (tm-30) REVERT: C 136 LYS cc_start: 0.7829 (pptt) cc_final: 0.7512 (pptt) REVERT: C 141 ASN cc_start: 0.8270 (m110) cc_final: 0.7258 (m110) REVERT: C 185 ASP cc_start: 0.7189 (p0) cc_final: 0.6933 (p0) REVERT: C 216 LYS cc_start: 0.6884 (tttp) cc_final: 0.6495 (tttt) REVERT: C 232 ASP cc_start: 0.7801 (t0) cc_final: 0.7432 (t0) REVERT: C 233 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: C 243 PHE cc_start: 0.8007 (t80) cc_final: 0.7507 (t80) REVERT: C 244 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7278 (mt-10) REVERT: C 264 TRP cc_start: 0.7565 (m-90) cc_final: 0.7279 (m-10) REVERT: C 272 GLU cc_start: 0.7556 (mp0) cc_final: 0.6808 (mp0) REVERT: G 106 MET cc_start: 0.5188 (ppp) cc_final: 0.4973 (tmm) REVERT: G 167 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8703 (ptmm) REVERT: G 169 TYR cc_start: 0.7552 (m-80) cc_final: 0.6912 (m-80) REVERT: G 182 PHE cc_start: 0.6720 (m-80) cc_final: 0.6497 (m-10) REVERT: G 198 ASP cc_start: 0.7434 (m-30) cc_final: 0.6981 (m-30) REVERT: G 209 ILE cc_start: 0.8898 (mm) cc_final: 0.8505 (tp) REVERT: G 214 PHE cc_start: 0.7105 (m-80) cc_final: 0.6741 (m-80) REVERT: G 216 LYS cc_start: 0.8381 (tptt) cc_final: 0.8158 (tptt) REVERT: G 224 TYR cc_start: 0.8518 (m-80) cc_final: 0.8183 (m-10) REVERT: G 235 ASP cc_start: 0.6331 (t70) cc_final: 0.5926 (m-30) REVERT: G 256 ASN cc_start: 0.7629 (t0) cc_final: 0.7327 (t0) REVERT: G 259 ARG cc_start: 0.5292 (ttm-80) cc_final: 0.4751 (tpp-160) REVERT: G 284 ARG cc_start: 0.7862 (ppt170) cc_final: 0.7425 (ttp-110) REVERT: G 300 LEU cc_start: 0.7972 (mt) cc_final: 0.7674 (mt) REVERT: G 309 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6614 (tm-30) REVERT: G 329 PHE cc_start: 0.8504 (m-80) cc_final: 0.8273 (m-10) REVERT: H 17 GLU cc_start: 0.6068 (tp30) cc_final: 0.5476 (mm-30) REVERT: H 29 GLU cc_start: 0.7156 (mp0) cc_final: 0.6351 (mp0) REVERT: H 35 THR cc_start: 0.6542 (p) cc_final: 0.6124 (t) REVERT: H 45 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6673 (mt) REVERT: H 98 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7359 (ttmm) REVERT: H 120 GLN cc_start: 0.8247 (mt0) cc_final: 0.7623 (mt0) REVERT: H 124 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7988 (mm-30) REVERT: H 173 ASN cc_start: 0.8977 (t0) cc_final: 0.8694 (t0) REVERT: H 265 TYR cc_start: 0.6308 (p90) cc_final: 0.5645 (p90) REVERT: H 290 PHE cc_start: 0.7530 (m-10) cc_final: 0.7265 (m-10) REVERT: H 291 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7130 (mtt90) REVERT: H 311 LEU cc_start: 0.7941 (mt) cc_final: 0.7733 (mt) outliers start: 68 outliers final: 36 residues processed: 838 average time/residue: 0.1718 time to fit residues: 221.9680 Evaluate side-chains 794 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 755 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 275 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 258 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 153 optimal weight: 0.0270 chunk 57 optimal weight: 0.0050 chunk 134 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 overall best weight: 1.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN I 17 ASN I 166 HIS ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 255 ASN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN F 195 GLN ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.156491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.132805 restraints weight = 55272.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.137159 restraints weight = 29982.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.140013 restraints weight = 18692.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.141939 restraints weight = 12916.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.143251 restraints weight = 9712.098| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24151 Z= 0.203 Angle : 0.732 17.378 33036 Z= 0.389 Chirality : 0.047 0.269 3667 Planarity : 0.005 0.072 3897 Dihedral : 18.154 100.486 4163 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 3.98 % Allowed : 19.98 % Favored : 76.04 % 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: -1.49 (0.16), residues: 2629 helix: -0.18 (0.17), residues: 801 sheet: -1.01 (0.26), residues: 404 loop : -1.46 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 291 TYR 0.030 0.002 TYR D 112 PHE 0.040 0.002 PHE G 243 TRP 0.027 0.002 TRP F 264 HIS 0.010 0.002 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (24151) covalent geometry : angle 0.73163 / 0.39 (33036) hydrogen bonds : bond 0.05675 / 3.84 ( 737) hydrogen bonds : angle 6.14968 / 4.27 ( 1941) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 786 time to evaluate : 0.678 Fit side-chains TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 24 ILE cc_start: 0.7823 (mm) cc_final: 0.7601 (mm) REVERT: A 61 ASP cc_start: 0.6986 (m-30) cc_final: 0.6562 (m-30) REVERT: A 75 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7408 (ptpp) REVERT: A 118 MET cc_start: 0.7939 (tpt) cc_final: 0.7498 (tpt) REVERT: A 181 LYS cc_start: 0.7340 (mmtt) cc_final: 0.6949 (mmtt) REVERT: A 186 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7776 (tpp80) REVERT: A 230 LYS cc_start: 0.7749 (tptt) cc_final: 0.7264 (tptt) REVERT: A 232 TYR cc_start: 0.7748 (m-10) cc_final: 0.7284 (m-10) REVERT: A 283 GLU cc_start: 0.8121 (mp0) cc_final: 0.7874 (mp0) REVERT: B 5 TYR cc_start: 0.6903 (m-80) cc_final: 0.6698 (m-80) REVERT: B 71 ARG cc_start: 0.8229 (tpt90) cc_final: 0.7965 (tpt90) REVERT: B 78 CYS cc_start: 0.6984 (t) cc_final: 0.6383 (t) REVERT: B 80 LEU cc_start: 0.8587 (tt) cc_final: 0.8371 (tt) REVERT: B 98 ASN cc_start: 0.8189 (p0) cc_final: 0.7520 (p0) REVERT: B 130 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7492 (mm-30) REVERT: B 192 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7902 (pt) REVERT: B 230 SER cc_start: 0.7394 (p) cc_final: 0.7166 (p) REVERT: I 92 PHE cc_start: 0.6773 (t80) cc_final: 0.6389 (t80) REVERT: I 165 LYS cc_start: 0.7135 (mmpt) cc_final: 0.6715 (mmtt) REVERT: D 45 LEU cc_start: 0.8568 (mt) cc_final: 0.8099 (mt) REVERT: D 92 ARG cc_start: 0.7983 (ttt90) cc_final: 0.7778 (ttt90) REVERT: D 121 LYS cc_start: 0.7877 (mmpt) cc_final: 0.7509 (mmpt) REVERT: D 125 TYR cc_start: 0.7566 (t80) cc_final: 0.7082 (t80) REVERT: D 194 GLN cc_start: 0.8116 (tp40) cc_final: 0.7794 (tp40) REVERT: D 204 ARG cc_start: 0.7531 (mmm160) cc_final: 0.7173 (mmm-85) REVERT: D 272 GLU cc_start: 0.8418 (mp0) cc_final: 0.7664 (mp0) REVERT: D 273 PHE cc_start: 0.7751 (p90) cc_final: 0.7227 (p90) REVERT: D 302 ASP cc_start: 0.6795 (m-30) cc_final: 0.6585 (m-30) REVERT: D 320 MET cc_start: 0.7813 (mmt) cc_final: 0.6949 (mmt) REVERT: E 21 PHE cc_start: 0.7602 (m-80) cc_final: 0.7314 (m-10) REVERT: E 43 PHE cc_start: 0.7546 (t80) cc_final: 0.7290 (t80) REVERT: E 44 LYS cc_start: 0.8465 (ptmt) cc_final: 0.7950 (ptpp) REVERT: E 86 THR cc_start: 0.7941 (p) cc_final: 0.7680 (p) REVERT: E 194 GLN cc_start: 0.8088 (tp40) cc_final: 0.7814 (tp40) REVERT: E 260 THR cc_start: 0.7993 (m) cc_final: 0.7718 (p) REVERT: E 268 TYR cc_start: 0.8127 (t80) cc_final: 0.7902 (t80) REVERT: F 34 GLN cc_start: 0.7342 (pt0) cc_final: 0.7122 (pt0) REVERT: F 85 SER cc_start: 0.7257 (p) cc_final: 0.6722 (m) REVERT: F 89 ASP cc_start: 0.7077 (p0) cc_final: 0.6612 (p0) REVERT: F 111 ASP cc_start: 0.6806 (t0) cc_final: 0.6074 (t0) REVERT: F 112 TYR cc_start: 0.7647 (t80) cc_final: 0.7179 (t80) REVERT: F 115 ARG cc_start: 0.8098 (ptp-110) cc_final: 0.7224 (ptp-110) REVERT: F 