Starting phenix.real_space_refine on Thu Mar 5 17:27:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjl_54946/03_2026/9sjl_54946.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjl_54946/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/9sjl_54946/03_2026/9sjl_54946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjl_54946/03_2026/9sjl_54946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sjl_54946/03_2026/9sjl_54946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjl_54946/03_2026/9sjl_54946.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.28, per 1000 atoms: 0.23 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: 1.93 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: 3.04 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: 4.09 Time building geometry restraints manager: 2.57 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=" 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=" N ARG A 142 " pdb=" CA ARG A 142 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.92e+00 bond pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.27e-02 6.20e+03 7.84e+00 bond pdb=" C LYS C 167 " pdb=" N GLU C 168 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.36e-02 5.41e+03 7.37e+00 ... (remaining 24146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 32235 2.11 - 4.22: 712 4.22 - 6.33: 71 6.33 - 8.43: 16 8.43 - 10.54: 2 Bond angle restraints: 33036 Sorted by residual: 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=" O3' U J 44 " pdb=" C3' U J 44 " pdb=" C2' U J 44 " ideal model delta sigma weight residual 109.50 116.17 -6.67 1.50e+00 4.44e-01 1.98e+01 angle pdb=" C TYR D 265 " pdb=" CA TYR D 265 " pdb=" CB TYR D 265 " ideal model delta sigma weight residual 109.42 116.10 -6.68 1.57e+00 4.06e-01 1.81e+01 angle pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" O THR A 69 " ideal model delta sigma weight residual 120.90 116.54 4.36 1.07e+00 8.73e-01 1.66e+01 angle pdb=" N ILE G 261 " pdb=" CA ILE G 261 " pdb=" C ILE G 261 " ideal model delta sigma weight residual 113.20 109.35 3.85 9.60e-01 1.09e+00 1.61e+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 - 0.100: 3528 0.100 - 0.200: 131 0.200 - 0.300: 4 0.300 - 0.400: 1 0.400 - 0.500: 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 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.24e+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: 4.770 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.500 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 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= 0.207 Angle : 0.743 10.542 33036 Z= 0.435 Chirality : 0.045 0.500 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 covalent geometry : bond 0.00399 (24151) covalent geometry : angle 0.74297 (33036) hydrogen bonds : bond 0.26679 ( 737) hydrogen bonds : angle 8.59645 ( 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 : 0.818 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: A 24 ILE cc_start: 0.8193 (mm) cc_final: 0.7992 (mm) REVERT: A 42 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8478 (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: 0.3495 (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: 0.6129 (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: 0.5631 (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: 0.6241 (m90) REVERT: B 22 ILE cc_start: 0.8098 (mm) cc_final: 0.7686 (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: 0.6806 (mtp) REVERT: B 179 MET cc_start: 0.7923 (mmm) cc_final: 0.7092 (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: 0.8183 (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: -0.3071 (ttm) REVERT: D 12 LEU cc_start: 0.7936 (tt) cc_final: 0.7593 (tt) REVERT: D 35 THR cc_start: 0.8067 (t) cc_final: 0.7820 (t) REVERT: D 45 LEU cc_start: 0.8491 (mt) cc_final: 0.8027 (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: 0.8005 (m-80) REVERT: D 178 ASN cc_start: 0.7627 (t0) cc_final: 0.7332 (t0) REVERT: D 204 ARG cc_start: 0.7548 (mmm160) cc_final: 0.7006 (mmm-85) REVERT: D 300 LEU cc_start: 0.7972 (mt) cc_final: 0.7691 (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: 0.7370 (mtmt) REVERT: E 134 LEU cc_start: 0.8524 (mm) cc_final: 0.8321 (mt) REVERT: E 194 GLN cc_start: 0.8173 (tp40) cc_final: 0.7910 (tp40) REVERT: E 206 TYR cc_start: 0.7084 (p90) cc_final: 0.6818 (p90) REVERT: E 229 MET cc_start: 0.4517 (tpt) cc_final: 0.3921 (tpt) REVERT: E 260 THR cc_start: 0.8146 (m) cc_final: 0.7689 (p) REVERT: E 291 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7591 (mmt90) REVERT: E 299 LYS cc_start: 0.8578 (mttt) cc_final: 0.8141 (mtmt) REVERT: E 332 LYS cc_start: 0.7175 (ttpt) cc_final: 0.6923 (mtpp) 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: 0.6808 (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: 0.7084 (p90) REVERT: F 207 LEU cc_start: 0.8385 (tp) cc_final: 0.7667 (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: 0.7506 (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: 0.7154 (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: 0.6880 (mt) REVERT: C 165 GLU cc_start: 0.8785 (pt0) cc_final: 0.8409 (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: 0.7053 (pm20) REVERT: C 198 ASP cc_start: 0.6811 (m-30) cc_final: 0.6601 (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: 0.6253 (tttt) REVERT: C 232 ASP cc_start: 0.7544 (t0) cc_final: 0.7324 (t0) REVERT: C 264 TRP cc_start: 0.7474 (m-90) cc_final: 0.7131 (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 23 ARG cc_start: 0.6887 (ttm110) cc_final: 0.6476 (ptp-110) REVERT: G 51 ASP cc_start: 0.6327 (m-30) cc_final: 0.6121 (m-30) REVERT: G 80 GLN cc_start: 0.7459 (mt0) cc_final: 0.7227 (mt0) REVERT: G 82 CYS cc_start: 0.7891 (t) cc_final: 0.7627 (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: 0.7053 (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: 0.8318 (mp) REVERT: G 167 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8586 (ptmm) REVERT: G 180 ASP cc_start: 0.8897 (m-30) cc_final: 0.8675 (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: 0.7461 (tm-30) REVERT: G 195 GLN cc_start: 0.8189 (mp-120) cc_final: 0.7451 (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: 0.8121 (mp) REVERT: G 224 TYR cc_start: 0.8588 (m-80) cc_final: 0.8239 (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: 0.7567 (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: 0.7971 (mm) REVERT: G 329 PHE cc_start: 0.8349 (m-80) cc_final: 0.8094 (m-80) REVERT: H 29 GLU cc_start: 0.7165 (mp0) cc_final: 0.6295 (mp0) REVERT: H 98 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7261 (ttmm) REVERT: H 141 ASN cc_start: 0.8432 (m110) cc_final: 0.8226 (m110) REVERT: H 164 ILE cc_start: 0.7974 (mp) cc_final: 0.7451 (mp) REVERT: H 168 GLU cc_start: 0.7333 (pp20) cc_final: 0.7101 (tm-30) REVERT: H 173 ASN cc_start: 0.9058 (t0) cc_final: 0.8643 (t0) REVERT: H 186 ASN cc_start: 0.7946 (t0) cc_final: 0.7278 (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: 0.5815 (m-40) REVERT: H 265 TYR cc_start: 0.5979 (p90) cc_final: 0.5215 (p90) REVERT: H 273 PHE cc_start: 0.6740 (p90) cc_final: 0.6323 (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: 0.7434 (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: 0.1745 time to fit residues: 252.2435 Evaluate side-chains 771 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 767 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 166 ASN ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN E 140 ASN E 255 ASN F 120 GLN ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 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 195 GLN H 255 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.165656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.140919 restraints weight = 54640.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.145448 restraints weight = 28769.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.148513 restraints weight = 17712.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.150546 restraints weight = 12116.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.151903 restraints weight = 9050.524| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24151 Z= 0.196 Angle : 0.724 13.254 33036 Z= 0.385 Chirality : 0.046 0.346 3667 Planarity : 0.006 0.052 3897 Dihedral : 18.237 101.557 4171 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 2.67 % Allowed : 13.46 % Favored : 83.87 % 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: -1.32 (0.16), residues: 2629 helix: 0.15 (0.18), residues: 806 sheet: -0.93 (0.25), residues: 439 loop : -1.49 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 41 TYR 0.029 0.002 TYR H 119 PHE 0.039 0.002 PHE H 200 TRP 0.033 0.002 TRP F 264 HIS 0.009 0.002 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00440 (24151) covalent geometry : angle 0.72364 (33036) hydrogen bonds : bond 0.05960 ( 737) hydrogen bonds : angle 6.43047 ( 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 899 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 836 time to evaluate : 0.847 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: 0.7872 (mm) cc_final: 0.7638 (mm) REVERT: A 61 ASP cc_start: 0.6920 (m-30) cc_final: 0.6487 (m-30) REVERT: A 69 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8019 (p) REVERT: A 118 MET cc_start: 0.8013 (tpt) cc_final: 0.7455 (tpt) REVERT: A 124 LYS cc_start: 0.7053 (ttpp) cc_final: 0.6648 (tttm) REVERT: A 175 ASP cc_start: 0.8563 (t0) cc_final: 0.8348 (t0) REVERT: A 181 LYS cc_start: 0.7553 (mmtt) cc_final: 0.7199 (mmtt) REVERT: A 186 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7266 (tpp80) REVERT: A 217 PRO cc_start: 0.5920 (Cg_exo) cc_final: 0.5252 (Cg_endo) REVERT: A 220 LEU cc_start: 0.7774 (mt) cc_final: 0.7541 (mt) REVERT: A 230 LYS cc_start: 0.7662 (tptt) cc_final: 0.7298 (tptt) REVERT: A 232 TYR cc_start: 0.7763 (m-10) cc_final: 0.7211 (m-80) REVERT: A 259 ILE cc_start: 0.6226 (OUTLIER) cc_final: 0.6018 (mp) REVERT: B 80 LEU cc_start: 0.8535 (tt) cc_final: 0.8263 (tt) REVERT: B 95 HIS cc_start: 0.7860 (p-80) cc_final: 0.7592 (p90) REVERT: B 97 MET cc_start: 0.7245 (tpp) cc_final: 0.6414 (tpp) REVERT: B 98 ASN cc_start: 0.8067 (p0) cc_final: 0.7139 (p0) REVERT: B 130 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7586 (mm-30) REVERT: B 146 ARG cc_start: 0.7059 (tpm170) cc_final: 0.6670 (tpm170) REVERT: B 175 MET cc_start: 0.6858 (mtp) cc_final: 0.6079 (mtp) REVERT: B 179 MET cc_start: 0.7753 (mmm) cc_final: 0.6916 (mmm) REVERT: B 192 ILE cc_start: 0.8153 (mp) cc_final: 0.7928 (pt) REVERT: I 92 PHE cc_start: 0.6794 (t80) cc_final: 0.6433 (t80) REVERT: I 165 LYS cc_start: 0.6884 (mmpt) cc_final: 0.6552 (mmtt) REVERT: D 45 LEU cc_start: 0.8520 (mt) cc_final: 0.8068 (mt) REVERT: D 121 LYS cc_start: 0.7967 (mmpt) cc_final: 0.7601 (mmpt) REVERT: D 125 TYR cc_start: 0.7413 (t80) cc_final: 0.6998 (t80) REVERT: D 194 GLN cc_start: 0.8044 (tp40) cc_final: 0.7700 (tp40) REVERT: D 204 ARG cc_start: 0.7647 (mmm160) cc_final: 0.7104 (mmm-85) REVERT: D 273 PHE cc_start: 0.7741 (p90) cc_final: 0.7289 (p90) REVERT: E 21 PHE cc_start: 0.7654 (m-80) cc_final: 0.7373 (m-80) REVERT: E 43 PHE cc_start: 0.7594 (t80) cc_final: 0.7342 (t80) REVERT: E 44 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8024 (ptmt) REVERT: E 85 SER cc_start: 0.7870 (t) cc_final: 0.7540 (m) REVERT: E 86 THR cc_start: 0.7841 (p) cc_final: 0.7410 (p) REVERT: E 134 LEU cc_start: 0.8400 (mm) cc_final: 0.8146 (mp) REVERT: E 138 TYR cc_start: 0.8077 (m-80) cc_final: 0.7771 (m-80) REVERT: E 194 GLN cc_start: 0.8274 (tp40) cc_final: 0.7937 (tp40) REVERT: E 221 MET cc_start: 0.5479 (tpp) cc_final: 0.5112 (tpp) REVERT: E 260 THR cc_start: 0.7936 (m) cc_final: 0.7654 (p) REVERT: E 268 TYR cc_start: 0.8129 (t80) cc_final: 0.7834 (t80) REVERT: E 291 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7269 (mmt90) REVERT: E 306 LEU cc_start: 0.7142 (mt) cc_final: 0.6472 (mp) REVERT: F 85 SER cc_start: 0.6909 (p) cc_final: 0.6539 (m) REVERT: F 111 ASP cc_start: 0.6855 (t0) cc_final: 0.6466 (t0) REVERT: F 112 TYR cc_start: 0.7599 (t80) cc_final: 0.7294 (t80) REVERT: F 115 ARG cc_start: 0.8217 (ptp-110) cc_final: 0.7094 (ptp-110) REVERT: F 204 ARG cc_start: 0.7847 (mmm160) cc_final: 0.6961 (mmm160) REVERT: F 207 LEU cc_start: 0.8612 (tp) cc_final: 0.7855 (mt) REVERT: F 229 MET cc_start: 0.5993 (ttt) cc_final: 0.5655 (ttt) REVERT: F 230 THR cc_start: 0.8422 (m) cc_final: 0.8167 (t) REVERT: F 263 THR cc_start: 0.7420 (p) cc_final: 0.7062 (t) REVERT: C 34 GLN cc_start: 0.6765 (pt0) cc_final: 0.6481 (pt0) REVERT: C 93 ILE cc_start: 0.7016 (mm) cc_final: 0.5963 (mt) REVERT: C 120 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 136 LYS cc_start: 0.7856 (pptt) cc_final: 0.7541 (pptt) REVERT: C 141 ASN cc_start: 0.8333 (m110) cc_final: 0.7779 (m110) REVERT: C 153 LYS cc_start: 0.7704 (mptt) cc_final: 0.7339 (mptt) REVERT: C 170 PRO cc_start: 0.8872 (Cg_exo) cc_final: 0.8664 (Cg_endo) REVERT: C 185 ASP cc_start: 0.7224 (p0) cc_final: 0.6955 (p0) REVERT: C 191 GLU cc_start: 0.7151 (tp30) cc_final: 0.5990 (tp30) REVERT: C 216 LYS cc_start: 0.7100 (tttp) cc_final: 0.6553 (tttp) REVERT: C 232 ASP cc_start: 0.7799 (t0) cc_final: 0.7383 (t0) REVERT: C 243 PHE cc_start: 0.8144 (t80) cc_final: 0.7833 (t80) REVERT: C 244 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7482 (mt-10) REVERT: C 264 TRP cc_start: 0.7547 (m-90) cc_final: 0.7263 (m-10) REVERT: C 272 GLU cc_start: 0.7578 (mp0) cc_final: 0.6860 (mp0) REVERT: G 113 ASN cc_start: 0.8495 (m-40) cc_final: 0.8255 (p0) REVERT: G 114 TYR cc_start: 0.8246 (t80) cc_final: 0.7974 (t80) REVERT: G 129 ASP cc_start: 0.7376 (t70) cc_final: 0.6984 (t0) REVERT: G 167 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8658 (ptmm) REVERT: G 169 TYR cc_start: 0.7531 (m-80) cc_final: 0.6839 (m-80) REVERT: G 198 ASP cc_start: 0.7515 (m-30) cc_final: 0.7051 (m-30) REVERT: G 208 ASN cc_start: 0.8141 (t0) cc_final: 0.7855 (t0) REVERT: G 209 ILE cc_start: 0.8875 (mm) cc_final: 0.8467 (tp) REVERT: G 214 PHE cc_start: 0.7115 (m-80) cc_final: 0.6791 (m-80) REVERT: G 217 ILE cc_start: 0.8277 (mp) cc_final: 0.8064 (mp) REVERT: G 224 TYR cc_start: 0.8550 (m-80) cc_final: 0.8263 (m-10) REVERT: G 235 ASP cc_start: 0.6391 (t70) cc_final: 0.5937 (m-30) REVERT: G 238 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7785 (ttpp) REVERT: G 243 PHE cc_start: 0.7306 (t80) cc_final: 0.7089 (t80) REVERT: G 249 MET cc_start: 0.7146 (ttt) cc_final: 0.6814 (ttt) REVERT: G 256 ASN cc_start: 0.7613 (t0) cc_final: 0.7269 (t0) REVERT: G 284 ARG cc_start: 0.7981 (ppt170) cc_final: 0.7488 (ttp-110) REVERT: G 300 LEU cc_start: 0.8031 (mt) cc_final: 0.7751 (mt) REVERT: G 309 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6868 (tm-30) REVERT: G 329 PHE cc_start: 0.8518 (m-80) cc_final: 0.8278 (m-10) REVERT: H 29 GLU cc_start: 0.6961 (mp0) cc_final: 0.6375 (mp0) REVERT: H 35 THR cc_start: 0.6636 (p) cc_final: 0.6427 (t) REVERT: H 98 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7318 (ttmm) REVERT: H 119 TYR cc_start: 0.8785 (m-10) cc_final: 0.8475 (m-80) REVERT: H 120 GLN cc_start: 0.8398 (mt0) cc_final: 0.7928 (mt0) REVERT: H 164 ILE cc_start: 0.7835 (mp) cc_final: 0.7625 (mp) REVERT: H 168 GLU cc_start: 0.7459 (pp20) cc_final: 0.7226 (tm-30) REVERT: H 173 ASN cc_start: 0.9051 (t0) cc_final: 0.8737 (t0) REVERT: H 180 ASP cc_start: 0.8127 (p0) cc_final: 0.6090 (m-30) REVERT: H 186 ASN cc_start: 0.7697 (t0) cc_final: 0.7070 (t0) REVERT: H 188 THR cc_start: 0.8465 (m) cc_final: 0.8177 (p) REVERT: H 189 ILE cc_start: 0.8778 (mt) cc_final: 0.8486 (mt) REVERT: H 265 TYR cc_start: 0.6288 (p90) cc_final: 0.6066 (p90) REVERT: H 273 PHE cc_start: 0.6954 (p90) cc_final: 0.6726 (p90) REVERT: H 290 PHE cc_start: 0.7548 (m-10) cc_final: 0.7253 (m-10) REVERT: H 304 MET cc_start: 0.7713 (mmt) cc_final: 0.7437 (mmt) REVERT: H 311 LEU cc_start: 0.7959 (mt) cc_final: 0.7326 (mt) REVERT: H 316 LYS cc_start: 0.9083 (tttp) cc_final: 0.8586 (tppt) outliers start: 63 outliers final: 36 residues processed: 854 average time/residue: 0.1779 time to fit residues: 231.6164 Evaluate side-chains 813 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 774 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 259 ILE 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 143 LYS 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 25 LEU Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 44 LYS Chi-restraints excluded: chain E residue 48 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 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 54 VAL Chi-restraints excluded: chain F residue 142 ILE 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 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 H residue 25 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 chunk 6 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 247 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN I 137 GLN I 166 HIS ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN F 195 GLN F 227 GLN C 140 ASN H 80 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.160269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.136780 restraints weight = 55739.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.141196 restraints weight = 29881.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.144051 restraints weight = 18500.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.146001 restraints weight = 12746.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.147288 restraints weight = 9534.524| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24151 Z= 0.148 Angle : 0.671 12.277 33036 Z= 0.352 Chirality : 0.044 0.255 3667 Planarity : 0.005 0.046 3897 Dihedral : 18.109 101.209 4165 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 3.39 % Allowed : 16.68 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2629 helix: 0.28 (0.18), residues: 789 sheet: -0.88 (0.25), residues: 425 loop : -1.38 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 291 TYR 0.022 0.002 TYR H 125 PHE 0.025 0.002 PHE D 297 TRP 0.051 0.002 TRP F 264 HIS 0.006 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00326 (24151) covalent geometry : angle 0.67094 (33036) hydrogen bonds : bond 0.05142 ( 737) hydrogen bonds : angle 5.90943 ( 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 899 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 819 time to evaluate : 0.782 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: A 24 ILE cc_start: 0.7832 (mm) cc_final: 0.7609 (mm) REVERT: A 61 ASP cc_start: 0.6938 (m-30) cc_final: 0.6508 (m-30) REVERT: A 75 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7340 (ptpp) REVERT: A 113 GLU cc_start: 0.8129 (pm20) cc_final: 0.7902 (pm20) REVERT: A 118 MET cc_start: 0.7981 (tpt) cc_final: 0.7517 (tpt) REVERT: A 124 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6671 (tttm) REVERT: A 175 ASP cc_start: 0.8492 (t0) cc_final: 0.8264 (t0) REVERT: A 186 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7417 (tpp80) REVERT: A 220 LEU cc_start: 0.7853 (mt) cc_final: 0.7652 (mt) REVERT: A 230 LYS cc_start: 0.7689 (tptt) cc_final: 0.7178 (tptt) REVERT: A 232 TYR cc_start: 0.7741 (m-10) cc_final: 0.7316 (m-80) REVERT: A 283 GLU cc_start: 0.8120 (mp0) cc_final: 0.7828 (mp0) REVERT: B 62 TYR cc_start: 0.5833 (p90) cc_final: 0.5519 (p90) REVERT: B 78 CYS cc_start: 0.6708 (t) cc_final: 0.6139 (t) REVERT: B 97 MET cc_start: 0.7273 (tpp) cc_final: 0.6631 (tpp) REVERT: B 98 ASN cc_start: 0.8077 (p0) cc_final: 0.7065 (p0) REVERT: B 130 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 143 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7762 (mttm) REVERT: B 144 LYS cc_start: 0.7901 (mmtm) cc_final: 0.7571 (mmpt) REVERT: B 175 MET cc_start: 0.6566 (mtp) cc_final: 0.5854 (mtp) REVERT: B 179 MET cc_start: 0.7560 (mmm) cc_final: 0.6697 (mmm) REVERT: B 230 SER cc_start: 0.7342 (p) cc_final: 0.7081 (p) REVERT: I 92 PHE cc_start: 0.6738 (t80) cc_final: 0.6354 (t80) REVERT: I 135 ASN cc_start: 0.6178 (m-40) cc_final: 0.5939 (m-40) REVERT: D 34 GLN cc_start: 0.7738 (pt0) cc_final: 0.6902 (pt0) REVERT: D 36 ASP cc_start: 0.7408 (t0) cc_final: 0.6103 (m-30) REVERT: D 45 LEU cc_start: 0.8552 (mt) cc_final: 0.8134 (mt) REVERT: D 92 ARG cc_start: 0.7954 (ttt-90) cc_final: 0.7727 (ttt90) REVERT: D 121 LYS cc_start: 0.7883 (mmpt) cc_final: 0.7518 (mmpt) REVERT: D 125 TYR cc_start: 0.7501 (t80) cc_final: 0.7108 (t80) REVERT: D 132 LEU cc_start: 0.7875 (tt) cc_final: 0.7664 (tp) REVERT: D 194 GLN cc_start: 0.8184 (tp40) cc_final: 0.7812 (tp-100) REVERT: D 204 ARG cc_start: 0.7509 (mmm160) cc_final: 0.7192 (mmm-85) REVERT: D 221 MET cc_start: 0.7421 (mpp) cc_final: 0.6830 (mpp) REVERT: D 262 ASP cc_start: 0.6478 (t70) cc_final: 0.6220 (t70) REVERT: D 273 PHE cc_start: 0.7696 (p90) cc_final: 0.7183 (p90) REVERT: E 44 LYS cc_start: 0.8340 (ptmt) cc_final: 0.7834 (ptpp) REVERT: E 62 MET cc_start: 0.7119 (mmm) cc_final: 0.6912 (mmm) REVERT: E 85 SER cc_start: 0.7873 (t) cc_final: 0.7556 (m) REVERT: E 134 LEU cc_start: 0.8418 (mm) cc_final: 0.8208 (mp) REVERT: E 136 LYS cc_start: 0.8575 (mttt) cc_final: 0.8316 (ttmt) REVERT: E 194 GLN cc_start: 0.8048 (tp40) cc_final: 0.7758 (tp40) REVERT: E 255 ASN cc_start: 0.8429 (t0) cc_final: 0.8207 (m-40) REVERT: E 260 THR cc_start: 0.7746 (m) cc_final: 0.7522 (p) REVERT: E 268 TYR cc_start: 0.7900 (t80) cc_final: 0.7666 (t80) REVERT: F 20 SER cc_start: 0.7633 (t) cc_final: 0.7376 (p) REVERT: F 39 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7744 (mtpp) REVERT: F 71 ILE cc_start: 0.7564 (tt) cc_final: 0.7088 (tt) REVERT: F 85 SER cc_start: 0.7059 (p) cc_final: 0.6800 (m) REVERT: F 89 ASP cc_start: 0.6911 (p0) cc_final: 0.6443 (p0) REVERT: F 111 ASP cc_start: 0.6773 (t0) cc_final: 0.6015 (t0) REVERT: F 112 TYR cc_start: 0.7562 (t80) cc_final: 0.7038 (t80) REVERT: F 115 ARG cc_start: 0.7986 (ptp-110) cc_final: 0.7179 (ptp-110) REVERT: F 136 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7621 (ttpp) REVERT: F 168 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5613 (tm-30) REVERT: F 204 ARG cc_start: 0.7785 (mmm160) cc_final: 0.6973 (mmm160) REVERT: F 205 GLU cc_start: 0.7275 (tt0) cc_final: 0.6909 (tt0) REVERT: F 207 LEU cc_start: 0.8640 (tp) cc_final: 0.7923 (mt) REVERT: F 224 TYR cc_start: 0.6689 (m-10) cc_final: 0.6466 (m-10) REVERT: F 229 MET cc_start: 0.6073 (ttt) cc_final: 0.5834 (ttt) REVERT: F 230 THR cc_start: 0.8395 (m) cc_final: 0.8045 (t) REVERT: F 264 TRP cc_start: 0.8048 (m-10) cc_final: 0.7676 (m-10) REVERT: F 267 ASP cc_start: 0.7663 (m-30) cc_final: 0.7405 (m-30) REVERT: F 313 ILE cc_start: 