136 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7717 (ttpt) REVERT: F 168 GLU cc_start: 0.5995 (pp20) cc_final: 0.5727 (tm-30) REVERT: F 204 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7028 (mmm160) REVERT: F 207 LEU cc_start: 0.8725 (tp) cc_final: 0.7996 (mt) REVERT: F 224 TYR cc_start: 0.6872 (m-10) cc_final: 0.6652 (m-10) REVERT: F 229 MET cc_start: 0.6167 (ttt) cc_final: 0.5820 (ttt) REVERT: F 230 THR cc_start: 0.8349 (m) cc_final: 0.8050 (t) REVERT: F 263 THR cc_start: 0.7307 (p) cc_final: 0.7051 (t) REVERT: F 267 ASP cc_start: 0.7710 (m-30) cc_final: 0.7443 (m-30) REVERT: C 34 GLN cc_start: 0.6715 (pt0) cc_final: 0.6434 (pt0) REVERT: C 44 LYS cc_start: 0.7804 (pttm) cc_final: 0.7534 (pttm) REVERT: C 93 ILE cc_start: 0.7030 (mm) cc_final: 0.6116 (mt) REVERT: C 120 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 141 ASN cc_start: 0.8036 (m110) cc_final: 0.7499 (m110) REVERT: C 232 ASP cc_start: 0.7852 (t0) cc_final: 0.7523 (t0) REVERT: C 233 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: C 243 PHE cc_start: 0.8067 (t80) cc_final: 0.7292 (t80) REVERT: C 244 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7227 (mt-10) REVERT: C 264 TRP cc_start: 0.7705 (m-90) cc_final: 0.7311 (m-10) REVERT: G 120 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: G 129 ASP cc_start: 0.7243 (t0) cc_final: 0.7042 (t0) REVERT: G 167 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8731 (ptmm) REVERT: G 169 TYR cc_start: 0.7595 (m-80) cc_final: 0.6980 (m-80) REVERT: G 198 ASP cc_start: 0.7459 (m-30) cc_final: 0.7108 (m-30) REVERT: G 214 PHE cc_start: 0.7103 (m-80) cc_final: 0.6863 (m-80) REVERT: G 241 PHE cc_start: 0.8191 (t80) cc_final: 0.7828 (t80) REVERT: G 256 ASN cc_start: 0.7670 (t0) cc_final: 0.7367 (t0) REVERT: G 259 ARG cc_start: 0.5384 (ttm-80) cc_final: 0.4886 (tpp-160) REVERT: G 284 ARG cc_start: 0.7902 (ppt170) cc_final: 0.7439 (ttp-110) REVERT: G 300 LEU cc_start: 0.8022 (mt) cc_final: 0.7740 (mt) REVERT: G 307 LYS cc_start: 0.8299 (mmtp) cc_final: 0.7879 (mmtp) REVERT: H 17 GLU cc_start: 0.6094 (tp30) cc_final: 0.5498 (mm-30) REVERT: H 26 ASN cc_start: 0.8095 (m-40) cc_final: 0.7784 (m-40) REVERT: H 29 GLU cc_start: 0.7236 (mp0) cc_final: 0.6436 (mp0) REVERT: H 35 THR cc_start: 0.6562 (p) cc_final: 0.6210 (t) REVERT: H 98 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7385 (ttmm) REVERT: H 120 GLN cc_start: 0.8249 (mt0) cc_final: 0.7932 (mt0) REVERT: H 173 ASN cc_start: 0.9019 (t0) cc_final: 0.8765 (t0) REVERT: H 224 TYR cc_start: 0.6725 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: H 265 TYR cc_start: 0.6287 (p90) cc_final: 0.5715 (p90) REVERT: H 290 PHE cc_start: 0.7562 (m-10) cc_final: 0.7301 (m-10) REVERT: H 291 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.7087 (mtt90) REVERT: H 311 LEU cc_start: 0.8002 (mt) cc_final: 0.7743 (mt) outliers start: 94 outliers final: 63 residues processed: 822 average time/residue: 0.1664 time to fit residues: 211.5880 Evaluate side-chains 816 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 749 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 270 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 185 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN B 184 GLN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.157937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.134492 restraints weight = 54965.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.138842 restraints weight = 29791.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.141617 restraints weight = 18464.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.143523 restraints weight = 12784.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.144818 restraints weight = 9619.403| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24151 Z= 0.167 Angle : 0.712 12.279 33036 Z= 0.377 Chirality : 0.046 0.251 3667 Planarity : 0.005 0.054 3897 Dihedral : 18.108 100.155 4162 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 4.02 % Allowed : 21.80 % Favored : 74.17 % 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: -1.45 (0.16), residues: 2629 helix: -0.13 (0.18), residues: 802 sheet: -0.85 (0.26), residues: 402 loop : -1.48 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 291 TYR 0.041 0.002 TYR D 112 PHE 0.038 0.002 PHE G 243 TRP 0.062 0.002 TRP F 264 HIS 0.008 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (24151) covalent geometry : angle 0.71184 / 0.38 (33036) hydrogen bonds : bond 0.05377 / 3.62 ( 737) hydrogen bonds : angle 6.00875 / 4.18 ( 1941) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 759 time to evaluate : 0.761 Fit side-chains TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.7792 (mm) cc_final: 0.7549 (mm) REVERT: A 75 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7410 (ptpp) REVERT: A 113 GLU cc_start: 0.8128 (pm20) cc_final: 0.7875 (pm20) REVERT: A 118 MET cc_start: 0.7913 (tpt) cc_final: 0.7488 (tpt) REVERT: A 171 TYR cc_start: 0.8025 (t80) cc_final: 0.7712 (t80) REVERT: A 186 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7822 (tpp80) REVERT: A 230 LYS cc_start: 0.7728 (tptt) cc_final: 0.7201 (tptt) REVERT: A 232 TYR cc_start: 0.7737 (m-10) cc_final: 0.7251 (m-10) REVERT: A 260 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7264 (mm) REVERT: A 264 LYS cc_start: 0.6759 (ptpp) cc_final: 0.6544 (ptmm) REVERT: B 78 CYS cc_start: 0.6862 (t) cc_final: 0.6018 (t) REVERT: B 80 LEU cc_start: 0.8581 (tt) cc_final: 0.8371 (tt) REVERT: B 97 MET cc_start: 0.7024 (tpp) cc_final: 0.6563 (tpp) REVERT: B 98 ASN cc_start: 0.8003 (p0) cc_final: 0.7521 (p0) REVERT: B 130 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 192 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7933 (pt) REVERT: B 224 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7723 (mm) REVERT: B 230 SER cc_start: 0.7468 (p) cc_final: 0.7247 (p) REVERT: I 20 ILE cc_start: 0.8470 (tp) cc_final: 0.7085 (tp) REVERT: I 25 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: I 92 PHE cc_start: 0.6801 (t80) cc_final: 0.6414 (t80) REVERT: I 165 LYS cc_start: 0.7099 (mmpt) cc_final: 0.6707 (mmtt) REVERT: D 34 GLN cc_start: 0.7746 (pt0) cc_final: 0.7191 (pt0) REVERT: D 45 LEU cc_start: 0.8540 (mt) cc_final: 0.8002 (mt) REVERT: D 121 LYS cc_start: 0.7856 (mmpt) cc_final: 0.7445 (mmpt) REVERT: D 125 TYR cc_start: 0.7545 (t80) cc_final: 0.7145 (t80) REVERT: D 169 TYR cc_start: 0.7835 (m-10) cc_final: 0.6596 (m-10) REVERT: D 180 ASP cc_start: 0.7643 (t0) cc_final: 0.7342 (t0) REVERT: D 194 GLN cc_start: 0.8167 (tp40) cc_final: 0.7832 (tp40) REVERT: D 204 ARG cc_start: 0.7528 (mmm160) cc_final: 0.7197 (mmm-85) REVERT: D 249 MET cc_start: 0.8300 (mtp) cc_final: 0.8099 (mtm) REVERT: D 272 GLU cc_start: 0.8362 (mp0) cc_final: 0.7797 (mp0) REVERT: D 291 ARG cc_start: 0.7590 (mmt90) cc_final: 0.7362 (mmt90) REVERT: D 320 MET cc_start: 0.7778 (mmt) cc_final: 0.6944 (mmt) REVERT: E 44 LYS cc_start: 0.8523 (ptmt) cc_final: 0.8034 (ptpp) REVERT: E 124 GLU cc_start: 0.7156 (tp30) cc_final: 0.6851 (tp30) REVERT: E 165 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6981 (tm-30) REVERT: E 194 GLN cc_start: 0.8038 (tp40) cc_final: 0.7742 (tp40) REVERT: E 255 ASN cc_start: 0.8433 (t0) cc_final: 0.8108 (t0) REVERT: E 268 TYR cc_start: 0.8039 (t80) cc_final: 0.7821 (t80) REVERT: F 34 GLN cc_start: 0.7325 (pt0) cc_final: 0.7083 (pt0) REVERT: F 85 SER cc_start: 0.7207 (p) cc_final: 0.6625 (m) REVERT: F 89 ASP cc_start: 0.7065 (p0) cc_final: 0.6599 (p0) REVERT: F 