0.7439 (pp) cc_final: 0.7183 (pp) REVERT: C 45 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6683 (mp) REVERT: C 84 LEU cc_start: 0.7712 (mt) cc_final: 0.7488 (mt) REVERT: C 136 LYS cc_start: 0.7832 (pptt) cc_final: 0.7514 (pptt) REVERT: C 141 ASN cc_start: 0.8249 (m110) cc_final: 0.7698 (m110) REVERT: C 185 ASP cc_start: 0.7083 (p0) cc_final: 0.6829 (p0) REVERT: C 232 ASP cc_start: 0.7824 (t0) cc_final: 0.7503 (t0) REVERT: C 243 PHE cc_start: 0.7965 (t80) cc_final: 0.7333 (t80) REVERT: C 244 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7163 (mt-10) REVERT: C 264 TRP cc_start: 0.7550 (m-90) cc_final: 0.7260 (m-10) REVERT: G 115 ARG cc_start: 0.8090 (ttp-110) cc_final: 0.7589 (ttp-110) REVERT: G 129 ASP cc_start: 0.7357 (t70) cc_final: 0.7026 (t0) REVERT: G 167 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8644 (ptmm) REVERT: G 169 TYR cc_start: 0.7561 (m-80) cc_final: 0.6815 (m-80) REVERT: G 198 ASP cc_start: 0.7352 (m-30) cc_final: 0.6968 (m-30) REVERT: G 214 PHE cc_start: 0.7043 (m-80) cc_final: 0.6842 (m-80) REVERT: G 242 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7354 (mmtt) REVERT: G 243 PHE cc_start: 0.7293 (t80) cc_final: 0.6943 (t80) REVERT: G 256 ASN cc_start: 0.7559 (t0) cc_final: 0.7248 (t0) REVERT: G 284 ARG cc_start: 0.7869 (ppt170) cc_final: 0.7385 (ttp-110) REVERT: G 300 LEU cc_start: 0.7951 (mt) cc_final: 0.7661 (mt) REVERT: G 306 LEU cc_start: 0.6891 (mt) cc_final: 0.6333 (mt) REVERT: G 307 LYS cc_start: 0.8302 (mmtp) cc_final: 0.7887 (mmtp) REVERT: G 309 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6789 (tm-30) REVERT: G 329 PHE cc_start: 0.8536 (m-80) cc_final: 0.8330 (m-10) REVERT: H 17 GLU cc_start: 0.6080 (tp30) cc_final: 0.5586 (mm-30) REVERT: H 23 ARG cc_start: 0.8063 (ptp-170) cc_final: 0.7788 (ptp-170) REVERT: H 26 ASN cc_start: 0.7877 (m-40) cc_final: 0.7674 (m-40) REVERT: H 35 THR cc_start: 0.6487 (p) cc_final: 0.6169 (t) REVERT: H 98 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7305 (ttmm) REVERT: H 100 LEU cc_start: 0.8213 (mt) cc_final: 0.7988 (tt) REVERT: H 120 GLN cc_start: 0.8281 (mt0) cc_final: 0.7625 (mt0) REVERT: H 124 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8052 (mm-30) REVERT: H 172 PHE cc_start: 0.8201 (m-10) cc_final: 0.7974 (m-10) REVERT: H 173 ASN cc_start: 0.8934 (t0) cc_final: 0.8619 (t0) REVERT: H 180 ASP cc_start: 0.8098 (p0) cc_final: 0.6180 (m-30) REVERT: H 186 ASN cc_start: 0.7526 (t0) cc_final: 0.6874 (t0) REVERT: H 188 THR cc_start: 0.8344 (m) cc_final: 0.7997 (p) REVERT: H 191 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8356 (mt-10) REVERT: H 224 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.6140 (m-80) REVERT: H 290 PHE cc_start: 0.7482 (m-10) cc_final: 0.7205 (m-10) REVERT: H 304 MET cc_start: 0.7571 (mmt) cc_final: 0.7309 (mmt) REVERT: H 311 LEU cc_start: 0.7969 (mt) cc_final: 0.7333 (mt) REVERT: H 316 LYS cc_start: 0.9075 (tttp) cc_final: 0.8635 (tppt) outliers start: 80 outliers final: 39 residues processed: 845 average time/residue: 0.1690 time to fit residues: 220.4255 Evaluate side-chains 816 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 772 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 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 249 CYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 143 LYS 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 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 102 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 E residue 323 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 37 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 168 GLU 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 178 ASN Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain G residue 39 LYS 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 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 224 TYR 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: 4.9990 chunk 200 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 206 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN D 80 GLN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN F 34 GLN F 120 GLN F 195 GLN F 208 ASN C 75 ASN C 190 ASN ** G 227 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 140 ASN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.151153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127463 restraints weight = 55212.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.131839 restraints weight = 29546.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.134690 restraints weight = 18292.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.136558 restraints weight = 12598.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.137857 restraints weight = 9485.923| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 24151 Z= 0.288 Angle : 0.786 14.236 33036 Z= 0.421 Chirality : 0.048 0.323 3667 Planarity : 0.006 0.124 3897 Dihedral : 18.228 106.398 4163 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.68 % Favored : 92.20 % Rotamer: Outliers : 5.00 % Allowed : 20.11 % Favored : 74.89 % 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: -1.65 (0.16), residues: 2629 helix: -0.21 (0.17), residues: 809 sheet: -1.05 (0.26), residues: 414 loop : -1.65 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 291 TYR 0.029 0.003 TYR F 224 PHE 0.031 0.003 PHE H 297 TRP 0.033 0.003 TRP F 149 HIS 0.011 0.002 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00624 (24151) covalent geometry : angle 0.78625 (33036) hydrogen bonds : bond 0.05908 ( 737) hydrogen bonds : angle 6.18879 ( 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 908 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 790 time to evaluate : 0.746 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: 0.7938 (mm) cc_final: 0.7702 (mm) REVERT: A 69 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8212 (m) REVERT: A 75 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7532 (ptpp) REVERT: A 118 MET cc_start: 0.8062 (tpt) cc_final: 0.7635 (tpt) REVERT: A 163 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6382 (mm) REVERT: A 171 TYR cc_start: 0.8165 (t80) cc_final: 0.7882 (t80) REVERT: A 175 ASP cc_start: 0.8557 (t0) cc_final: 0.8322 (t0) REVERT: A 186 ARG cc_start: 0.8334 (tpp80) cc_final: 0.7850 (tpp80) REVERT: A 230 LYS cc_start: 0.7831 (tptt) cc_final: 0.7438 (tptt) REVERT: A 283 GLU cc_start: 0.8221 (mp0) cc_final: 0.8019 (mp0) REVERT: B 22 ILE cc_start: 0.7909 (mm) cc_final: 0.7708 (mm) REVERT: B 23 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6701 (tp) REVERT: B 62 TYR cc_start: 0.7029 (p90) cc_final: 0.6714 (p90) REVERT: B 78 CYS cc_start: 0.7235 (t) cc_final: 0.6465 (t) REVERT: B 97 MET cc_start: 0.7503 (tpp) cc_final: 0.7194 (tpp) REVERT: B 98 ASN cc_start: 0.8458 (p0) cc_final: 0.7777 (p0) REVERT: B 99 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: B 130 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 142 TYR cc_start: 0.6881 (p90) cc_final: 0.6642 (p90) REVERT: B 143 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7980 (mttm) REVERT: B 250 TYR cc_start: 0.5479 (m-10) cc_final: 0.5260 (m-10) REVERT: B 252 CYS cc_start: 0.6562 (p) cc_final: 0.6232 (p) REVERT: I 22 GLU cc_start: 0.8369 (tp30) cc_final: 0.8158 (tp30) REVERT: I 135 ASN cc_start: 0.6386 (m-40) cc_final: 0.6081 (m-40) REVERT: I 165 LYS cc_start: 0.7085 (mmpt) cc_final: 0.6752 (mmtt) REVERT: D 33 TRP cc_start: 0.8260 (m100) cc_final: 0.7840 (m100) REVERT: D 34 GLN cc_start: 0.7742 (pt0) cc_final: 0.7465 (pt0) REVERT: D 36 ASP cc_start: 0.7376 (t0) cc_final: 0.6497 (m-30) REVERT: D 69 LYS cc_start: 0.8409 (pttt) cc_final: 0.8067 (pttp) REVERT: D 121 LYS cc_start: 0.8008 (mmpt) cc_final: 0.7646 (mmpt) REVERT: D 125 TYR cc_start: 0.7631 (t80) cc_final: 0.7158 (t80) REVERT: D 156 GLU cc_start: 0.6958 (pt0) cc_final: 0.6650 (pt0) REVERT: D 194 GLN cc_start: 0.8347 (tp40) cc_final: 0.7668 (tp40) REVERT: D 204 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7401 (mmm-85) REVERT: D 272 GLU cc_start: 0.8454 (mp0) cc_final: 0.7728 (mp0) REVERT: D 291 ARG cc_start: 0.7619 (mmt90) cc_final: 0.6405 (mmt90) REVERT: E 86 THR cc_start: 0.8122 (p) cc_final: 0.7894 (p) REVERT: E 194 GLN cc_start: 0.8113 (tp40) cc_final: 0.7827 (tp40) REVERT: E 200 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: E 268 TYR cc_start: 0.8393 (t80) cc_final: 0.8191 (t80) REVERT: F 20 SER cc_start: 0.7963 (t) cc_final: 0.7652 (p) REVERT: F 40 ARG cc_start: 0.8520 (ptt90) cc_final: 0.8058 (ptp90) REVERT: F 89 ASP cc_start: 0.7296 (p0) cc_final: 0.6952 (p0) REVERT: F 104 GLU cc_start: 0.8624 (mp0) cc_final: 0.8052 (mp0) REVERT: F 112 TYR cc_start: 0.7772 (t80) cc_final: 0.7492 (t80) REVERT: F 136 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7703 (ttpt) REVERT: F 194 GLN cc_start: 0.8259 (tp40) cc_final: 0.8053 (tp-100) REVERT: F 204 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7158 (mmm160) REVERT: F 205 GLU cc_start: 0.7505 (tt0) cc_final: 0.7051 (tt0) REVERT: F 207 LEU cc_start: 0.8792 (tp) cc_final: 0.8072 (mt) REVERT: F 230 THR cc_start: 0.8245 (m) cc_final: 0.7826 (t) REVERT: F 263 THR cc_start: 0.7430 (p) cc_final: 0.6818 (t) REVERT: C 31 LYS cc_start: 0.8704 (ptmt) cc_final: 0.8367 (ptmt) REVERT: C 45 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6996 (mp) REVERT: C 141 ASN cc_start: 0.8314 (m110) cc_final: 0.7804 (m110) REVERT: C 151 ASN cc_start: 0.7102 (m-40) cc_final: 0.6818 (m-40) REVERT: C 221 MET cc_start: 0.6182 (mmm) cc_final: 0.5908 (mmt) REVERT: C 232 ASP cc_start: 0.7870 (t0) cc_final: 0.7436 (t0) REVERT: C 243 PHE cc_start: 0.8249 (t80) cc_final: 0.7273 (t80) REVERT: C 244 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7302 (mt-10) REVERT: C 272 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7581 (mm-30) REVERT: G 113 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8063 (p0) REVERT: G 120 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: G 129 ASP cc_start: 0.7585 (t70) cc_final: 0.7259 (t0) REVERT: G 133 THR cc_start: 0.9076 (m) cc_final: 0.8803 (t) REVERT: G 191 GLU cc_start: 0.8320 (tp30) cc_final: 0.7953 (tp30) REVERT: G 198 ASP cc_start: 0.7512 (m-30) cc_final: 0.7194 (m-30) REVERT: G 214 PHE cc_start: 0.7268 (m-80) cc_final: 0.7059 (m-80) REVERT: G 216 LYS cc_start: 0.8192 (tptt) cc_final: 0.7971 (tptt) REVERT: G 243 PHE cc_start: 0.7599 (t80) cc_final: 0.7092 (t80) REVERT: G 256 ASN cc_start: 0.7755 (t0) cc_final: 0.7370 (t0) REVERT: G 284 ARG cc_start: 0.8046 (ppt170) cc_final: 0.7510 (ttp-110) REVERT: G 300 LEU cc_start: 0.8008 (mt) cc_final: 0.7620 (mt) REVERT: G 307 LYS cc_start: 0.8344 (mmtp) cc_final: 0.7896 (mmtp) REVERT: G 309 GLU cc_start: 0.7233 (tm-30) cc_final: 0.7004 (tm-30) REVERT: H 17 GLU cc_start: 0.6440 (tp30) cc_final: 0.6012 (mm-30) REVERT: H 98 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7994 (mmmt) REVERT: H 100 LEU cc_start: 0.8567 (mt) cc_final: 0.8283 (mt) REVERT: H 121 LYS cc_start: 0.8320 (mppt) cc_final: 0.8078 (mmtm) REVERT: H 150 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.7352 (ttt180) REVERT: H 173 ASN cc_start: 0.9094 (t0) cc_final: 0.8868 (t0) REVERT: H 189 ILE cc_start: 0.8837 (mt) cc_final: 0.8127 (mt) REVERT: H 191 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8475 (mt-10) REVERT: H 249 MET cc_start: 0.7454 (mtp) cc_final: 0.7053 (mtp) REVERT: H 268 TYR cc_start: 0.7683 (t80) cc_final: 0.7102 (t80) REVERT: H 291 ARG cc_start: 0.7520 (mtt-85) cc_final: 0.7091 (mtt90) REVERT: H 304 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7219 (mmt) REVERT: H 311 LEU cc_start: 0.8122 (mt) cc_final: 0.7204 (mt) REVERT: H 316 LYS cc_start: 0.9118 (tttp) cc_final: 0.8630 (tppt) REVERT: H 328 MET cc_start: 0.4971 (ptt) cc_final: 0.4699 (ptt) outliers start: 118 outliers final: 62 residues processed: 841 average time/residue: 0.1657 time to fit residues: 215.6178 Evaluate side-chains 811 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 739 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 164 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 23 ILE 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 80 LEU Chi-restraints excluded: chain B residue 99 GLN 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 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 D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 296 SER 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 158 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 200 PHE 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 84 LEU Chi-restraints excluded: chain F residue 137 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 C residue 45 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 91 LEU 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 82 CYS Chi-restraints excluded: chain G residue 113 ASN 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 H residue 36 ASP 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 Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 304 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 185 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 304 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN I 120 HIS D 140 ASN D 195 GLN D 256 ASN E 26 ASN F 120 GLN G 227 GLN ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.156281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.132429 restraints weight = 54597.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.136809 restraints weight = 29483.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.139661 restraints weight = 18353.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.141583 restraints weight = 12678.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.142799 restraints weight = 9516.311| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.4782 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= 0.158 Angle : 0.705 13.587 33036 Z= 0.368 Chirality : 0.045 0.437 3667 Planarity : 0.005 0.082 3897 Dihedral : 18.059 103.939 4163 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 4.06 % Allowed : 23.03 % Favored : 72.90 % 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: -0.03 (0.18), residues: 807 sheet: -0.85 (0.26), residues: 405 loop : -1.48 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 291 TYR 0.033 0.002 TYR D 112 PHE 0.032 0.002 PHE E 131 TRP 0.053 0.002 TRP F 264 HIS 0.007 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00354 (24151) covalent geometry : angle 0.70548 (33036) hydrogen bonds : bond 0.04923 ( 737) hydrogen bonds : angle 5.82653 ( 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 862 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 766 time to evaluate : 0.978 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: A 24 ILE cc_start: 0.7930 (mm) cc_final: 0.7712 (mm) REVERT: A 118 MET cc_start: 0.8026 (tpt) cc_final: 0.7605 (tpt) REVERT: A 124 LYS cc_start: 0.7198 (ttpp) cc_final: 0.6681 (tttm) REVERT: A 171 TYR cc_start: 0.8153 (t80) cc_final: 0.7901 (t80) REVERT: A 175 ASP cc_start: 0.8505 (t0) cc_final: 0.8268 (t0) REVERT: A 186 ARG cc_start: 0.8329 (tpp80) cc_final: 0.7952 (ttm-80) REVERT: A 228 LEU cc_start: 0.8123 (mm) cc_final: 0.7916 (mm) REVERT: A 283 GLU cc_start: 0.8294 (mp0) cc_final: 0.7865 (mp0) REVERT: B 78 CYS cc_start: 0.6871 (t) cc_final: 0.6304 (t) REVERT: B 98 ASN cc_start: 0.8281 (p0) cc_final: 0.7880 (p0) REVERT: B 105 ASN cc_start: 0.7717 (t0) cc_final: 0.7410 (t0) REVERT: B 144 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7451 (mmpt) REVERT: B 224 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7724 (mm) REVERT: B 244 LYS cc_start: 0.8258 (mmmm) cc_final: 0.8041 (mmmm) REVERT: B 252 CYS cc_start: 0.6449 (p) cc_final: 0.6097 (p) REVERT: I 23 ASP cc_start: 0.7967 (t0) cc_final: 0.7735 (t0) REVERT: I 92 PHE cc_start: 0.6945 (t80) cc_final: 0.6617 (t80) REVERT: I 115 MET cc_start: -0.3341 (tpp) cc_final: -0.4101 (ttm) REVERT: I 135 ASN cc_start: 0.6501 (m-40) cc_final: 0.6228 (m-40) REVERT: I 165 LYS cc_start: 0.7184 (mmpt) cc_final: 0.6776 (mmtt) REVERT: D 33 TRP cc_start: 0.8023 (m100) cc_final: 0.7743 (m100) REVERT: D 36 ASP cc_start: 0.7298 (t0) cc_final: 0.6418 (m-30) REVERT: D 69 LYS cc_start: 0.8348 (pttt) cc_final: 0.7984 (pttp) REVERT: D 78 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8094 (tppp) REVERT: D 121 LYS cc_start: 0.8007 (mmpt) cc_final: 0.7623 (mmpt) REVERT: D 125 TYR cc_start: 0.7657 (t80) cc_final: 0.7166 (t80) REVERT: D 165 GLU cc_start: 0.7163 (tp30) cc_final: 0.6842 (tp30) REVERT: D 194 GLN cc_start: 0.8316 (tp40) cc_final: 0.7699 (tp-100) REVERT: D 204 ARG cc_start: 0.7663 (mmm160) cc_final: 0.7366 (mmm-85) REVERT: D 241 PHE cc_start: 0.8675 (t80) cc_final: 0.8468 (t80) REVERT: D 272 GLU cc_start: 0.8376 (mp0) cc_final: 0.7735 (mp0) REVERT: D 290 PHE cc_start: 0.5935 (m-80) cc_final: 0.5714 (m-80) REVERT: D 291 ARG cc_start: 0.7698 (mmt90) cc_final: 0.6499 (mmt90) REVERT: D 320 MET cc_start: 0.7949 (mmt) cc_final: 0.7036 (mmt) REVERT: D 322 ILE cc_start: 0.8236 (mm) cc_final: 0.8029 (tt) REVERT: E 15 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8155 (mtm-85) REVERT: E 72 MET cc_start: 0.3896 (mmm) cc_final: 0.3527 (mmm) REVERT: E 111 ASP cc_start: 0.7114 (t0) cc_final: 0.6873 (t70) REVERT: E 114 TYR cc_start: 0.7856 (t80) cc_final: 0.7566 (t80) REVERT: E 118 ILE cc_start: 0.8712 (mm) cc_final: 0.8397 (mm) REVERT: E 194 GLN cc_start: 0.7988 (tp40) cc_final: 0.7450 (tp40) REVERT: E 200 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: E 224 TYR cc_start: 0.7028 (m-80) cc_final: 0.6679 (m-10) REVERT: E 229 MET cc_start: 0.3976 (tpt) cc_final: 0.3618 (tpt) REVERT: E 268 TYR cc_start: 0.8160 (t80) cc_final: 0.7941 (t80) REVERT: F 44 LYS cc_start: 0.8534 (ptmt) cc_final: 0.8223 (ptmm) REVERT: F 89 ASP cc_start: 0.7309 (p0) cc_final: 0.6950 (p0) REVERT: F 104 GLU cc_start: 0.8602 (mp0) cc_final: 0.8334 (mp0) REVERT: F 112 TYR cc_start: 0.7590 (t80) cc_final: 0.7158 (t80) REVERT: F 136 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7525 (mmmm) REVERT: F 204 ARG cc_start: 0.7867 (mmm160) cc_final: 0.6964 (mmm160) REVERT: F 205 GLU cc_start: 0.7473 (tt0) cc_final: 0.6988 (tt0) REVERT: F 207 LEU cc_start: 0.8707 (tp) cc_final: 0.8035 (mt) REVERT: F 230 THR cc_start: 0.8272 (m) cc_final: 0.7897 (t) REVERT: F 249 MET cc_start: 0.6631 (tmm) cc_final: 0.5999 (tmm) REVERT: C 31 LYS cc_start: 0.8643 (ptmt) cc_final: 0.8241 (ptmt) REVERT: C 45 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7096 (mp) REVERT: C 73 ASP cc_start: 0.7708 (m-30) cc_final: 0.7485 (m-30) REVERT: C 80 GLN cc_start: 0.8594 (mm-40) cc_final: 0.7693 (mt0) REVERT: C 120 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8444 (pp30) REVERT: C 141 ASN cc_start: 0.8333 (m110) cc_final: 0.7162 (m110) REVERT: C 151 ASN cc_start: 0.7103 (m-40) cc_final: 0.6804 (m-40) REVERT: C 216 LYS cc_start: 0.6793 (tttp) cc_final: 0.6580 (tttt) REVERT: C 221 MET cc_start: 0.6067 (mmm) cc_final: 0.5723 (mmt) REVERT: C 232 ASP cc_start: 0.7854 (t0) cc_final: 0.7438 (t0) REVERT: C 243 PHE cc_start: 0.8080 (t80) cc_final: 0.7118 (t80) REVERT: C 244 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6936 (mt-10) REVERT: C 309 GLU cc_start: 0.8079 (tp30) cc_final: 0.7852 (tp30) REVERT: C 312 PRO cc_start: 0.7199 (Cg_exo) cc_final: 0.6982 (Cg_endo) REVERT: G 51 ASP cc_start: 0.7901 (m-30) cc_final: 0.7578 (m-30) REVERT: G 89 ASP cc_start: 0.7929 (m-30) cc_final: 0.7640 (m-30) REVERT: G 120 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: G 129 ASP cc_start: 0.7518 (t70) cc_final: 0.7205 (t0) REVERT: G 133 THR cc_start: 0.9019 (m) cc_final: 0.8692 (t) REVERT: G 167 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8627 (ptmm) REVERT: G 172 PHE cc_start: 0.6216 (m-10) cc_final: 0.5972 (m-10) REVERT: G 198 ASP cc_start: 0.7390 (m-30) cc_final: 0.7102 (m-30) REVERT: G 214 PHE cc_start: 0.7274 (m-80) cc_final: 0.7031 (m-80) REVERT: G 243 PHE cc_start: 0.7622 (t80) cc_final: 0.7247 (t80) REVERT: G 256 ASN cc_start: 0.7647 (t0) cc_final: 0.7371 (t0) REVERT: G 264 TRP cc_start: 0.7505 (m-90) cc_final: 0.7167 (m-90) REVERT: G 284 ARG cc_start: 0.7861 (ppt170) cc_final: 0.7395 (ttp-110) REVERT: G 300 LEU cc_start: 0.8011 (mt) cc_final: 0.7708 (mt) REVERT: G 306 LEU cc_start: 0.6973 (mt) cc_final: 0.6349 (mt) REVERT: G 307 LYS cc_start: 0.8353 (mmtp) cc_final: 0.7880 (mmtp) REVERT: G 309 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7098 (tm-30) REVERT: H 17 GLU cc_start: 0.6217 (tp30) cc_final: 0.5983 (mm-30) REVERT: H 35 THR cc_start: 0.6428 (p) cc_final: 0.6124 (t) REVERT: H 45 LEU cc_start: 0.7144 (mt) cc_final: 0.6860 (mt) REVERT: H 100 LEU cc_start: 0.8406 (mt) cc_final: 0.8206 (mt) REVERT: H 120 GLN cc_start: 0.8220 (mt0) cc_final: 0.7843 (mt0) REVERT: H 121 LYS cc_start: 0.8300 (mppt) cc_final: 0.8037 (mmtm) REVERT: H 146 ARG cc_start: 0.8390 (mtp85) cc_final: 0.7913 (mtp-110) REVERT: H 150 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7320 (ttt180) REVERT: H 173 ASN cc_start: 0.9008 (t0) cc_final: 0.8705 (t0) REVERT: H 186 ASN cc_start: 0.6646 (p0) cc_final: 0.6384 (p0) REVERT: H 200 PHE cc_start: 0.7326 (m-80) cc_final: 0.6951 (m-80) REVERT: H 205 GLU cc_start: 0.7744 (tp30) cc_final: 0.7500 (tp30) REVERT: H 290 PHE cc_start: 0.7527 (m-10) cc_final: 0.7074 (m-10) REVERT: H 291 ARG cc_start: 0.7496 (mtt-85) cc_final: 0.6967 (mtt90) REVERT: H 304 MET cc_start: 0.7636 (mmt) cc_final: 0.7024 (mmt) REVERT: H 311 LEU cc_start: 0.8131 (mt) cc_final: 0.7174 (mt) REVERT: H 316 LYS cc_start: 0.9112 (tttp) cc_final: 0.8541 (tppt) REVERT: H 328 MET cc_start: 0.5139 (ptt) cc_final: 0.4862 (ptt) outliers start: 96 outliers final: 58 residues processed: 807 average time/residue: 0.1624 time to fit residues: 201.8422 Evaluate side-chains 806 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 743 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 190 VAL 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 I residue 157 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 44 LYS 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 200 PHE 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 84 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 113 ASN 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 229 MET 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 164 ILE 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: 2.9990 chunk 126 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 123 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 chunk 250 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 60 HIS F 41 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN F 195 GLN ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN H 41 HIS ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.151265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.127725 restraints weight = 54703.