111 ASP cc_start: 0.6817 (t0) cc_final: 0.6113 (t0) REVERT: F 112 TYR cc_start: 0.7579 (t80) cc_final: 0.7112 (t80) REVERT: F 115 ARG cc_start: 0.8069 (ptp-110) cc_final: 0.7219 (ptp-110) REVERT: F 136 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7674 (ttpt) REVERT: F 194 GLN cc_start: 0.8068 (tp40) cc_final: 0.7759 (tp-100) REVERT: F 204 ARG cc_start: 0.7794 (mmm160) cc_final: 0.6967 (mmm160) REVERT: F 207 LEU cc_start: 0.8655 (tp) cc_final: 0.7912 (mt) REVERT: F 229 MET cc_start: 0.6171 (ttt) cc_final: 0.5902 (ttt) REVERT: F 230 THR cc_start: 0.8314 (m) cc_final: 0.8013 (t) REVERT: F 267 ASP cc_start: 0.7715 (m-30) cc_final: 0.7464 (m-30) REVERT: C 44 LYS cc_start: 0.7796 (pttm) cc_final: 0.7509 (pttm) REVERT: C 73 ASP cc_start: 0.7842 (m-30) cc_final: 0.7126 (m-30) REVERT: C 78 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8470 (tppt) REVERT: C 80 GLN cc_start: 0.8552 (mm-40) cc_final: 0.7500 (mt0) REVERT: C 93 ILE cc_start: 0.6937 (mm) cc_final: 0.6050 (mt) REVERT: C 120 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7643 (tm-30) REVERT: C 141 ASN cc_start: 0.8060 (m110) cc_final: 0.7501 (m110) REVERT: C 216 LYS cc_start: 0.6725 (tttp) cc_final: 0.6455 (ttpt) REVERT: C 221 MET cc_start: 0.6125 (mmm) cc_final: 0.5818 (mmm) REVERT: C 228 GLU cc_start: 0.6278 (mp0) cc_final: 0.5819 (mp0) REVERT: C 232 ASP cc_start: 0.7824 (t0) cc_final: 0.7440 (t0) REVERT: C 243 PHE cc_start: 0.8089 (t80) cc_final: 0.7268 (t80) REVERT: C 244 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7156 (mt-10) REVERT: C 272 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7613 (mm-30) REVERT: G 12 LEU cc_start: 0.7959 (mt) cc_final: 0.7016 (pt) REVERT: G 113 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.7611 (t0) REVERT: G 120 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: G 129 ASP cc_start: 0.7243 (t0) cc_final: 0.7020 (t0) REVERT: G 133 THR cc_start: 0.9062 (m) cc_final: 0.8741 (t) REVERT: G 167 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8701 (ptmm) REVERT: G 169 TYR cc_start: 0.7573 (m-80) cc_final: 0.6976 (m-80) REVERT: G 198 ASP cc_start: 0.7412 (m-30) cc_final: 0.7064 (m-30) REVERT: G 214 PHE cc_start: 0.7169 (m-80) cc_final: 0.6923 (m-80) REVERT: G 221 MET cc_start: 0.6751 (tpp) cc_final: 0.6144 (tpt) REVERT: G 241 PHE cc_start: 0.8142 (t80) cc_final: 0.7901 (t80) REVERT: G 242 LYS cc_start: 0.7903 (mptt) cc_final: 0.7679 (mptt) REVERT: G 256 ASN cc_start: 0.7606 (t0) cc_final: 0.7273 (t0) REVERT: G 259 ARG cc_start: 0.5380 (ttm-80) cc_final: 0.4904 (tpp-160) REVERT: G 284 ARG cc_start: 0.7840 (ppt170) cc_final: 0.7317 (ttp-110) REVERT: G 300 LEU cc_start: 0.8074 (mt) cc_final: 0.7826 (mt) REVERT: G 307 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7838 (mmtp) REVERT: H 17 GLU cc_start: 0.6094 (tp30) cc_final: 0.5607 (mm-30) REVERT: H 29 GLU cc_start: 0.7306 (mp0) cc_final: 0.6413 (mp0) REVERT: H 35 THR cc_start: 0.6417 (p) cc_final: 0.6107 (t) REVERT: H 98 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7931 (mmmt) REVERT: H 173 ASN cc_start: 0.8998 (t0) cc_final: 0.8713 (t0) REVERT: H 224 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: H 229 MET cc_start: 0.2187 (ttm) cc_final: 0.1965 (ttt) REVERT: H 290 PHE cc_start: 0.7508 (m-10) cc_final: 0.7260 (m-10) REVERT: H 311 LEU cc_start: 0.7968 (mt) cc_final: 0.7682 (mt) REVERT: H 328 MET cc_start: 0.4843 (ptt) cc_final: 0.4522 (ptt) outliers start: 95 outliers final: 61 residues processed: 804 average time/residue: 0.1657 time to fit residues: 205.7921 Evaluate side-chains 794 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 726 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 224 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 0 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 126 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 250 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.159027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.135272 restraints weight = 55143.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.139827 restraints weight = 29320.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.142781 restraints weight = 17977.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.144788 restraints weight = 12279.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.146143 restraints weight = 9108.452| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24151 Z= 0.152 Angle : 0.704 11.873 33036 Z= 0.373 Chirality : 0.046 0.257 3667 Planarity : 0.005 0.051 3897 Dihedral : 18.049 98.863 4162 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 3.68 % Allowed : 23.33 % Favored : 72.99 % 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: -1.39 (0.16), residues: 2629 helix: -0.05 (0.18), residues: 801 sheet: -0.90 (0.26), residues: 415 loop : -1.44 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 291 TYR 0.037 0.002 TYR F 268 PHE 0.038 0.002 PHE G 243 TRP 0.075 0.002 TRP F 264 HIS 0.008 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (24151) covalent geometry : angle 0.70396 / 0.37 (33036) hydrogen bonds : bond 0.05133 / 3.44 ( 737) hydrogen bonds : angle 5.88003 / 4.08 ( 1941) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 760 time to evaluate : 0.846 Fit side-chains TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.7832 (mm) cc_final: 0.7607 (mm) REVERT: A 75 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7384 (ptpp) REVERT: A 76 GLU cc_start: 0.8658 (tp30) cc_final: 0.8427 (tp30) REVERT: A 113 GLU cc_start: 0.8125 (pm20) cc_final: 0.7841 (pm20) REVERT: A 118 MET cc_start: 0.7908 (tpt) cc_final: 0.7513 (tpt) REVERT: A 171 TYR cc_start: 0.8067 (t80) cc_final: 0.7736 (t80) REVERT: A 186 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7748 (tpp80) REVERT: A 221 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 230 LYS cc_start: 0.7668 (tptt) cc_final: 0.7110 (tptt) REVERT: A 232 TYR cc_start: 0.7746 (m-10) cc_final: 0.7200 (m-10) REVERT: A 260 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7221 (mm) REVERT: A 264 LYS cc_start: 0.6776 (ptpp) cc_final: 0.6445 (ptmm) REVERT: A 281 LYS cc_start: 0.7565 (mmmm) cc_final: 0.7338 (mmmm) REVERT: B 22 ILE cc_start: 0.7604 (mm) cc_final: 0.7378 (mm) REVERT: B 78 CYS cc_start: 0.7031 (t) cc_final: 0.6327 (t) REVERT: B 80 LEU cc_start: 0.8591 (tt) cc_final: 0.8378 (tt) REVERT: B 97 MET cc_start: 0.6943 (tpp) cc_final: 0.6687 (tpp) REVERT: B 98 ASN cc_start: 0.7974 (p0) cc_final: 0.7642 (p0) REVERT: B 192 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7979 (pt) REVERT: B 224 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7657 (mm) REVERT: I 92 PHE cc_start: 0.6888 (t80) cc_final: 0.6521 (t80) REVERT: I 165 LYS cc_start: 0.7106 (mmpt) cc_final: 0.6762 (mmtt) REVERT: D 23 ARG cc_start: 0.7776 (ptt-90) cc_final: 0.7530 (ptt90) REVERT: D 33 TRP cc_start: 0.8038 (m100) cc_final: 0.7743 (m100) REVERT: D 34 GLN cc_start: 0.7760 (pt0) cc_final: 0.7270 (pt0) REVERT: D 121 LYS cc_start: 0.7926 (mmpt) cc_final: 0.7512 (mmpt) REVERT: D 125 TYR cc_start: 0.7591 (t80) cc_final: 0.7148 (t80) REVERT: D 178 ASN cc_start: 0.8193 (t0) cc_final: 0.7930 (t0) REVERT: D 194 GLN cc_start: 0.8239 (tp40) cc_final: 0.7933 (tp40) REVERT: D 204 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7280 (mmm-85) REVERT: D 272 GLU cc_start: 0.8412 (mp0) cc_final: 0.8210 (mp0) REVERT: D 302 ASP cc_start: 0.6734 (m-30) cc_final: 0.6510 (m-30) REVERT: D 320 MET cc_start: 0.7839 (mmt) cc_final: 0.6929 (mmt) REVERT: E 25 LEU cc_start: 0.8302 (mp) cc_final: 0.8007 (mp) REVERT: E 44 LYS cc_start: 0.8564 (ptmt) cc_final: 0.8290 (ptmt) REVERT: E 124 GLU cc_start: 0.7209 (tp30) cc_final: 0.6868 (tp30) REVERT: E 191 GLU cc_start: 0.8010 (pm20) cc_final: 0.7809 (pm20) REVERT: E 194 GLN cc_start: 0.8091 (tp40) cc_final: 0.7827 (tp40) REVERT: E 255 ASN cc_start: 0.8417 (t0) cc_final: 0.8171 (t0) REVERT: E 268 TYR cc_start: 0.8043 (t80) cc_final: 0.7741 (t80) REVERT: F 34 GLN cc_start: 0.7280 (pt0) cc_final: 0.7046 (pt0) REVERT: F 85 SER cc_start: 0.7150 (p) cc_final: 0.6625 (m) REVERT: F 89 ASP cc_start: 0.7124 (p0) cc_final: 0.6696 (p0) REVERT: F 111 ASP cc_start: 0.6833 (t0) cc_final: 0.6111 (t0) REVERT: F 112 TYR cc_start: 0.7526 (t80) cc_final: 0.7083 (t80) REVERT: F 115 ARG cc_start: 0.8128 (ptp-110) cc_final: 0.7216 (ptp-110) REVERT: F 136 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7673 (ttpt) REVERT: F 204 ARG cc_start: 0.7794 (mmm160) cc_final: 0.7003 (mmm160) REVERT: F 207 LEU cc_start: 0.8586 (tp) cc_final: 0.7836 (mt) REVERT: F 213 CYS cc_start: 0.7779 (t) cc_final: 0.7261 (t) REVERT: F 229 MET cc_start: 0.6254 (ttt) cc_final: 0.5974 (ttt) REVERT: F 230 THR cc_start: 0.8336 (m) cc_final: 0.8024 (t) REVERT: F 267 ASP cc_start: 0.7769 (m-30) cc_final: 0.7498 (m-30) REVERT: F 311 LEU cc_start: 0.7784 (tp) cc_final: 0.7558 (tp) REVERT: F 328 MET cc_start: 0.4604 (ppp) cc_final: 0.2977 (ptt) REVERT: C 44 LYS cc_start: 0.7760 (pttm) cc_final: 0.7458 (pttm) REVERT: C 47 LEU cc_start: 0.7717 (mt) cc_final: 0.7197 (mt) REVERT: C 80 GLN cc_start: 0.8618 (mm-40) cc_final: 0.7297 (mt0) REVERT: C 93 ILE cc_start: 0.6879 (mm) cc_final: 0.5994 (mt) REVERT: C 120 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 141 ASN cc_start: 0.8124 (m110) cc_final: 0.7556 (m110) REVERT: C 151 ASN cc_start: 0.7123 (m-40) cc_final: 0.6776 (m-40) REVERT: C 221 MET cc_start: 0.6145 (mmm) cc_final: 0.5797 (mmm) REVERT: C 228 GLU cc_start: 0.6316 (mp0) cc_final: 0.6002 (mp0) REVERT: C 232 ASP cc_start: 0.7773 (t0) cc_final: 0.7460 (t0) REVERT: C 243 PHE cc_start: 0.8169 (t80) cc_final: 0.7231 (t80) REVERT: C 244 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7190 (mt-10) REVERT: C 272 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7607 (mm-30) REVERT: G 120 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: G 129 ASP cc_start: 0.7251 (t0) cc_final: 0.6998 (t0) REVERT: G 133 THR cc_start: 0.9055 (m) cc_final: 0.8720 (t) REVERT: G 169 TYR cc_start: 0.7503 (m-80) cc_final: 0.6827 (m-80) REVERT: G 198 ASP cc_start: 0.7422 (m-30) cc_final: 0.7092 (m-30) REVERT: G 214 PHE cc_start: 0.7224 (m-80) cc_final: 0.6976 (m-80) REVERT: G 216 LYS cc_start: 0.7962 (tptt) cc_final: 0.7700 (mptt) REVERT: G 242 LYS cc_start: 0.7860 (mptt) cc_final: 0.7634 (mptt) REVERT: G 256 ASN cc_start: 0.7543 (t0) cc_final: 0.7272 (t0) REVERT: G 259 ARG cc_start: 0.5216 (ttm-80) cc_final: 0.4788 (tpp-160) REVERT: G 284 ARG cc_start: 0.7833 (ppt170) cc_final: 0.7390 (ttp-110) REVERT: G 300 LEU cc_start: 0.8071 (mt) cc_final: 0.7708 (mt) REVERT: G 307 LYS cc_start: 0.8283 (mmtp) cc_final: 0.7811 (mmtp) REVERT: G 329 PHE cc_start: 0.8279 (m-10) cc_final: 0.7921 (m-10) REVERT: H 17 GLU cc_start: 0.6181 (tp30) cc_final: 0.5762 (mm-30) REVERT: H 29 GLU cc_start: 0.7342 (mp0) cc_final: 0.6415 (mp0) REVERT: H 35 THR cc_start: 0.6396 (p) cc_final: 0.6143 (t) REVERT: H 98 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7892 (mmmt) REVERT: H 119 TYR cc_start: 0.8459 (m-80) cc_final: 0.8239 (m-80) REVERT: H 120 GLN cc_start: 0.8205 (mt0) cc_final: 0.7817 (mt0) REVERT: H 150 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.6634 (ttp-170) REVERT: H 173 ASN cc_start: 0.9013 (t0) cc_final: 0.8687 (t0) REVERT: H 191 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8255 (mt-10) REVERT: H 198 ASP cc_start: 0.8184 (m-30) cc_final: 0.7917 (m-30) REVERT: H 224 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.6357 (m-80) REVERT: H 229 MET cc_start: 0.2167 (ttm) cc_final: 0.1908 (ttt) REVERT: H 311 LEU cc_start: 0.7958 (mt) cc_final: 0.7637 (mt) REVERT: H 328 MET cc_start: 0.4754 (ptt) cc_final: 0.4473 (ptt) outliers start: 87 outliers final: 55 residues processed: 798 average time/residue: 0.1645 time to fit residues: 202.8858 Evaluate side-chains 777 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 717 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 224 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 250 optimal weight: 0.6980 chunk 243 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 206 ASN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN I 135 ASN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.157425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.133628 restraints weight = 55270.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.138103 restraints weight = 29576.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.141049 restraints weight = 18285.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.142993 restraints weight = 12508.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.144347 restraints weight = 9356.503| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24151 Z= 0.176 Angle : 0.724 11.873 33036 Z= 0.384 Chirality : 0.047 0.275 3667 Planarity : 0.005 0.058 3897 Dihedral : 18.033 98.609 4162 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.43 % Favored : 93.53 % Rotamer: Outliers : 4.11 % Allowed : 24.72 % Favored : 71.17 % 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: -1.36 (0.16), residues: 2629 helix: -0.04 (0.18), residues: 803 sheet: -0.90 (0.26), residues: 404 loop : -1.40 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 291 TYR 0.026 0.002 TYR H 112 PHE 0.038 0.002 PHE G 243 TRP 0.046 0.002 TRP F 264 HIS 0.008 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (24151) covalent geometry : angle 0.72431 / 0.38 (33036) hydrogen bonds : bond 0.05121 / 3.45 ( 737) hydrogen bonds : angle 5.92769 / 4.12 ( 1941) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 745 time to evaluate : 0.831 Fit side-chains TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.7864 (mm) cc_final: 0.7659 (mm) REVERT: A 30 SER cc_start: 0.8860 (m) cc_final: 0.8558 (p) REVERT: A 75 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7377 (ptpp) REVERT: A 118 MET cc_start: 0.7924 (tpt) cc_final: 0.7552 (tpt) REVERT: A 163 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6570 (mm) REVERT: A 171 TYR cc_start: 0.8164 (t80) cc_final: 0.7831 (t80) REVERT: A 186 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7770 (tpp80) REVERT: A 230 LYS cc_start: 0.7675 (tptt) cc_final: 0.7080 (tptt) REVERT: A 232 TYR cc_start: 0.7696 (m-10) cc_final: 0.7110 (m-10) REVERT: A 264 LYS cc_start: 0.6842 (ptpp) cc_final: 0.6624 (ptmm) REVERT: A 281 LYS cc_start: 0.7559 (mmmm) cc_final: 0.7313 (mmmm) REVERT: A 283 GLU cc_start: 0.8217 (mp0) cc_final: 0.7807 (mp0) REVERT: B 78 CYS cc_start: 0.7087 (t) cc_final: 0.6411 (t) REVERT: B 80 LEU cc_start: 0.8631 (tt) cc_final: 0.8418 (tt) REVERT: B 98 ASN cc_start: 0.8076 (p0) cc_final: 0.7696 (p0) REVERT: B 192 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8042 (pt) REVERT: B 217 PHE cc_start: 0.5141 (m-80) cc_final: 0.4840 (m-80) REVERT: B 252 CYS cc_start: 0.6580 (p) cc_final: 0.6202 (p) REVERT: I 25 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: I 92 PHE cc_start: 0.6923 (t80) cc_final: 0.6555 (t80) REVERT: I 165 LYS cc_start: 0.7160 (mmpt) cc_final: 0.6846 (mmtt) REVERT: D 23 ARG cc_start: 0.7833 (ptt-90) cc_final: 0.7582 (ptt90) REVERT: D 33 TRP cc_start: 0.8079 (m100) cc_final: 0.7778 (m100) REVERT: D 121 LYS cc_start: 0.7974 (mmpt) cc_final: 0.7598 (mmpt) REVERT: D 125 TYR cc_start: 0.7639 (t80) cc_final: 0.7130 (t80) REVERT: D 178 ASN cc_start: 0.8260 (t0) cc_final: 0.8002 (t0) REVERT: D 194 GLN cc_start: 0.8310 (tp40) cc_final: 0.8020 (tp40) REVERT: D 204 ARG cc_start: 0.7680 (mmm160) cc_final: 0.7335 (mmm-85) REVERT: D 272 GLU cc_start: 0.8350 (mp0) cc_final: 0.7677 (mp0) REVERT: D 291 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7371 (mmt180) REVERT: D 320 MET cc_start: 0.7933 (mmt) cc_final: 0.7008 (mmt) REVERT: E 25 LEU cc_start: 0.8261 (mp) cc_final: 0.7915 (mp) REVERT: E 114 TYR cc_start: 0.7627 (t80) cc_final: 0.7214 (t80) REVERT: E 118 ILE cc_start: 0.8684 (mm) cc_final: 0.8379 (mm) REVERT: E 124 GLU cc_start: 0.7289 (tp30) cc_final: 0.7032 (tp30) REVERT: E 194 GLN cc_start: 0.8076 (tp40) cc_final: 0.7814 (tp40) REVERT: E 229 MET cc_start: 0.3728 (tpt) cc_final: 0.3383 (tpt) REVERT: E 255 ASN cc_start: 0.8431 (t0) cc_final: 0.8160 (t0) REVERT: E 268 TYR cc_start: 0.8126 (t80) cc_final: 0.7881 (t80) REVERT: F 34 GLN cc_start: 0.7325 (pt0) cc_final: 0.7058 (pt0) REVERT: F 40 ARG cc_start: 0.8465 (ptt90) cc_final: 0.8143 (ptp-170) REVERT: F 85 SER cc_start: 0.7198 (p) cc_final: 0.6660 (m) REVERT: F 89 ASP cc_start: 0.7146 (p0) cc_final: 0.6777 (p0) REVERT: F 112 TYR cc_start: 0.7569 (t80) cc_final: 0.7198 (t80) REVERT: F 136 LYS cc_start: 0.7994 (mtpt) cc_final: 0.7652 (ttpt) REVERT: F 175 LYS cc_start: 0.6944 (ptpp) cc_final: 0.6499 (ptpp) REVERT: F 204 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7071 (mmm160) REVERT: F 207 LEU cc_start: 0.8647 (tp) cc_final: 0.7899 (mt) REVERT: F 208 ASN cc_start: 0.7750 (m110) cc_final: 0.7503 (m110) REVERT: F 213 CYS cc_start: 0.7807 (t) cc_final: 0.7278 (t) REVERT: F 215 VAL cc_start: 0.7646 (t) cc_final: 0.7443 (m) REVERT: F 230 THR cc_start: 0.8316 (m) cc_final: 0.7980 (t) REVERT: F 267 ASP cc_start: 0.7857 (m-30) cc_final: 0.7578 (m-30) REVERT: F 311 LEU cc_start: 0.7769 (tp) cc_final: 0.7532 (tp) REVERT: C 31 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8351 (pttt) REVERT: C 44 LYS cc_start: 0.7797 (pttm) cc_final: 0.7454 (pttm) REVERT: C 80 GLN cc_start: 0.8625 (mm-40) cc_final: 0.7680 (mt0) REVERT: C 141 ASN cc_start: 0.8145 (m110) cc_final: 0.7598 (m110) REVERT: C 151 ASN cc_start: 0.7120 (m-40) cc_final: 0.6763 (m-40) REVERT: C 156 GLU cc_start: 0.7167 (tt0) cc_final: 0.6578 (tt0) REVERT: C 216 LYS cc_start: 0.6900 (ptmt) cc_final: 0.6233 (ptmt) REVERT: C 232 ASP cc_start: 0.7873 (t0) cc_final: 0.7524 (t0) REVERT: C 243 PHE cc_start: 0.8204 (t80) cc_final: 0.7274 (t80) REVERT: C 244 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7171 (mt-10) REVERT: C 272 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7614 (mm-30) REVERT: G 120 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: G 129 ASP cc_start: 0.7327 (t0) cc_final: 0.7002 (t0) REVERT: G 133 THR cc_start: 0.9037 (m) cc_final: 0.8723 (t) REVERT: G 198 ASP cc_start: 0.7467 (m-30) cc_final: 0.7139 (m-30) REVERT: G 214 PHE cc_start: 0.7281 (m-80) cc_final: 0.7002 (m-80) REVERT: G 216 LYS cc_start: 0.8082 (tptt) cc_final: 0.7824 (mptt) REVERT: G 221 MET cc_start: 0.6841 (tpp) cc_final: 0.6186 (tpt) REVERT: G 230 THR cc_start: 0.6677 (p) cc_final: 0.6215 (m) REVERT: G 241 PHE cc_start: 0.8057 (t80) cc_final: 0.7701 (t80) REVERT: G 256 ASN cc_start: 0.7572 (t0) cc_final: 0.7310 (t0) REVERT: G 259 ARG cc_start: 0.5209 (ttm-80) cc_final: 0.4781 (tpp-160) REVERT: G 300 LEU cc_start: 0.8049 (mt) cc_final: 0.7753 (mt) REVERT: G 307 LYS cc_start: 0.8325 (mmtp) cc_final: 0.7867 (mmtp) REVERT: G 329 PHE cc_start: 0.8384 (m-10) cc_final: 0.8171 (m-10) REVERT: H 17 GLU cc_start: 0.6212 (tp30) cc_final: 0.5829 (mm-30) REVERT: H 35 THR cc_start: 0.6505 (p) cc_final: 0.6269 (t) REVERT: H 45 LEU cc_start: 0.7064 (mt) cc_final: 0.6859 (mt) REVERT: H 98 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7983 (mmmt) REVERT: H 120 GLN cc_start: 0.8248 (mt0) cc_final: 0.7866 (mt0) REVERT: H 173 ASN cc_start: 0.9035 (t0) cc_final: 0.8722 (t0) REVERT: H 191 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8179 (mt-10) REVERT: H 200 PHE cc_start: 0.7380 (m-80) cc_final: 0.7015 (m-80) REVERT: H 229 MET cc_start: 0.2321 (ttm) cc_final: 0.2038 (ttt) REVERT: H 304 MET cc_start: 0.7642 (mmt) cc_final: 0.6964 (mmt) REVERT: H 311 LEU cc_start: 0.8003 (mt) cc_final: 0.7102 (mt) outliers start: 97 outliers final: 66 residues processed: 787 average time/residue: 0.1558 time to fit residues: 190.9593 Evaluate side-chains 786 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 716 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 224 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 194 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 141 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 250 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 233 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.158354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.134953 restraints weight = 55286.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.139288 restraints weight = 30016.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.142126 restraints weight = 18689.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.143972 restraints weight = 12890.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.145275 restraints weight = 9770.497| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24151 Z= 0.158 Angle : 0.724 10.883 33036 Z= 0.382 Chirality : 0.046 0.256 3667 Planarity : 0.005 0.059 3897 Dihedral : 17.997 98.117 4162 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 3.22 % Allowed : 25.87 % Favored : 70.91 % 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: -1.36 (0.16), residues: 2629 helix: -0.04 (0.18), residues: 800 sheet: -0.80 (0.25), residues: 411 loop : -1.44 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 291 TYR 0.029 0.002 TYR F 268 PHE 0.036 0.002 PHE G 243 TRP 0.042 0.002 TRP F 264 HIS 0.032 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (24151) covalent geometry : angle 0.72396 / 0.38 (33036) hydrogen bonds : bond 0.04957 / 3.34 ( 737) hydrogen bonds : angle 5.88841 / 4.08 ( 1941) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 730 time to evaluate : 0.798 Fit side-chains TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.7871 (mm) cc_final: 0.7667 (mm) REVERT: A 30 SER cc_start: 0.8838 (m) cc_final: 0.8546 (p) REVERT: A 75 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7361 (ptpp) REVERT: A 118 MET cc_start: 0.7905 (tpt) cc_final: 0.7548 (tpt) REVERT: A 133 LEU cc_start: 0.8893 (mt) cc_final: 0.8580 (mt) REVERT: A 170 ASN cc_start: 0.8793 (t0) cc_final: 0.8371 (t0) REVERT: A 171 TYR cc_start: 0.8190 (t80) cc_final: 0.7783 (t80) REVERT: A 186 ARG cc_start: 0.8064 (tpp80) cc_final: 0.7792 (tpp80) REVERT: A 230 LYS cc_start: 0.7634 (tptt) cc_final: 0.7387 (tptt) REVERT: A 264 LYS cc_start: 0.6908 (ptpp) cc_final: 0.6624 (ptmm) REVERT: A 281 LYS cc_start: 0.7511 (mmmm) cc_final: 0.7251 (mmmm) REVERT: A 283 GLU cc_start: 0.8205 (mp0) cc_final: 0.7827 (mp0) REVERT: B 78 CYS cc_start: 0.6938 (t) cc_final: 0.6347 (t) REVERT: B 80 LEU cc_start: 0.8608 (tt) cc_final: 0.8399 (tt) REVERT: B 98 ASN cc_start: 0.7987 (p0) cc_final: 0.7709 (p0) REVERT: B 130 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7400 (mp0) REVERT: B 192 ILE cc_start: 0.8301 (mp) cc_final: 0.8061 (pt) REVERT: B 217 PHE cc_start: 0.5033 (m-80) cc_final: 0.4736 (m-80) REVERT: B 224 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7615 (mm) REVERT: B 252 CYS cc_start: 0.6333 (p) cc_final: 0.6017 (p) REVERT: I 25 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: I 92 PHE cc_start: 0.6922 (t80) cc_final: 0.6529 (t80) REVERT: I 136 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8160 (tm-30) REVERT: I 165 LYS cc_start: 0.7205 (mmpt) cc_final: 0.6795 (mmtt) REVERT: D 33 TRP cc_start: 0.8018 (m100) cc_final: 0.7766 (m100) REVERT: D 125 TYR cc_start: 0.7622 (t80) cc_final: 0.7151 (t80) REVERT: D 178 ASN cc_start: 0.8234 (t0) cc_final: 0.7990 (t0) REVERT: D 194 GLN cc_start: 0.8284 (tp40) cc_final: 0.8037 (tp40) REVERT: D 204 ARG cc_start: 0.7602 (mmm160) cc_final: 0.7291 (mmm-85) REVERT: D 271 TYR cc_start: 0.8463 (m-80) cc_final: 0.8232 (m-80) REVERT: D 272 GLU cc_start: 0.8325 (mp0) cc_final: 0.7670 (mp0) REVERT: D 291 ARG cc_start: 0.7645 (mmt90) cc_final: 0.7266 (mmt90) REVERT: D 320 MET cc_start: 0.7862 (mmt) cc_final: 0.7041 (mmt) REVERT: E 25 LEU cc_start: 0.8227 (mp) cc_final: 0.7905 (mp) REVERT: E 44 LYS cc_start: 0.8499 (ptmt) cc_final: 0.8212 (ptmm) REVERT: E 111 ASP cc_start: 0.7042 (t0) cc_final: 0.6836 (t70) REVERT: E 114 TYR cc_start: 0.7589 (t80) cc_final: 0.7120 (t80) REVERT: E 118 ILE cc_start: 0.8668 (mm) cc_final: 0.8355 (mm) REVERT: E 124 GLU cc_start: 0.7207 (tp30) cc_final: 0.6994 (tp30) REVERT: E 194 GLN cc_start: 0.8025 (tp40) cc_final: 0.7563 (tp-100) REVERT: E 229 MET cc_start: 0.3664 (tpt) cc_final: 0.3362 (tpt) REVERT: E 255 ASN cc_start: 0.8394 (t0) cc_final: 0.8157 (t0) REVERT: E 268 TYR cc_start: 0.8035 (t80) cc_final: 0.7786 (t80) REVERT: E 291 ARG cc_start: 0.7294 (mmt90) cc_final: 0.7069 (mmt90) REVERT: F 34 GLN cc_start: 0.7299 (pt0) cc_final: 0.7078 (pt0) REVERT: F 85 SER cc_start: 0.7245 (p) cc_final: 0.6894 (m) REVERT: F 89 ASP cc_start: 0.7031 (p0) cc_final: 0.6666 (p0) REVERT: F 112 TYR cc_start: 0.7464 (t80) cc_final: 0.7042 (t80) REVERT: F 136 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7724 (ttpt) REVERT: F 162 VAL cc_start: 0.8760 (t) cc_final: 0.8533 (m) REVERT: F 204 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7089 (mmm160) REVERT: F 207 LEU cc_start: 0.8565 (tp) cc_final: 0.7867 (mt) REVERT: F 208 ASN cc_start: 0.7730 (m110) cc_final: 0.7480 (m110) REVERT: F 230 THR cc_start: 0.8257 (m) cc_final: 0.7913 (t) REVERT: F 263 THR cc_start: 0.7187 (p) cc_final: 0.6778 (t) REVERT: F 268 TYR cc_start: 0.6814 (t80) cc_final: 0.6189 (t80) REVERT: F 311 LEU cc_start: 0.7899 (tp) cc_final: 0.7689 (tp) REVERT: C 31 LYS cc_start: 0.8629 (ptmt) cc_final: 0.8290 (ptmt) REVERT: C 44 LYS cc_start: 0.7777 (pttm) cc_final: 0.7481 (pttm) REVERT: C 78 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8519 (tppt) REVERT: C 80 GLN cc_start: 0.8583 (mm-40) cc_final: 0.7769 (mt0) REVERT: C 141 ASN cc_start: 0.8117 (m110) cc_final: 0.7590 (m110) REVERT: C 151 ASN cc_start: 0.7076 (m-40) cc_final: 0.6743 (m-40) REVERT: C 153 LYS cc_start: 0.8448 (mmmm) cc_final: 0.7796 (mtpp) REVERT: C 203 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7676 (mtmt) REVERT: C 221 MET cc_start: 0.5878 (mmm) cc_final: 0.5557 (mmm) REVERT: C 232 ASP cc_start: 0.7904 (t0) cc_final: 0.7548 (t0) REVERT: C 243 PHE cc_start: 0.8152 (t80) cc_final: 0.7276 (t80) REVERT: C 244 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7128 (mt-10) REVERT: C 272 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7567 (mm-30) REVERT: C 304 MET cc_start: 0.7775 (tpt) cc_final: 0.6499 (tpt) REVERT: C 312 PRO cc_start: 0.7048 (Cg_exo) cc_final: 0.6839 (Cg_endo) REVERT: G 103 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7720 (ttpp) REVERT: G 120 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: G 129 ASP cc_start: 0.7287 (t0) cc_final: 0.7019 (t0) REVERT: G 133 THR cc_start: 0.8994 (m) cc_final: 0.8688 (t) REVERT: G 198 ASP cc_start: 0.7372 (m-30) cc_final: 0.7059 (m-30) REVERT: G 214 PHE cc_start: 0.7256 (m-80) cc_final: 0.6992 (m-80) REVERT: G 216 LYS cc_start: 0.8013 (tptt) cc_final: 0.7799 (mptt) REVERT: G 221 MET cc_start: 0.6824 (tpp) cc_final: 0.6175 (tpt) REVERT: G 230 THR cc_start: 0.6690 (p) cc_final: 0.6209 (m) REVERT: G 256 ASN cc_start: 0.7488 (t0) cc_final: 0.7285 (t0) REVERT: G 259 ARG cc_start: 0.5172 (ttm-80) cc_final: 0.4866 (tpp-160) REVERT: G 264 TRP cc_start: 0.7442 (m-90) cc_final: 0.7168 (m-90) REVERT: G 284 ARG cc_start: 0.6766 (mtm-85) cc_final: 0.6564 (mtt180) REVERT: G 300 LEU cc_start: 0.8046 (mt) cc_final: 0.7736 (mt) REVERT: G 307 LYS cc_start: 0.8304 (mmtp) cc_final: 0.7849 (mmtp) REVERT: G 329 PHE cc_start: 0.8377 (m-10) cc_final: 0.8162 (m-10) REVERT: H 17 GLU cc_start: 0.6058 (tp30) cc_final: 0.5757 (mm-30) REVERT: H 35 THR cc_start: 0.6472 (p) cc_final: 0.6240 (t) REVERT: H 150 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7284 (ttt180) REVERT: H 173 ASN cc_start: 0.8958 (t0) cc_final: 0.8647 (t0) REVERT: H 191 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8118 (mt-10) REVERT: H 229 MET cc_start: 0.2386 (ttm) cc_final: 0.2107 (ttt) REVERT: H 304 MET cc_start: 0.7596 (mmt) cc_final: 0.6891 (mmt) REVERT: H 311 LEU cc_start: 0.8006 (mt) cc_final: 0.7111 (mt) outliers start: 76 outliers final: 61 residues processed: 762 average time/residue: 0.1616 time to fit residues: 190.7686 Evaluate side-chains 780 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 716 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 224 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 148 optimal weight: 0.4980 chunk 93 optimal weight: 0.0270 chunk 198 optimal weight: 0.0060 chunk 5 optimal weight: 0.0170 chunk 7 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 261 optimal weight: 0.0010 chunk 38 optimal weight: 4.9990 overall best weight: 0.1098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 304 HIS I 135 ASN I 166 HIS ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.158623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.135080 restraints weight = 55406.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.139460 restraints weight = 29745.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.142343 restraints weight = 18430.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.144237 restraints weight = 12661.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.145545 restraints weight = 9557.501| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24151 Z= 0.150 Angle : 0.737 16.987 33036 Z= 0.386 Chirality : 0.046 0.251 3667 Planarity : 0.005 0.065 3897 Dihedral : 17.914 96.070 4162 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 2.79 % Allowed : 27.39 % Favored : 69.81 % 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: -1.36 (0.16), residues: 2629 helix: -0.02 (0.18), residues: 801 sheet: -0.77 (0.26), residues: 396 loop : -1.46 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 15 TYR 0.052 0.002 TYR H 119 PHE 0.032 0.002 PHE G 243 TRP 0.040 0.002 TRP F 264 HIS 0.006 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (24151) covalent geometry : angle 0.73716 / 0.39 (33036) hydrogen bonds : bond 0.04802 / 3.22 ( 737) hydrogen bonds : angle 5.79039 / 4.00 ( 1941) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 728 time to evaluate : 0.809 Fit side-chains TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 24 ILE cc_start: 0.7896 (mm) cc_final: 0.7678 (mm) REVERT: A 75 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7385 (ptpp) REVERT: A 95 MET cc_start: 0.3402 (tmm) cc_final: 0.3148 (tmm) REVERT: A 118 MET cc_start: 0.7935 (tpt) cc_final: 0.7599 (tpt) REVERT: A 133 LEU cc_start: 0.8755 (mt) cc_final: 0.8372 (mt) REVERT: A 170 ASN cc_start: 0.8784 (t0) cc_final: 0.8485 (t0) REVERT: A 171 TYR cc_start: 0.8242 (t80) cc_final: 0.7802 (t80) REVERT: A 186 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7583 (tpp80) REVERT: A 230 LYS cc_start: 0.7601 (tptt) cc_final: 0.6993 (tptt) REVERT: A 232 TYR cc_start: 0.7665 (m-10) cc_final: 0.7003 (m-10) REVERT: A 264 LYS cc_start: 0.6972 (ptpp) cc_final: 0.6691 (ptmm) REVERT: A 281 LYS cc_start: 0.7443 (mmmm) cc_final: 0.7171 (mmmm) REVERT: A 283 GLU cc_start: 0.8178 (mp0) cc_final: 0.7817 (mp0) REVERT: B 78 CYS cc_start: 0.6932 (t) cc_final: 0.6302 (t) REVERT: B 98 ASN cc_start: 0.7850 (p0) cc_final: 0.7449 (p0) REVERT: B 134 ILE cc_start: 0.7790 (mm) cc_final: 0.7578 (tp) REVERT: B 192 ILE cc_start: 0.8291 (mp) cc_final: 0.8078 (pt) REVERT: B 224 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7510 (mm) REVERT: B 252 CYS cc_start: 0.6515 (p) cc_final: 0.6147 (p) REVERT: I 9 LYS cc_start: 0.8359 (mttt) cc_final: 0.8020 (mtmt) REVERT: I 25 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: I 92 PHE cc_start: 0.6930 (t80) cc_final: 0.6585 (t80) REVERT: I 135 ASN cc_start: 0.6040 (m110) cc_final: 0.5725 (m-40) REVERT: I 136 GLN cc_start: 0.8281 (tm-30) cc_final: 0.8036 (tm-30) REVERT: I 165 LYS cc_start: 0.7233 (mmpt) cc_final: 0.6825 (mmtt) REVERT: D 33 TRP cc_start: 0.7918 (m100) cc_final: 0.7707 (m100) REVERT: D 36 ASP cc_start: 0.7185 (t0) cc_final: 0.6073 (m-30) REVERT: D 125 TYR cc_start: 0.7610 (t80) cc_final: 0.7318 (t80) REVERT: D 272 GLU cc_start: 0.8230 (mp0) cc_final: 0.7661 (mp0) REVERT: D 320 MET cc_start: 0.7967 (mmt) cc_final: 0.7240 (mmt) REVERT: E 43 PHE cc_start: 0.7463 (t80) cc_final: 0.7235 (t80) REVERT: E 44 LYS cc_start: 0.8432 (ptmt) cc_final: 0.7920 (ptpp) REVERT: E 48 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7689 (mp) REVERT: E 114 TYR cc_start: 0.7550 (t80) cc_final: 0.7248 (t80) REVERT: E 118 ILE cc_start: 0.8643 (mm) cc_final: 0.8415 (mm) REVERT: E 194 GLN cc_start: 0.8003 (tp40) cc_final: 0.7508 (tp-100) REVERT: E 195 GLN cc_start: 0.8966 (mt0) cc_final: 0.8196 (tt0) REVERT: E 229 MET cc_start: 0.3582 (tpt) cc_final: 0.3350 (tpt) REVERT: E 255 ASN cc_start: 0.8322 (t0) cc_final: 0.8112 (t0) REVERT: E 268 TYR cc_start: 0.7920 (t80) cc_final: 0.7637 (t80) REVERT: F 34 GLN cc_start: 0.7194 (pt0) cc_final: 0.6956 (pt0) REVERT: F 85 SER cc_start: 0.7164 (p) cc_final: 0.6408 (m) REVERT: F 89 ASP cc_start: 0.6960 (p0) cc_final: 0.6549 (p0) REVERT: F 92 ARG cc_start: 0.6180 (mtp180) cc_final: 0.3100 (mtp-110) REVERT: F 204 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7089 (mmm160) REVERT: F 207 LEU cc_start: 0.8478 (tp) cc_final: 0.7781 (mt) REVERT: F 208 ASN cc_start: 0.7712 (m110) cc_final: 0.7495 (m-40) REVERT: F 230 THR cc_start: 0.8243 (m) cc_final: 0.7924 (t) REVERT: F 311 LEU cc_start: 0.7956 (tp) cc_final: 0.7735 (tp) REVERT: F 328 MET cc_start: 0.4477 (ppp) cc_final: 0.2985 (ptt) REVERT: C 31 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8252 (ptmt) REVERT: C 44 LYS cc_start: 0.7730 (pttm) cc_final: 0.7386 (pttm) REVERT: C 78 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8815 (mmtt) REVERT: C 80 GLN cc_start: 0.8546 (mm-40) cc_final: 0.7792 (mt0) REVERT: C 141 ASN cc_start: 0.8142 (m110) cc_final: 0.7616 (m110) REVERT: C 153 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7917 (ttmt) REVERT: C 221 MET cc_start: 0.5577 (mmm) cc_final: 0.5251 (mmm) REVERT: C 232 ASP cc_start: 0.7883 (t0) cc_final: 0.7521 (t0) REVERT: C 243 PHE cc_start: 0.8076 (t80) cc_final: 0.7097 (t80) REVERT: C 244 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6752 (mt-10) REVERT: C 272 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7532 (mm-30) REVERT: C 312 PRO cc_start: 0.6977 (Cg_exo) cc_final: 0.6741 (Cg_endo) REVERT: G 103 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7713 (ttpp) REVERT: G 120 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: G 121 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8135 (mmtp) REVERT: G 129 ASP cc_start: 0.7294 (t0) cc_final: 0.6980 (t0) REVERT: G 133 THR cc_start: 0.8989 (m) cc_final: 0.8662 (t) REVERT: G 198 ASP cc_start: 0.7375 (m-30) cc_final: 0.7073 (m-30) REVERT: G 214 PHE cc_start: 0.7272 (m-80) cc_final: 0.6983 (m-80) REVERT: G 221 MET cc_start: 0.6736 (tpp) cc_final: 0.6087 (tpt) REVERT: G 230 THR cc_start: 0.6676 (p) cc_final: 0.6203 (m) REVERT: G 256 ASN cc_start: 0.7389 (t0) cc_final: 0.7182 (t0) REVERT: G 259 ARG cc_start: 0.5037 (ttm-80) cc_final: 0.4648 (tpp-160) REVERT: G 300 LEU cc_start: 0.8020 (mt) cc_final: 0.7706 (mt) REVERT: G 307 LYS cc_start: 0.8315 (mmtp) cc_final: 0.7862 (mmtp) REVERT: G 329 PHE cc_start: 0.8345 (m-10) cc_final: 0.8139 (m-10) REVERT: H 17 GLU cc_start: 0.6061 (tp30) cc_final: 0.5768 (mm-30) REVERT: H 120 GLN cc_start: 0.8202 (mt0) cc_final: 0.7848 (mt0) REVERT: H 173 ASN cc_start: 0.8873 (t0) cc_final: 0.8506 (t0) REVERT: H 191 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8056 (mt-10) REVERT: H 205 GLU cc_start: 0.7572 (tp30) cc_final: 0.7351 (tp30) REVERT: H 224 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: H 249 MET cc_start: 0.7164 (mtp) cc_final: 0.6837 (mtp) REVERT: H 291 ARG cc_start: 0.7459 (mtt-85) cc_final: 0.6943 (mtt-85) REVERT: H 304 MET cc_start: 0.7535 (mmt) cc_final: 0.6942 (mmt) REVERT: H 311 LEU cc_start: 0.7973 (mt) cc_final: 0.7025 (mt) REVERT: H 316 LYS cc_start: 0.8961 (tptm) cc_final: 0.8456 (tppt) outliers start: 66 outliers final: 49 residues processed: 756 average time/residue: 0.1623 time to fit residues: 190.6858 Evaluate side-chains 755 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 701 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 189 optimal weight: 0.6980 chunk 203 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 235 optimal weight: 0.0670 chunk 226 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 256 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 159 HIS A 304 HIS B 204 HIS I 166 HIS D 140 ASN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** 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 = 0.4327 r_free = 0.4327 target = 0.160002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.136745 restraints weight = 50511.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.141196 restraints weight = 26912.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.144073 restraints weight = 16400.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.145983 restraints weight = 11077.