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.131984 restraints weight = 29505.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.134769 restraints weight = 18384.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.136597 restraints weight = 12725.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.137842 restraints weight = 9651.446| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 0.071 24151 Z= 0.189 Angle : 0.716 13.149 33036 Z= 0.376 Chirality : 0.046 0.368 3667 Planarity : 0.005 0.067 3897 Dihedral : 17.993 103.700 4162 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.35 % Favored : 93.61 % Rotamer: Outliers : 4.32 % Allowed : 24.30 % Favored : 71.38 % 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: 0.03 (0.18), residues: 808 sheet: -0.66 (0.27), residues: 383 loop : -1.49 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 129 TYR 0.048 0.002 TYR H 119 PHE 0.025 0.002 PHE G 241 TRP 0.069 0.002 TRP F 264 HIS 0.017 0.002 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00426 (24151) covalent geometry : angle 0.71646 (33036) hydrogen bonds : bond 0.04870 ( 737) hydrogen bonds : angle 5.80558 ( 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 865 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 763 time to evaluate : 0.793 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: A 24 ILE cc_start: 0.7937 (mm) cc_final: 0.7720 (mm) REVERT: A 45 GLU cc_start: 0.7626 (tp30) cc_final: 0.7324 (tm-30) REVERT: A 114 LEU cc_start: 0.8002 (mm) cc_final: 0.7752 (mt) REVERT: A 118 MET cc_start: 0.8033 (tpt) cc_final: 0.7674 (tpt) REVERT: A 124 LYS cc_start: 0.7194 (ttpp) cc_final: 0.6664 (tttm) REVERT: A 163 ILE cc_start: 0.6724 (mm) cc_final: 0.6175 (mm) REVERT: A 171 TYR cc_start: 0.8193 (t80) cc_final: 0.7970 (t80) REVERT: A 175 ASP cc_start: 0.8508 (t0) cc_final: 0.8247 (t0) REVERT: A 186 ARG cc_start: 0.8357 (tpp80) cc_final: 0.8000 (ttm-80) REVERT: A 208 TRP cc_start: 0.7406 (m-10) cc_final: 0.7156 (m-10) REVERT: A 230 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7540 (ttpt) REVERT: A 283 GLU cc_start: 0.8281 (mp0) cc_final: 0.7958 (mp0) REVERT: B 40 GLU cc_start: 0.8067 (tt0) cc_final: 0.7811 (tt0) REVERT: B 78 CYS cc_start: 0.6907 (t) cc_final: 0.5991 (t) REVERT: B 98 ASN cc_start: 0.8206 (p0) cc_final: 0.7583 (p0) REVERT: B 99 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: B 105 ASN cc_start: 0.7766 (t0) cc_final: 0.7445 (t0) REVERT: B 119 MET cc_start: 0.4826 (OUTLIER) cc_final: 0.3969 (tpt) REVERT: B 130 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 144 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7488 (mmpt) REVERT: B 244 LYS cc_start: 0.8295 (mmmm) cc_final: 0.8057 (mmmm) REVERT: B 252 CYS cc_start: 0.6542 (p) cc_final: 0.6259 (p) REVERT: I 25 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.6224 (m-80) REVERT: I 115 MET cc_start: -0.3371 (tpp) cc_final: -0.4214 (ttp) REVERT: I 135 ASN cc_start: 0.6537 (m-40) cc_final: 0.6236 (m-40) REVERT: I 165 LYS cc_start: 0.7233 (mmpt) cc_final: 0.6839 (mmtt) REVERT: D 33 TRP cc_start: 0.8034 (m100) cc_final: 0.7772 (m100) REVERT: D 36 ASP cc_start: 0.7329 (t0) cc_final: 0.6556 (m-30) REVERT: D 78 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7835 (tptt) REVERT: D 125 TYR cc_start: 0.7649 (t80) cc_final: 0.7166 (t80) REVERT: D 140 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7722 (m-40) REVERT: D 204 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7362 (mmm-85) REVERT: D 272 GLU cc_start: 0.8341 (mp0) cc_final: 0.7988 (mp0) REVERT: D 290 PHE cc_start: 0.5958 (m-80) cc_final: 0.5652 (m-80) REVERT: D 291 ARG cc_start: 0.7807 (mmt90) cc_final: 0.6620 (mmt90) REVERT: D 320 MET cc_start: 0.7974 (mmt) cc_final: 0.7096 (mmt) REVERT: E 15 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8067 (mtm-85) REVERT: E 34 GLN cc_start: 0.7681 (pm20) cc_final: 0.7376 (pm20) REVERT: E 72 MET cc_start: 0.4074 (mmm) cc_final: 0.3763 (mmm) REVERT: E 118 ILE cc_start: 0.8677 (mm) cc_final: 0.8398 (mm) REVERT: E 124 GLU cc_start: 0.7096 (tp30) cc_final: 0.6732 (tp30) REVERT: E 194 GLN cc_start: 0.8002 (tp40) cc_final: 0.7437 (tp40) REVERT: E 229 MET cc_start: 0.3953 (tpt) cc_final: 0.3706 (tpt) REVERT: E 253 LYS cc_start: 0.8416 (tptm) cc_final: 0.8162 (mmmt) REVERT: E 260 THR cc_start: 0.8362 (m) cc_final: 0.8010 (p) REVERT: E 328 MET cc_start: 0.7472 (ttt) cc_final: 0.7181 (tpp) REVERT: F 44 LYS cc_start: 0.8562 (ptmt) cc_final: 0.8242 (ptmm) REVERT: F 51 ASP cc_start: 0.8924 (p0) cc_final: 0.7866 (t0) REVERT: F 89 ASP cc_start: 0.7244 (p0) cc_final: 0.6933 (p0) REVERT: F 92 ARG cc_start: 0.6937 (mtp180) cc_final: 0.4165 (mtp180) REVERT: F 104 GLU cc_start: 0.8666 (mp0) cc_final: 0.8293 (mp0) REVERT: F 112 TYR cc_start: 0.7632 (t80) cc_final: 0.7239 (t80) REVERT: F 136 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7730 (ttpt) REVERT: F 192 ILE cc_start: 0.8761 (mm) cc_final: 0.8530 (mm) REVERT: F 204 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7019 (mmm160) REVERT: F 205 GLU cc_start: 0.7509 (tt0) cc_final: 0.7007 (tt0) REVERT: F 207 LEU cc_start: 0.8612 (tp) cc_final: 0.7981 (mt) REVERT: F 230 THR cc_start: 0.8252 (m) cc_final: 0.7857 (t) REVERT: F 249 MET cc_start: 0.6880 (tmm) cc_final: 0.6005 (tmm) REVERT: C 31 LYS cc_start: 0.8613 (ptmt) cc_final: 0.8215 (ptmt) REVERT: C 45 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7145 (mp) REVERT: C 80 GLN cc_start: 0.8629 (mm-40) cc_final: 0.7771 (mt0) REVERT: C 141 ASN cc_start: 0.8295 (m110) cc_final: 0.7714 (m110) REVERT: C 156 GLU cc_start: 0.7660 (tt0) cc_final: 0.6842 (tt0) REVERT: C 221 MET cc_start: 0.6158 (mmm) cc_final: 0.5946 (mmt) REVERT: C 232 ASP cc_start: 0.7817 (t0) cc_final: 0.7417 (t0) REVERT: C 243 PHE cc_start: 0.8092 (t80) cc_final: 0.7509 (t80) REVERT: C 244 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7236 (mt-10) REVERT: C 312 PRO cc_start: 0.7299 (Cg_exo) cc_final: 0.6971 (Cg_endo) REVERT: C 316 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7846 (mtmt) REVERT: G 89 ASP cc_start: 0.8020 (m-30) cc_final: 0.7794 (m-30) REVERT: G 113 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.7999 (p0) REVERT: G 115 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7758 (ttp-110) REVERT: G 120 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: G 129 ASP cc_start: 0.7552 (t70) cc_final: 0.7287 (t0) REVERT: G 133 THR cc_start: 0.8986 (m) cc_final: 0.8741 (t) REVERT: G 198 ASP cc_start: 0.7361 (m-30) cc_final: 0.7074 (m-30) REVERT: G 221 MET cc_start: 0.6906 (tpp) cc_final: 0.6344 (tpt) REVERT: G 243 PHE cc_start: 0.7575 (t80) cc_final: 0.7187 (t80) REVERT: G 256 ASN cc_start: 0.7615 (t0) cc_final: 0.7400 (t0) REVERT: G 264 TRP cc_start: 0.7538 (m-90) cc_final: 0.7188 (m-90) REVERT: G 300 LEU cc_start: 0.8026 (mt) cc_final: 0.7652 (mt) REVERT: G 306 LEU cc_start: 0.6969 (mt) cc_final: 0.6229 (mt) REVERT: G 307 LYS cc_start: 0.8331 (mmtp) cc_final: 0.7874 (mmtp) REVERT: H 35 THR cc_start: 0.6385 (p) cc_final: 0.6074 (t) REVERT: H 120 GLN cc_start: 0.8190 (mt0) cc_final: 0.7819 (mt0) REVERT: H 121 LYS cc_start: 0.8262 (mppt) cc_final: 0.8013 (mmtm) REVERT: H 146 ARG cc_start: 0.8385 (mtp85) cc_final: 0.7886 (mtp-110) REVERT: H 150 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7342 (ttt180) REVERT: H 173 ASN cc_start: 0.9006 (t0) cc_final: 0.8726 (t0) REVERT: H 191 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8367 (mt-10) REVERT: H 200 PHE cc_start: 0.7342 (m-80) cc_final: 0.7002 (m-80) REVERT: H 295 LYS cc_start: 0.6057 (mmmt) cc_final: 0.5386 (mtpt) REVERT: H 304 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6959 (mmt) REVERT: H 311 LEU cc_start: 0.8161 (mt) cc_final: 0.7246 (mt) REVERT: H 316 LYS cc_start: 0.9107 (tttp) cc_final: 0.8552 (tppt) outliers start: 102 outliers final: 70 residues processed: 807 average time/residue: 0.1634 time to fit residues: 203.2600 Evaluate side-chains 815 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 736 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 157 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 5 ILE 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 I residue 140 CYS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN 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 86 THR 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 199 THR Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 142 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 305 ILE Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 113 ASN 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 229 MET Chi-restraints excluded: chain G residue 246 SER 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 224 TYR Chi-restraints excluded: chain H residue 304 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 206 ASN A 304 HIS ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN C 77 GLN ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 ASN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.153026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.129621 restraints weight = 55107.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.133930 restraints weight = 29787.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.136681 restraints weight = 18482.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.138592 restraints weight = 12825.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.139777 restraints weight = 9645.506| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24151 Z= 0.161 Angle : 0.713 11.717 33036 Z= 0.372 Chirality : 0.045 0.310 3667 Planarity : 0.005 0.063 3897 Dihedral : 17.917 102.538 4162 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 4.02 % Allowed : 25.66 % Favored : 70.32 % 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: -1.32 (0.16), residues: 2629 helix: -0.01 (0.18), residues: 806 sheet: -0.68 (0.27), residues: 379 loop : -1.45 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 129 TYR 0.054 0.002 TYR H 119 PHE 0.034 0.002 PHE G 297 TRP 0.049 0.002 TRP F 264 HIS 0.007 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00366 (24151) covalent geometry : angle 0.71263 (33036) hydrogen bonds : bond 0.04697 ( 737) hydrogen bonds : angle 5.72178 ( 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 849 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 754 time to evaluate : 0.897 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.7911 (mm) cc_final: 0.7688 (mm) REVERT: A 104 MET cc_start: 0.4590 (mmm) cc_final: 0.4356 (mmp) REVERT: A 113 GLU cc_start: 0.8065 (pm20) cc_final: 0.7853 (pm20) REVERT: A 118 MET cc_start: 0.8004 (tpt) cc_final: 0.7643 (tpt) REVERT: A 129 ARG cc_start: 0.7995 (tmt170) cc_final: 0.7145 (ttp80) REVERT: A 133 LEU cc_start: 0.8900 (mt) cc_final: 0.8239 (mt) REVERT: A 163 ILE cc_start: 0.6671 (mm) cc_final: 0.6108 (mm) REVERT: A 171 TYR cc_start: 0.8198 (t80) cc_final: 0.7978 (t80) REVERT: A 175 ASP cc_start: 0.8547 (t0) cc_final: 0.8321 (t0) REVERT: A 186 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7976 (ttm-80) REVERT: A 264 LYS cc_start: 0.7189 (ptpp) cc_final: 0.6817 (ptmm) REVERT: A 283 GLU