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.147260 restraints weight = 8178.784| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24151 Z= 0.156 Angle : 0.746 12.487 33036 Z= 0.391 Chirality : 0.046 0.351 3667 Planarity : 0.005 0.066 3897 Dihedral : 17.886 96.210 4162 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 2.67 % Allowed : 28.03 % Favored : 69.31 % 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: -1.36 (0.16), residues: 2629 helix: -0.06 (0.18), residues: 807 sheet: -0.71 (0.26), residues: 396 loop : -1.46 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 129 TYR 0.057 0.002 TYR H 119 PHE 0.036 0.002 PHE D 290 TRP 0.095 0.002 TRP F 264 HIS 0.008 0.001 HIS F 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (24151) covalent geometry : angle 0.74629 / 0.39 (33036) hydrogen bonds : bond 0.04761 / 3.20 ( 737) hydrogen bonds : angle 5.81521 / 4.00 ( 1941) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 711 time to evaluate : 0.812 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN A 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 24 ILE cc_start: 0.7867 (mm) cc_final: 0.7654 (mm) REVERT: A 118 MET cc_start: 0.7966 (tpt) cc_final: 0.7646 (tpt) REVERT: A 133 LEU cc_start: 0.8811 (mt) cc_final: 0.8451 (mt) REVERT: A 171 TYR cc_start: 0.8241 (t80) cc_final: 0.7886 (t80) REVERT: A 186 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7761 (tpp80) REVERT: A 205 LYS cc_start: 0.7084 (mmpt) cc_final: 0.6148 (mmtt) REVERT: A 230 LYS cc_start: 0.7612 (tptt) cc_final: 0.7295 (tptt) REVERT: A 232 TYR cc_start: 0.7615 (m-10) cc_final: 0.7317 (m-10) REVERT: A 264 LYS cc_start: 0.7046 (ptpp) cc_final: 0.6788 (ptmm) REVERT: A 281 LYS cc_start: 0.7418 (mmmm) cc_final: 0.7117 (mmmm) REVERT: A 283 GLU cc_start: 0.8161 (mp0) cc_final: 0.7751 (mp0) REVERT: B 78 CYS cc_start: 0.6960 (t) cc_final: 0.6367 (t) REVERT: B 98 ASN cc_start: 0.7871 (p0) cc_final: 0.7446 (p0) REVERT: B 192 ILE cc_start: 0.8315 (mp) cc_final: 0.8077 (pt) REVERT: B 224 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7460 (mm) REVERT: B 252 CYS cc_start: 0.6378 (p) cc_final: 0.6035 (p) REVERT: I 92 PHE cc_start: 0.6947 (t80) cc_final: 0.6602 (t80) REVERT: I 135 ASN cc_start: 0.5915 (m110) cc_final: 0.5710 (m-40) REVERT: I 136 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8059 (tm-30) REVERT: I 165 LYS cc_start: 0.7254 (mmpt) cc_final: 0.6857 (mmtt) REVERT: D 28 THR cc_start: 0.7467 (m) cc_final: 0.6086 (p) REVERT: D 36 ASP cc_start: 0.7317 (t0) cc_final: 0.6465 (m-30) REVERT: D 125 TYR cc_start: 0.7640 (t80) cc_final: 0.7345 (t80) REVERT: D 272 GLU cc_start: 0.8156 (mp0) cc_final: 0.7594 (mp0) REVERT: D 320 MET cc_start: 0.7924 (mmt) cc_final: 0.7007 (mmt) REVERT: E 44 LYS cc_start: 0.8503 (ptmt) cc_final: 0.8232 (ptmm) REVERT: E 114 TYR cc_start: 0.7579 (t80) cc_final: 0.7279 (t80) REVERT: E 118 ILE cc_start: 0.8649 (mm) cc_final: 0.8425 (mm) REVERT: E 194 GLN cc_start: 0.8009 (tp40) cc_final: 0.7521 (tp-100) REVERT: E 195 GLN cc_start: 0.8979 (mt0) cc_final: 0.8223 (tt0) REVERT: E 229 MET cc_start: 0.3558 (tpt) cc_final: 0.3321 (tpt) REVERT: E 268 TYR cc_start: 0.7913 (t80) cc_final: 0.7672 (t80) REVERT: E 291 ARG cc_start: 0.7201 (mmt90) cc_final: 0.6965 (mmt90) REVERT: F 39 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7750 (mtpp) REVERT: F 85 SER cc_start: 0.7139 (p) cc_final: 0.6879 (m) REVERT: F 89 ASP cc_start: 0.6884 (p0) cc_final: 0.6498 (p0) REVERT: F 92 ARG cc_start: 0.6373 (mtp180) cc_final: 0.3274 (mtp-110) REVERT: F 200 PHE cc_start: 0.8236 (m-10) cc_final: 0.7950 (m-80) REVERT: F 204 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7128 (mmm160) REVERT: F 207 LEU cc_start: 0.8531 (tp) cc_final: 0.7819 (mt) REVERT: F 208 ASN cc_start: 0.7718 (m110) cc_final: 0.7442 (m110) REVERT: F 230 THR cc_start: 0.8289 (m) cc_final: 0.7958 (t) REVERT: F 311 LEU cc_start: 0.8007 (tp) cc_final: 0.7786 (tp) REVERT: C 31 LYS cc_start: 0.8597 (ptmt) cc_final: 0.8172 (ptmt) REVERT: C 44 LYS cc_start: 0.7772 (pttm) cc_final: 0.7390 (pttm) REVERT: C 80 GLN cc_start: 0.8506 (mm-40) cc_final: 0.7817 (mt0) REVERT: C 141 ASN cc_start: 0.8124 (m110) cc_final: 0.7640 (m110) REVERT: C 153 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8053 (ttmt) REVERT: C 221 MET cc_start: 0.5679 (mmm) cc_final: 0.5291 (mmm) REVERT: C 232 ASP cc_start: 0.7907 (t0) cc_final: 0.7541 (t0) REVERT: C 243 PHE cc_start: 0.8034 (t80) cc_final: 0.7358 (t80) REVERT: C 244 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6924 (mt-10) REVERT: C 272 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7580 (mm-30) REVERT: C 312 PRO cc_start: 0.7087 (Cg_exo) cc_final: 0.6855 (Cg_endo) REVERT: G 103 LYS cc_start: 0.7894 (ttpp) cc_final: 0.7636 (ttpp) REVERT: G 120 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: G 121 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8134 (mmtp) REVERT: G 129 ASP cc_start: 0.7327 (t0) cc_final: 0.7057 (t0) REVERT: G 133 THR cc_start: 0.8969 (m) cc_final: 0.8675 (t) REVERT: G 198 ASP cc_start: 0.7366 (m-30) cc_final: 0.7072 (m-30) REVERT: G 214 PHE cc_start: 0.7260 (m-80) cc_final: 0.7014 (m-80) REVERT: G 221 MET cc_start: 0.6822 (tpp) cc_final: 0.6210 (tpt) REVERT: G 230 THR cc_start: 0.6647 (p) cc_final: 0.6110 (m) REVERT: G 259 ARG cc_start: 0.5141 (ttm-80) cc_final: 0.4861 (tpp-160) REVERT: G 264 TRP cc_start: 0.7573 (m-90) cc_final: 0.7253 (m-90) REVERT: G 300 LEU cc_start: 0.7999 (mt) cc_final: 0.7744 (mt) REVERT: G 307 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7845 (mmtp) REVERT: H 17 GLU cc_start: 0.5902 (tp30) cc_final: 0.5691 (mm-30) REVERT: H 23 ARG cc_start: 0.8115 (ptp90) cc_final: 0.7810 (ptp-170) REVERT: H 98 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7599 (ttmm) REVERT: H 173 ASN cc_start: 0.8844 (t0) cc_final: 0.8488 (t0) REVERT: H 200 PHE cc_start: 0.7279 (m-80) cc_final: 0.7011 (m-80) REVERT: H 205 GLU cc_start: 0.7621 (tp30) cc_final: 0.7311 (tp30) REVERT: H 224 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: H 249 MET cc_start: 0.7132 (mtp) cc_final: 0.6752 (mtp) REVERT: H 304 MET cc_start: 0.7437 (mmt) cc_final: 0.6688 (mmt) REVERT: H 311 LEU cc_start: 0.8021 (mt) cc_final: 0.7036 (mt) REVERT: H 316 LYS cc_start: 0.8965 (tptm) cc_final: 0.8490 (tppt) outliers start: 63 outliers final: 48 residues processed: 742 average time/residue: 0.1624 time to fit residues: 186.2466 Evaluate side-chains 751 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 700 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 224 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 43 optimal weight: 0.8980 chunk 251 optimal weight: 0.4980 chunk 263 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 123 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 159 HIS A 304 HIS B 204 HIS I 166 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** 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 = 0.4334 r_free = 0.4334 target = 0.160462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.137224 restraints weight = 50151.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.141721 restraints weight = 26747.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.144590 restraints weight = 16268.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.146511 restraints weight = 10989.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.147766 restraints weight = 8111.350| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 24151 Z= 0.160 Angle : 0.760 12.589 33036 Z= 0.397 Chirality : 0.046 0.381 3667 Planarity : 0.005 0.083 3897 Dihedral : 17.875 95.772 4162 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 2.37 % Allowed : 28.20 % Favored : 69.43 % 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: -1.35 (0.16), residues: 2629 helix: -0.05 (0.18), residues: 802 sheet: -0.71 (0.26), residues: 389 loop : -1.45 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 129 TYR 0.056 0.002 TYR H 119 PHE 0.076 0.002 PHE D 290 TRP 0.074 0.003 TRP F 264 HIS 0.029 0.002 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (24151) covalent geometry : angle 0.75968 / 0.40 (33036) hydrogen bonds : bond 0.04821 / 3.24 ( 737) hydrogen bonds : angle 5.79277 / 3.99 ( 1941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5278.00 seconds wall clock time: 92 minutes 10.64 seconds (5530.64 seconds total)