cc_start: 0.8253 (mp0) cc_final: 0.7901 (mp0) REVERT: B 78 CYS cc_start: 0.6824 (t) cc_final: 0.5887 (t) REVERT: B 98 ASN cc_start: 0.8089 (p0) cc_final: 0.7752 (p0) REVERT: B 119 MET cc_start: 0.4836 (OUTLIER) cc_final: 0.4004 (tpt) REVERT: B 130 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 166 ASN cc_start: 0.9174 (m-40) cc_final: 0.8567 (t0) REVERT: B 179 MET cc_start: 0.7888 (mmm) cc_final: 0.7289 (mmm) REVERT: B 224 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7276 (mm) REVERT: B 244 LYS cc_start: 0.8363 (mmmm) cc_final: 0.8133 (mmmm) REVERT: I 63 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8049 (mm-30) REVERT: I 92 PHE cc_start: 0.7084 (t80) cc_final: 0.6803 (t80) REVERT: I 115 MET cc_start: -0.3377 (tpp) cc_final: -0.4100 (ttp) REVERT: I 135 ASN cc_start: 0.6539 (m-40) cc_final: 0.6094 (m110) REVERT: I 136 GLN cc_start: 0.8348 (tm-30) cc_final: 0.8144 (tm-30) REVERT: D 36 ASP cc_start: 0.7295 (t0) cc_final: 0.6537 (m-30) REVERT: D 78 LYS cc_start: 0.8509 (ttmm) cc_final: 0.7815 (tptt) REVERT: D 125 TYR cc_start: 0.7611 (t80) cc_final: 0.7304 (t80) REVERT: D 165 GLU cc_start: 0.7207 (tp30) cc_final: 0.6916 (tp30) REVERT: D 194 GLN cc_start: 0.8250 (tp40) cc_final: 0.7956 (tp40) REVERT: D 204 ARG cc_start: 0.7588 (mmm160) cc_final: 0.7370 (mmm-85) REVERT: D 205 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5680 (pt0) REVERT: D 272 GLU cc_start: 0.8262 (mp0) cc_final: 0.7799 (mp0) REVERT: D 278 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8508 (mm-30) REVERT: D 290 PHE cc_start: 0.5882 (m-80) cc_final: 0.5609 (m-80) REVERT: D 291 ARG cc_start: 0.7730 (mmt90) cc_final: 0.6589 (mmt90) REVERT: D 320 MET cc_start: 0.7987 (mmt) cc_final: 0.7025 (mmt) REVERT: E 15 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7981 (mtm-85) REVERT: E 48 LEU cc_start: 0.8149 (mp) cc_final: 0.7881 (mp) REVERT: E 72 MET cc_start: 0.4142 (mmm) cc_final: 0.3924 (mmm) REVERT: E 118 ILE cc_start: 0.8633 (mm) cc_final: 0.8348 (mm) REVERT: E 194 GLN cc_start: 0.7939 (tp40) cc_final: 0.7370 (tp-100) REVERT: E 229 MET cc_start: 0.3895 (tpt) cc_final: 0.3666 (tpt) REVERT: E 260 THR cc_start: 0.8259 (m) cc_final: 0.7967 (p) REVERT: F 44 LYS cc_start: 0.8566 (ptmt) cc_final: 0.8268 (ptmm) REVERT: F 51 ASP cc_start: 0.8913 (p0) cc_final: 0.7875 (t0) REVERT: F 89 ASP cc_start: 0.7120 (p0) cc_final: 0.6824 (p0) REVERT: F 92 ARG cc_start: 0.6952 (mtp180) cc_final: 0.4122 (mtp180) REVERT: F 104 GLU cc_start: 0.8674 (mp0) cc_final: 0.8283 (mp0) REVERT: F 112 TYR cc_start: 0.7585 (t80) cc_final: 0.7133 (t80) REVERT: F 115 ARG cc_start: 0.8198 (ptp-110) cc_final: 0.7816 (ptp-110) REVERT: F 136 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7677 (ttpt) REVERT: F 192 ILE cc_start: 0.8733 (mm) cc_final: 0.8499 (mm) REVERT: F 200 PHE cc_start: 0.8243 (m-10) cc_final: 0.8037 (m-80) REVERT: F 204 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7041 (mmm160) REVERT: F 205 GLU cc_start: 0.7482 (tt0) cc_final: 0.6980 (tt0) REVERT: F 207 LEU cc_start: 0.8517 (tp) cc_final: 0.7908 (mt) REVERT: F 230 THR cc_start: 0.8242 (m) cc_final: 0.7834 (t) REVERT: F 249 MET cc_start: 0.6900 (tmm) cc_final: 0.6282 (tmm) REVERT: C 31 LYS cc_start: 0.8561 (ptmt) cc_final: 0.8139 (ptmt) REVERT: C 45 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7135 (mp) REVERT: C 80 GLN cc_start: 0.8600 (mm-40) cc_final: 0.7707 (mt0) REVERT: C 121 LYS cc_start: 0.8208 (tppp) cc_final: 0.7961 (mmmt) REVERT: C 141 ASN cc_start: 0.8371 (m110) cc_final: 0.7804 (m110) REVERT: C 151 ASN cc_start: 0.6999 (m-40) cc_final: 0.6715 (m-40) REVERT: C 242 LYS cc_start: 0.8364 (tppp) cc_final: 0.8075 (tptp) REVERT: C 243 PHE cc_start: 0.8055 (t80) cc_final: 0.7201 (t80) REVERT: C 244 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6964 (mt-10) REVERT: C 312 PRO cc_start: 0.7208 (Cg_exo) cc_final: 0.6910 (Cg_endo) REVERT: C 316 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7868 (mtmt) REVERT: G 89 ASP cc_start: 0.7953 (m-30) cc_final: 0.7661 (m-30) REVERT: G 115 ARG cc_start: 0.8116 (ttp-110) cc_final: 0.7785 (ttp-110) REVERT: G 120 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: G 121 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8230 (mmtt) REVERT: G 129 ASP cc_start: 0.7556 (t70) cc_final: 0.7272 (t0) REVERT: G 133 THR cc_start: 0.8962 (m) cc_final: 0.8672 (t) REVERT: G 198 ASP cc_start: 0.7308 (m-30) cc_final: 0.7032 (m-30) REVERT: G 243 PHE cc_start: 0.7565 (t80) cc_final: 0.7169 (t80) REVERT: G 264 TRP cc_start: 0.7542 (m-90) cc_final: 0.7177 (m-90) REVERT: G 284 ARG cc_start: 0.7531 (ptt-90) cc_final: 0.7261 (ptt-90) REVERT: G 306 LEU cc_start: 0.6746 (mt) cc_final: 0.6117 (mt) REVERT: G 307 LYS cc_start: 0.8315 (mmtp) cc_final: 0.7842 (mmtp) REVERT: H 35 THR cc_start: 0.6226 (p) cc_final: 0.5963 (t) REVERT: H 98 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7605 (ttmm) REVERT: H 120 GLN cc_start: 0.8178 (mt0) cc_final: 0.7700 (mt0) REVERT: H 124 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8252 (mt-10) REVERT: H 125 TYR cc_start: 0.8281 (t80) cc_final: 0.7912 (t80) REVERT: H 146 ARG cc_start: 0.8340 (mtp85) cc_final: 0.7825 (mtp-110) REVERT: H 150 ARG cc_start: 0.7919 (ttp-170) cc_final: 0.7341 (ttt180) REVERT: H 173 ASN cc_start: 0.8930 (t0) cc_final: 0.8620 (t0) REVERT: H 191 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8264 (mt-10) REVERT: H 200 PHE cc_start: 0.7365 (m-80) cc_final: 0.7034 (m-80) REVERT: H 208 ASN cc_start: 0.7956 (m-40) cc_final: 0.6968 (m-40) REVERT: H 239 LYS cc_start: 0.8774 (tptp) cc_final: 0.8466 (tptt) REVERT: H 295 LYS cc_start: 0.5598 (mmmt) cc_final: 0.5049 (mtpt) REVERT: H 299 LYS cc_start: 0.8958 (tptp) cc_final: 0.8734 (tptp) REVERT: H 304 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6952 (mmt) REVERT: H 311 LEU cc_start: 0.8146 (mt) cc_final: 0.7249 (mt) REVERT: H 316 LYS cc_start: 0.9093 (tttp) cc_final: 0.8508 (tppt) outliers start: 95 outliers final: 68 residues processed: 796 average time/residue: 0.1607 time to fit residues: 197.0353 Evaluate side-chains 804 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 730 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 157 SER 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 15 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 304 MET 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 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 E residue 322 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 164 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 C residue 45 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 113 ASN 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 229 MET Chi-restraints excluded: chain G residue 246 SER 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 111 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 304 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 194 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 250 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 206 ASN A 304 HIS B 53 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN F 208 ASN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 ASN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.156275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.132372 restraints weight = 54827.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.136679 restraints weight = 29300.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.139550 restraints weight = 18300.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.141509 restraints weight = 12700.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.142838 restraints weight = 9579.038| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24151 Z= 0.165 Angle : 0.726 11.565 33036 Z= 0.379 Chirality : 0.045 0.280 3667 Planarity : 0.005 0.120 3897 Dihedral : 17.878 101.364 4162 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.50 % Favored : 93.42 % Rotamer: Outliers : 3.85 % Allowed : 26.93 % Favored : 69.22 % 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: -1.30 (0.16), residues: 2629 helix: 0.03 (0.18), residues: 804 sheet: -0.66 (0.27), residues: 373 loop : -1.45 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 15 TYR 0.037 0.002 TYR H 119 PHE 0.028 0.002 PHE F 241 TRP 0.042 0.002 TRP F 264 HIS 0.008 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00375 (24151) covalent geometry : angle 0.72607 (33036) hydrogen bonds : bond 0.04732 ( 737) hydrogen bonds : angle 5.73596 ( 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 831 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 740 time to evaluate : 0.713 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: A 5 LYS cc_start: 0.7016 (ttmt) cc_final: 0.6514 (mtmt) REVERT: A 24 ILE cc_start: 0.7965 (mm) cc_final: 0.7735 (mm) REVERT: A 118 MET cc_start: 0.8041 (tpt) cc_final: 0.7676 (tpt) REVERT: A 129 ARG cc_start: 0.7996 (tmt170) cc_final: 0.7177 (ttp80) REVERT: A 133 LEU cc_start: 0.8875 (mt) cc_final: 0.8051 (mt) REVERT: A 171 TYR cc_start: 0.8251 (t80) cc_final: 0.8002 (t80) REVERT: A 186 ARG cc_start: 0.8304 (tpp80) cc_final: 0.7982 (ttm-80) REVERT: A 264 LYS cc_start: 0.7301 (ptpp) cc_final: 0.6934 (ptmm) REVERT: A 283 GLU cc_start: 0.8277 (mp0) cc_final: 0.7907 (mp0) REVERT: B 40 GLU cc_start: 0.8332 (tt0) cc_final: 0.8019 (mt-10) REVERT: B 78 CYS cc_start: 0.7130 (t) cc_final: 0.6517 (t) REVERT: B 97 MET cc_start: 0.7440 (tpp) cc_final: 0.7062 (tpt) REVERT: B 119 MET cc_start: 0.4962 (OUTLIER) cc_final: 0.4186 (tpt) REVERT: B 130 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7865 (mm-30) REVERT: B 166 ASN cc_start: 0.9217 (m-40) cc_final: 0.8540 (t0) REVERT: B 179 MET cc_start: 0.7938 (mmm) cc_final: 0.7315 (mmm) REVERT: B 224 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7306 (mm) REVERT: B 244 LYS cc_start: 0.8397 (mmmm) cc_final: 0.8187 (mmmm) REVERT: I 115 MET cc_start: -0.3391 (tpp) cc_final: -0.3990 (ttp) REVERT: I 135 ASN cc_start: 0.6636 (m-40) cc_final: 0.6204 (m110) REVERT: D 34 GLN cc_start: 0.7717 (pt0) cc_final: 0.7324 (pt0) REVERT: D 36 ASP cc_start: 0.7419 (t0) cc_final: 0.6873 (m-30) REVERT: D 78 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7920 (tptt) REVERT: D 125 TYR cc_start: 0.7646 (t80) cc_final: 0.7365 (t80) REVERT: D 194 GLN cc_start: 0.8251 (tp40) cc_final: 0.7956 (tp40) REVERT: D 204 ARG cc_start: 0.7650 (mmm160) cc_final: 0.7390 (mmm-85) REVERT: D 205 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5794 (pt0) REVERT: D 272 GLU cc_start: 0.8299 (mp0) cc_final: 0.7793 (mp0) REVERT: D 278 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8413 (mm-30) REVERT: D 290 PHE cc_start: 0.5886 (m-80) cc_final: 0.5556 (m-80) REVERT: D 291 ARG cc_start: 0.7769 (mmt90) cc_final: 0.6559 (mmt90) REVERT: D 320 MET cc_start: 0.8171 (mmt) cc_final: 0.7088 (mmt) REVERT: E 15 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7904 (mtm-85) REVERT: E 44 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8658 (mtpt) REVERT: E 48 LEU cc_start: 0.8187 (mp) cc_final: 0.7935 (mp) REVERT: E 118 ILE cc_start: 0.8600 (mm) cc_final: 0.8319 (mm) REVERT: E 194 GLN cc_start: 0.8040 (tp40) cc_final: 0.7445 (tp-100) REVERT: E 260 THR cc_start: 0.8335 (m) cc_final: 0.7898 (p) REVERT: E 328 MET cc_start: 0.7370 (tpp) cc_final: 0.7052 (tpt) REVERT: F 51 ASP cc_start: 0.8889 (p0) cc_final: 0.7958 (t0) REVERT: F 89 ASP cc_start: 0.7162 (p0) cc_final: 0.6835 (p0) REVERT: F 104 GLU cc_start: 0.8683 (mp0) cc_final: 0.8263 (mp0) REVERT: F 115 ARG cc_start: 0.8214 (ptp-110) cc_final: 0.7976 (ptp-110) REVERT: F 136 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7716 (ttpt) REVERT: F 137 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7783 (tpp-160) REVERT: F 204 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7194 (mmm160) REVERT: F 205 GLU cc_start: 0.7539 (tt0) cc_final: 0.7042 (tt0) REVERT: F 207 LEU cc_start: 0.8460 (tp) cc_final: 0.8241 (tp) REVERT: F 230 THR cc_start: 0.8226 (m) cc_final: 0.7789 (t) REVERT: F 249 MET cc_start: 0.6827 (tmm) cc_final: 0.6323 (tmm) REVERT: F 311 LEU cc_start: 0.8259 (tp) cc_final: 0.7953 (tp) REVERT: C 31 LYS cc_start: 0.8624 (ptmt) cc_final: 0.8167 (ptmt) REVERT: C 45 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7086 (mp) REVERT: C 80 GLN cc_start: 0.8583 (mm-40) cc_final: 0.7829 (mt0) REVERT: C 121 LYS cc_start: 0.8152 (tppp) cc_final: 0.7231 (mmmm) REVERT: C 141 ASN cc_start: 0.8404 (m110) cc_final: 0.7772 (m110) REVERT: C 151 ASN cc_start: 0.7103 (m-40) cc_final: 0.6901 (m-40) REVERT: C 243 PHE cc_start: 0.8077 (t80) cc_final: 0.6858 (t80) REVERT: C 244 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6859 (mt-10) REVERT: C 272 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7588 (mm-30) REVERT: C 312 PRO cc_start: 0.7251 (Cg_exo) cc_final: 0.6899 (Cg_endo) REVERT: C 316 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7900 (mtmt) REVERT: G 89 ASP cc_start: 0.8022 (m-30) cc_final: 0.7732 (m-30) REVERT: G 121 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8389 (mmtt) REVERT: G 129 ASP cc_start: 0.7568 (t70) cc_final: 0.7299 (t0) REVERT: G 133 THR cc_start: 0.8978 (m) cc_final: 0.8698 (t) REVERT: G 198 ASP cc_start: 0.7332 (m-30) cc_final: 0.7039 (m-30) REVERT: G 221 MET cc_start: 0.6912 (tpp) cc_final: 0.6218 (tpt) REVERT: G 243 PHE cc_start: 0.7618 (t80) cc_final: 0.7238 (t80) REVERT: G 264 TRP cc_start: 0.7557 (m-90) cc_final: 0.7198 (m-90) REVERT: G 284 ARG cc_start: 0.7683 (ptt-90) cc_final: 0.7405 (ptt-90) REVERT: G 307 LYS cc_start: 0.8393 (mmtp) cc_final: 0.7900 (mmtp) REVERT: H 35 THR cc_start: 0.6185 (p) cc_final: 0.5934 (t) REVERT: H 120 GLN cc_start: 0.8127 (mt0) cc_final: 0.7597 (mt0) REVERT: H 121 LYS cc_start: 0.8360 (mppt) cc_final: 0.7968 (mttm) REVERT: H 124 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8342 (mt-10) REVERT: H 125 TYR cc_start: 0.8333 (t80) cc_final: 0.8080 (t80) REVERT: H 146 ARG cc_start: 0.8379 (mtp85) cc_final: 0.7855 (mtp-110) REVERT: H 150 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7391 (ttt180) REVERT: H 173 ASN cc_start: 0.8965 (t0) cc_final: 0.8625 (t0) REVERT: H 191 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8307 (mt-10) REVERT: H 200 PHE cc_start: 0.7479 (m-80) cc_final: 0.7154 (m-80) REVERT: H 239 LYS cc_start: 0.8789 (tptp) cc_final: 0.8567 (tptt) REVERT: H 240 LEU cc_start: 0.8071 (mp) cc_final: 0.7838 (mp) REVERT: H 272 GLU cc_start: 0.7559 (mp0) cc_final: 0.7308 (mp0) REVERT: H 291 ARG cc_start: 0.7505 (mtt-85) cc_final: 0.6967 (mtt-85) REVERT: H 295 LYS cc_start: 0.5720 (mmmt) cc_final: 0.5098 (mtpt) REVERT: H 299 LYS cc_start: 0.9025 (tptp) cc_final: 0.8748 (tptp) REVERT: H 304 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6820 (mmt) REVERT: H 309 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6730 (mt-10) REVERT: H 311 LEU cc_start: 0.8123 (mt) cc_final: 0.7060 (mt) REVERT: H 316 LYS cc_start: 0.9103 (tttp) cc_final: 0.8494 (tppt) outliers start: 91 outliers final: 65 residues processed: 780 average time/residue: 0.1680 time to fit residues: 202.4220 Evaluate side-chains 782 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 710 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 5 ILE 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 140 CYS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 109 CYS 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 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 102 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 190 ASN 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 37 PHE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 164 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 C residue 45 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain G residue 39 LYS 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 229 MET Chi-restraints excluded: chain G residue 246 SER 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 164 ILE Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 304 MET 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: 0.8980 chunk 198 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 206 ASN A 304 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN D 255 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4260 r_free = 0.4260 target = 0.155028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.131615 restraints weight = 55014.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.135938 restraints weight = 29886.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.138704 restraints weight = 18605.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.140589 restraints weight = 12895.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.141816 restraints weight = 9754.033| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24151 Z= 0.152 Angle : 0.740 11.619 33036 Z= 0.386 Chirality : 0.045 0.285 3667 Planarity : 0.005 0.051 3897 Dihedral : 17.824 99.497 4162 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 3.73 % Allowed : 27.69 % Favored : 68.59 % 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: -1.28 (0.16), residues: 2629 helix: 0.02 (0.18), residues: 805 sheet: -0.57 (0.27), residues: 377 loop : -1.44 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 115 TYR 0.046 0.002 TYR H 119 PHE 0.040 0.002 PHE D 241 TRP 0.078 0.002 TRP F 264 HIS 0.017 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00347 (24151) covalent geometry : angle 0.73986 (33036) hydrogen bonds : bond 0.04608 ( 737) hydrogen bonds : angle 5.64846 ( 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 810 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 722 time to evaluate : 0.881 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: A 5 LYS cc_start: 0.6982 (ttmt) cc_final: 0.6530 (mtmt) REVERT: A 24 ILE cc_start: 0.7963 (mm) cc_final: 0.7746 (mm) REVERT: A 118 MET cc_start: 0.8025 (tpt) cc_final: 0.7721 (tpt) REVERT: A 129 ARG cc_start: 0.7949 (tmt170) cc_final: 0.7188 (ttp80) REVERT: A 133 LEU cc_start: 0.8864 (mt) cc_final: 0.7969 (mt) REVERT: A 171 TYR cc_start: 0.8216 (t80) cc_final: 0.7976 (t80) REVERT: A 186 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7989 (ttm-80) REVERT: A 264 LYS cc_start: 0.7346 (ptpp) cc_final: 0.6980 (ptmm) REVERT: A 283 GLU cc_start: 0.8385 (mp0) cc_final: 0.8001 (mp0) REVERT: B 37 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7655 (mmm-85) REVERT: B 78 CYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6332 (t) REVERT: B 119 MET cc_start: 0.4941 (OUTLIER) cc_final: 0.4174 (tpt) REVERT: B 179 MET cc_start: 0.7866 (mmm) cc_final: 0.7189 (mmm) REVERT: B 224 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7145 (mm) REVERT: B 244 LYS cc_start: 0.8422 (mmmm) cc_final: 0.8205 (mmmm) REVERT: I 92 PHE cc_start: 0.7222 (t80) cc_final: 0.6912 (t80) REVERT: I 115 MET cc_start: -0.3462 (tpp) cc_final: -0.4039 (ttp) REVERT: I 135 ASN cc_start: 0.6559 (m-40) cc_final: 0.6086 (m110) REVERT: D 34 GLN cc_start: 0.7579 (pt0) cc_final: 0.7261 (pt0) REVERT: D 36 ASP cc_start: 0.7316 (t0) cc_final: 0.6686 (m-30) REVERT: D 78 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8022 (tptt) REVERT: D 194 GLN cc_start: 0.8248 (tp40) cc_final: 0.7941 (tp40) REVERT: D 204 ARG cc_start: 0.7565 (mmm160) cc_final: 0.7351 (mmm-85) REVERT: D 205 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5719 (pt0) REVERT: D 208 ASN cc_start: 0.7551 (p0) cc_final: 0.6860 (p0) REVERT: D 272 GLU cc_start: 0.8254 (mp0) cc_final: 0.7770 (mp0) REVERT: D 278 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8372 (mm-30) REVERT: D 320 MET cc_start: 0.8166 (mmt) cc_final: 0.7114 (mmt) REVERT: E 15 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7881 (mtm-85) REVERT: E 118 ILE cc_start: 0.8564 (mm) cc_final: 0.8272 (mm) REVERT: E 194 GLN cc_start: 0.7999 (tp40) cc_final: 0.7391 (tp-100) REVERT: E 240 LEU cc_start: 0.9023 (mm) cc_final: 0.8799 (mp) REVERT: E 260 THR cc_start: 0.8182 (m) cc_final: 0.7850 (p) REVERT: E 332 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7074 (tttt) REVERT: F 89 ASP cc_start: 0.7013 (p0) cc_final: 0.6722 (p0) REVERT: F 104 GLU cc_start: 0.8688 (mp0) cc_final: 0.8256 (mp0) REVERT: F 115 ARG cc_start: 0.8170 (ptp-110) cc_final: 0.7966 (ptp-110) REVERT: F 136 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7643 (ttpt) REVERT: F 137 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7742 (tpp-160) REVERT: F 204 ARG cc_start: 0.7861 (mmm160) cc_final: 0.7243 (mmm160) REVERT: F 311 LEU cc_start: 0.8254 (tp) cc_final: 0.7937 (tp) REVERT: C 44 LYS cc_start: 0.7974 (pttm) cc_final: 0.7648 (tttm) REVERT: C 45 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7182 (mp) REVERT: C 80 GLN cc_start: 0.8550 (mm-40) cc_final: 0.7719 (mt0) REVERT: C 141 ASN cc_start: 0.8425 (m110) cc_final: 0.7889 (m110) REVERT: C 243 PHE cc_start: 0.8006 (t80) cc_final: 0.6773 (t80) REVERT: C 244 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6757 (mt-10) REVERT: C 312 PRO cc_start: 0.7240 (Cg_exo) cc_final: 0.6880 (Cg_endo) REVERT: C 316 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7899 (mtmt) REVERT: G 39 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6560 (ptmt) REVERT: G 89 ASP cc_start: 0.8052 (m-30) cc_final: 0.7713 (m-30) REVERT: G 129 ASP cc_start: 0.7498 (t70) cc_final: 0.7277 (t70) REVERT: G 133 THR cc_start: 0.8941 (m) cc_final: 0.8653 (t) REVERT: G 198 ASP cc_start: 0.7294 (m-30) cc_final: 0.6988 (m-30) REVERT: G 221 MET cc_start: 0.6836 (tpp) cc_final: 0.6260 (tpt) REVERT: G 243 PHE cc_start: 0.7576 (t80) cc_final: 0.7196 (t80) REVERT: G 264 TRP cc_start: 0.7570 (m-90) cc_final: 0.7161 (m-90) REVERT: G 307 LYS cc_start: 0.8370 (mmtp) cc_final: 0.7878 (mmtp) REVERT: H 35 THR cc_start: 0.6176 (p) cc_final: 0.5931 (t) REVERT: H 120 GLN cc_start: 0.8130 (mt0) cc_final: 0.7600 (mt0) REVERT: H 121 LYS cc_start: 0.8347 (mppt) cc_final: 0.7977 (mttm) REVERT: H 125 TYR cc_start: 0.8342 (t80) cc_final: 0.8069 (t80) REVERT: H 146 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7844 (mtp-110) REVERT: H 167 LYS cc_start: 0.8073 (tptt) cc_final: 0.7771 (tptt) REVERT: H 173 ASN cc_start: 0.8873 (t0) cc_final: 0.8514 (t0) REVERT: H 191 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8293 (mt-10) REVERT: H 200 PHE cc_start: 0.7382 (m-80) cc_final: 0.7173 (m-80) REVERT: H 272 GLU cc_start: 0.7451 (mp0) cc_final: 0.7222 (mp0) REVERT: H 291 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.7002 (mtt-85) REVERT: H 295 LYS cc_start: 0.5897 (mmmt) cc_final: 0.5323 (mtpt) REVERT: H 299 LYS cc_start: 0.8987 (tptp) cc_final: 0.8719 (tptp) REVERT: H 304 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6736 (mmt) REVERT: H 311 LEU cc_start: 0.8113 (mt) cc_final: 0.7050 (mt) REVERT: H 316 LYS cc_start: 0.9085 (tttp) cc_final: 0.8455 (tppt) outliers start: 88 outliers final: 66 residues processed: 761 average time/residue: 0.1711 time to fit residues: 201.1958 Evaluate side-chains 790 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 716 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 190 VAL 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 5 ILE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 102 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 190 ASN Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 137 ARG Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 91 LEU 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 C residue 305 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 112 TYR 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 229 MET Chi-restraints excluded: chain G residue 246 SER 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 162 VAL Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 304 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 189 optimal weight: 3.9990 chunk 203 optimal weight: 0.0470 chunk 61 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 235 optimal weight: 0.0980 chunk 226 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 234 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 overall best weight: 0.4680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 206 ASN A 304 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.157566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.133993 restraints weight = 55290.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.138332 restraints weight = 29525.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.141259 restraints weight = 18337.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.143145 restraints weight = 12586.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.144371 restraints weight = 9501.250| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24151 Z= 0.150 Angle : 0.748 11.031 33036 Z= 0.390 Chirality : 0.045 0.244 3667 Planarity : 0.005 0.051 3897 Dihedral : 17.768 98.512 4162 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.88 % Rotamer: Outliers : 3.30 % Allowed : 28.70 % Favored : 67.99 % 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: -1.28 (0.16), residues: 2629 helix: -0.01 (0.18), residues: 807 sheet: -0.58 (0.27), residues: 380 loop : -1.42 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 15 TYR 0.048 0.002 TYR H 119 PHE 0.031 0.002 PHE A 152 TRP 0.066 0.002 TRP F 264 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00344 (24151) covalent geometry : angle 0.74803 (33036) hydrogen bonds : bond 0.04581 ( 737) hydrogen bonds : angle 5.65949 ( 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 798 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 720 time to evaluate : 0.719 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 5 LYS cc_start: 0.6883 (ttmt) cc_final: 0.6456 (mtmt) REVERT: A 24 ILE cc_start: 0.7996 (mm) cc_final: 0.7770 (mm) REVERT: A 45 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7393 (tp30) REVERT: A 118 MET cc_start: 0.7971 (tpt) cc_final: 0.7717 (tpt) REVERT: A 129 ARG cc_start: 0.7954 (tmt170) cc_final: 0.7293 (ttp80) REVERT: A 133 LEU cc_start: 0.8816 (mt) cc_final: 0.7882 (mt) REVERT: A 171 TYR cc_start: 0.8190 (t80) cc_final: 0.7987 (t80) REVERT: A 186 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7985 (ttm-80) REVERT: A 283 GLU cc_start: 0.8413 (mp0) cc_final: 0.8043 (mp0) REVERT: B 78 CYS cc_start: 0.6742 (t) cc_final: 0.6266 (t) REVERT: B 88 ASN cc_start: 0.8963 (t0) cc_final: 0.8731 (t0) REVERT: B 163 ARG cc_start: 0.7099 (mpt-90) cc_final: 0.6763 (mpt-90) REVERT: B 179 MET cc_start: 0.7859 (mmm) cc_final: 0.7182 (mmm) REVERT: B 252 CYS cc_start: 0.6538 (p) cc_final: 0.6189 (p) REVERT: I 92 PHE cc_start: 0.7366 (t80) cc_final: 0.7003 (t80) REVERT: I 115 MET cc_start: -0.3542 (tpp) cc_final: -0.4014 (ttp) REVERT: I 135 ASN cc_start: 0.6624 (m-40) cc_final: 0.6141 (m110) REVERT: D 33 TRP cc_start: 0.7500 (m-10) cc_final: 0.7267 (m-10) REVERT: D 34 GLN cc_start: 0.7508 (pt0) cc_final: 0.7193 (pt0) REVERT: D 36 ASP cc_start: 0.7174 (t0) cc_final: 0.6822 (m-30) REVERT: D 194 GLN cc_start: 0.8298 (tp40) cc_final: 0.7726 (tp40) REVERT: D 228 GLU cc_start: 0.8067 (tp30) cc_final: 0.7743 (tp30) REVERT: D 272 GLU cc_start: 0.8210 (mp0) cc_final: 0.7746 (mp0) REVERT: D 278 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8329 (mm-30) REVERT: D 320 MET cc_start: 0.8134 (mmt) cc_final: 0.7229 (mmt) REVERT: E 15 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7821 (mtm-85) REVERT: E 48 LEU cc_start: 0.8099 (mp) cc_final: 0.7880 (mp) REVERT: E 118 ILE cc_start: 0.8552 (mm) cc_final: 0.8278 (mm) REVERT: E 124 GLU cc_start: 0.6972 (tp30) cc_final: 0.6679 (tp30) REVERT: E 194 GLN cc_start: 0.8024 (tp40) cc_final: 0.7447 (tp-100) REVERT: E 240 LEU cc_start: 0.9016 (mm) cc_final: 0.8790 (mp) REVERT: E 260 THR cc_start: 0.8182 (m) cc_final: 0.7850 (p) REVERT: E 291 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6553 (mtt-85) REVERT: E 299 LYS cc_start: 0.8418 (mttt) cc_final: 0.8046 (mtmt) REVERT: E 332 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7054 (tttt) REVERT: F 89 ASP cc_start: 0.6980 (p0) cc_final: 0.6683 (p0) REVERT: F 104 GLU cc_start: 0.8674 (mp0) cc_final: 0.8235 (mp0) REVERT: F 136 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7697 (ttpt) REVERT: F 137 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7755 (tpp-160) REVERT: F 192 ILE cc_start: 0.8705 (mm) cc_final: 0.8378 (mm) REVERT: F 204 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7210 (mmm160) REVERT: F 207 LEU cc_start: 0.8233 (tp) cc_final: 0.7673 (mp) REVERT: F 230 THR cc_start: 0.8216 (m) cc_final: 0.7764 (t) REVERT: F 244 GLU cc_start: 0.7674 (mp0) cc_final: 0.7416 (pp20) REVERT: F 311 LEU cc_start: 0.8254 (tp) cc_final: 0.7960 (tp) REVERT: F 328 MET cc_start: 0.6022 (ppp) cc_final: 0.4363 (ppp) REVERT: C 44 LYS cc_start: 0.7950 (pttm) cc_final: 0.7601 (tttm) REVERT: C 45 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7140 (mp) REVERT: C 80 GLN cc_start: 0.8525 (mm-40) cc_final: 0.7725 (mt0) REVERT: C 141 ASN cc_start: 0.8382 (m110) cc_final: 0.7866 (m110) REVERT: C 243 PHE cc_start: 0.7955 (t80) cc_final: 0.6624 (t80) REVERT: C 244 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6636 (mt-10) REVERT: C 312 PRO cc_start: 0.7316 (Cg_exo) cc_final: 0.6965 (Cg_endo) REVERT: C 316 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7905 (mtmt) REVERT: G 39 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6492 (ptmt) REVERT: G 89 ASP cc_start: 0.8045 (m-30) cc_final: 0.7753 (m-30) REVERT: G 121 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8288 (mmtp) REVERT: G 129 ASP cc_start: 0.7460 (t70) cc_final: 0.7258 (t70) REVERT: G 133 THR cc_start: 0.8940 (m) cc_final: 0.8659 (t) REVERT: G 167 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8454 (ptmt) REVERT: G 198 ASP cc_start: 0.7274 (m-30) cc_final: 0.6973 (m-30) REVERT: G 221 MET cc_start: 0.6792 (tpp) cc_final: 0.6231 (tpt) REVERT: G 242 LYS cc_start: 0.7573 (mmmm) cc_final: 0.7223 (mmtt) REVERT: G 243 PHE cc_start: 0.7639 (t80) cc_final: 0.7241 (t80) REVERT: G 264 TRP cc_start: 0.7602 (m-90) cc_final: 0.7143 (m-90) REVERT: G 307 LYS cc_start: 0.8369 (mmtp) cc_final: 0.7886 (mmtp) REVERT: H 35 THR cc_start: 0.6128 (p) cc_final: 0.5898 (t) REVERT: H 115 ARG cc_start: 0.7442 (mtt-85) cc_final: 0.6999 (mtt180) REVERT: H 120 GLN cc_start: 0.8190 (mt0) cc_final: 0.6984 (mt0) REVERT: H 121 LYS cc_start: 0.8368 (mppt) cc_final: 0.7999 (mttm) REVERT: H 124 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8087 (mp0) REVERT: H 125 TYR cc_start: 0.8345 (t80) cc_final: 0.8097 (t80) REVERT: H 146 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7854 (mtp-110) REVERT: H 150 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7463 (ttt180) REVERT: H 167 LYS cc_start: 0.8176 (tptt) cc_final: 0.7920 (tptt) REVERT: H 173 ASN cc_start: 0.8803 (t0) cc_final: 0.8440 (t0) REVERT: H 191 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8267 (mt-10) REVERT: H 224 TYR cc_start: 0.8197 (m-80) cc_final: 0.7426 (m-80) REVERT: H 268 TYR cc_start: 0.7391 (t80) cc_final: 0.6498 (t80) REVERT: H 272 GLU cc_start: 0.7414 (mp0) cc_final: 0.7188 (mp0) REVERT: H 295 LYS cc_start: 0.5880 (mmmt) cc_final: 0.5332 (mtmt) REVERT: H 299 LYS cc_start: 0.9039 (tptp) cc_final: 0.8755 (tptp) REVERT: H 304 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6616 (mmt) REVERT: H 311 LEU cc_start: 0.8114 (mt) cc_final: 0.7115 (mt) REVERT: H 316 LYS cc_start: 0.9050 (tttp) cc_final: 0.8426 (tppt) outliers start: 78 outliers final: 62 residues processed: 757 average time/residue: 0.1666 time to fit residues: 195.1600 Evaluate side-chains 776 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 711 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 109 CYS 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 D residue 304 MET Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 102 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 F residue 28 THR Chi-restraints excluded: chain F residue 37 PHE Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 91 LEU 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 C residue 305 ILE Chi-restraints excluded: chain G residue 39 LYS 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 229 MET Chi-restraints excluded: chain G residue 246 SER 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 162 VAL Chi-restraints excluded: chain H residue 304 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 43 optimal weight: 1.9990 chunk 251 optimal weight: 0.1980 chunk 263 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 136 optimal weight: 0.4980 chunk 195 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 206 ASN A 304 HIS ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.157790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.134203 restraints weight = 55330.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.138642 restraints weight = 29649.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.141479 restraints weight = 18347.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.143392 restraints weight = 12663.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.144691 restraints weight = 9522.368| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24151 Z= 0.154 Angle : 0.750 10.912 33036 Z= 0.392 Chirality : 0.045 0.254 3667 Planarity : 0.005 0.053 3897 Dihedral : 17.725 98.362 4162 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.88 % Rotamer: Outliers : 3.05 % Allowed : 29.21 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.16), residues: 2629 helix: -0.09 (0.18), residues: 809 sheet: -0.59 (0.27), residues: 384 loop : -1.42 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 15 TYR 0.049 0.002 TYR H 119 PHE 0.058 0.002 PHE D 290 TRP 0.059 0.002 TRP F 264 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00354 (24151) covalent geometry : angle 0.74966 (33036) hydrogen bonds : bond 0.04619 ( 737) hydrogen bonds : angle 5.67304 ( 1941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5269.23 seconds wall clock time: 91 minutes 53.76 seconds (5513.76 seconds total)