Starting phenix.real_space_refine on Thu Mar 5 16:16:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjd_54944/03_2026/9sjd_54944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjd_54944/03_2026/9sjd_54944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sjd_54944/03_2026/9sjd_54944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjd_54944/03_2026/9sjd_54944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sjd_54944/03_2026/9sjd_54944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjd_54944/03_2026/9sjd_54944.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 93 5.49 5 S 114 5.16 5 C 14469 2.51 5 N 3882 2.21 5 O 4618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23176 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2703 Classifications: {'peptide': 337} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1986 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "I" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1082 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain breaks: 3 Chain: "L" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2621 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain: "E" Number of atoms: 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: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2628 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "G" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2512 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 2 Chain: "H" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2393 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "K" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1288 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 13} Link IDs: {'rna2p': 27, 'rna3p': 32} Time building chain proxies: 4.77, per 1000 atoms: 0.21 Number of scatterers: 23176 At special positions: 0 Unit cell: (118.175, 144.275, 156.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 93 15.00 O 4618 8.00 N 3882 7.00 C 14469 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: 1.78 Conformation dependent library (CDL) restraints added in 873.0 milliseconds 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4982 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 36 sheets defined 33.0% alpha, 9.5% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 4.124A pdb=" N LEU A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.590A pdb=" N TYR A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 93 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.637A pdb=" N ILE A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 180 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.681A pdb=" N GLU A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.594A pdb=" N VAL A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.672A pdb=" N GLU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.635A pdb=" N PHE B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 4.033A pdb=" N GLU B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.865A pdb=" N LEU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'I' and resid 15 through 23 Processing helix chain 'I' and resid 24 through 35 removed outlier: 3.565A pdb=" N SER I 30 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 72 removed outlier: 3.869A pdb=" N LEU I 68 " --> pdb=" O ASP I 64 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 78 through 81 removed outlier: 3.644A pdb=" N THR I 81 " --> pdb=" O ALA I 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 78 through 81' Processing helix chain 'D' and resid 63 through 71 removed outlier: 4.153A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 201 removed outlier: 3.580A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.511A pdb=" N TYR D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 63 through 70 removed outlier: 4.074A pdb=" N LYS E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 186 through 201 Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.886A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 4.270A 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 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 186 through 201 removed outlier: 3.615A pdb=" N GLN F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.637A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 63 through 71 removed outlier: 4.175A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.654A 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 306 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 186 through 201 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.561A pdb=" N ILE G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 313 through 326 removed outlier: 3.787A pdb=" N TYR G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET G 320 " --> pdb=" O LYS G 316 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 324 " --> pdb=" O MET G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.747A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 Processing helix chain 'H' and resid 267 through 272 Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 296 through 305 removed outlier: 4.525A pdb=" N ASP H 302 " --> pdb=" O TYR H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 326 removed outlier: 3.829A pdb=" N TYR H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET H 320 " --> pdb=" O LYS H 316 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA H 321 " --> pdb=" O HIS H 317 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG H 325 " --> pdb=" O ALA H 321 " (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 151 through 153 removed outlier: 4.288A pdb=" N ASP B 214 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.660A pdb=" N VAL B 24 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 6 through 17 current: chain 'B' and resid 101 through 112 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 101 through 112 current: chain 'B' and resid 137 through 139 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 139 current: chain 'B' and resid 225 through 229 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 225 through 229 current: chain 'B' and resid 252 through 253 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA8, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.641A pdb=" N GLY B 195 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 40 through 42 removed outlier: 6.237A pdb=" N SER I 3 " --> pdb=" O GLU I 89 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU I 89 " --> pdb=" O SER I 3 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE I 5 " --> pdb=" O LYS I 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS I 87 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE I 7 " --> pdb=" O LYS I 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 99 through 100 removed outlier: 3.709A pdb=" N ALA I 142 " --> pdb=" O LEU I 159 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 106 through 109 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 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 167 through 168 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.321A 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: 3.506A 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 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 168 current: chain 'E' and resid 246 through 249 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AC1, first strand: chain 'E' and resid 282 through 283 removed outlier: 4.031A pdb=" N ALA E 283 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE E 288 " --> pdb=" O ALA E 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, 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=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 57 removed outlier: 4.541A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AC5, first strand: chain 'F' and resid 282 through 283 removed outlier: 4.428A pdb=" N ALA F 283 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE F 288 " --> pdb=" O ALA F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 106 through 109 Processing sheet with id=AC7, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 172 through 173 current: chain 'C' and resid 246 through 249 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 50 through 57 removed outlier: 4.110A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 260 through 262 Processing sheet with id=AD1, first strand: chain 'G' and resid 106 through 109 removed outlier: 3.680A pdb=" N SER G 108 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing sheet with id=AD2, 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=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 50 through 56 removed outlier: 3.619A pdb=" N ASN G 75 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 227 through 228 removed outlier: 4.886A pdb=" N LYS G 239 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 20 through 21 removed outlier: 6.918A pdb=" N SER H 20 " --> pdb=" O TYR H 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 45 through 46 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.915A pdb=" N CYS H 82 " --> pdb=" O VAL H 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AD9, first strand: chain 'H' and resid 260 through 262 608 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.32 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: 6805 1.33 - 1.46: 4592 1.46 - 1.58: 12110 1.58 - 1.70: 185 1.70 - 1.82: 181 Bond restraints: 23873 Sorted by residual: bond pdb=" C ASP A 99 " pdb=" N GLY A 100 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" N ILE H 261 " pdb=" CA ILE H 261 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N GLU C 165 " pdb=" CA GLU C 165 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.24e-02 6.50e+03 8.33e+00 bond pdb=" C ILE A 14 " pdb=" N PRO A 15 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.12e-02 7.97e+03 7.90e+00 bond pdb=" C MET A 97 " pdb=" N SER A 98 " ideal model delta sigma weight residual 1.332 1.371 -0.038 1.40e-02 5.10e+03 7.44e+00 ... (remaining 23868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 32159 2.38 - 4.75: 449 4.75 - 7.13: 48 7.13 - 9.51: 11 9.51 - 11.88: 2 Bond angle restraints: 32669 Sorted by residual: angle pdb=" CA PHE H 147 " pdb=" C PHE H 147 " pdb=" N LEU H 148 " ideal model delta sigma weight residual 118.43 126.96 -8.53 1.33e+00 5.65e-01 4.11e+01 angle pdb=" N ILE C 164 " pdb=" CA ILE C 164 " pdb=" C ILE C 164 " ideal model delta sigma weight residual 110.05 104.62 5.43 1.09e+00 8.42e-01 2.48e+01 angle pdb=" C ILE G 313 " pdb=" N GLU G 314 " pdb=" CA GLU G 314 " ideal model delta sigma weight residual 121.54 112.12 9.42 1.91e+00 2.74e-01 2.43e+01 angle pdb=" CA ARG A 265 " pdb=" CB ARG A 265 " pdb=" CG ARG A 265 " ideal model delta sigma weight residual 114.10 123.85 -9.75 2.00e+00 2.50e-01 2.38e+01 angle pdb=" O MET A 97 " pdb=" C MET A 97 " pdb=" N SER A 98 " ideal model delta sigma weight residual 123.21 128.34 -5.13 1.27e+00 6.20e-01 1.63e+01 ... (remaining 32664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 13435 33.14 - 66.27: 928 66.27 - 99.41: 76 99.41 - 132.54: 1 132.54 - 165.68: 2 Dihedral angle restraints: 14442 sinusoidal: 6732 harmonic: 7710 Sorted by residual: dihedral pdb=" O4' A J 39 " pdb=" C1' A J 39 " pdb=" N9 A J 39 " pdb=" C4 A J 39 " ideal model delta sinusoidal sigma weight residual 254.00 167.57 86.43 1 1.70e+01 3.46e-03 3.11e+01 dihedral pdb=" CA MET G 320 " pdb=" C MET G 320 " pdb=" N ALA G 321 " pdb=" CA ALA G 321 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" O4' A J 45 " pdb=" C1' A J 45 " pdb=" N9 A J 45 " pdb=" C4 A J 45 " ideal model delta sinusoidal sigma weight residual -106.00 -178.95 72.95 1 1.70e+01 3.46e-03 2.35e+01 ... (remaining 14439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3498 0.102 - 0.205: 122 0.205 - 0.307: 4 0.307 - 0.410: 0 0.410 - 0.512: 3 Chirality restraints: 3627 Sorted by residual: chirality pdb=" P U J 42 " pdb=" OP1 U J 42 " pdb=" OP2 U J 42 " pdb=" O5' U J 42 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.57e+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 -2.88 -0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" P DA L 2 " pdb=" OP1 DA L 2 " pdb=" OP2 DA L 2 " pdb=" O5' DA L 2 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.44 2.00e-01 2.50e+01 4.95e+00 ... (remaining 3624 not shown) Planarity restraints: 3839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 149 " -0.022 2.00e-02 2.50e+03 1.85e-02 8.53e+00 pdb=" CG TRP H 149 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP H 149 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP H 149 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 149 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 149 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 149 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 149 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 149 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 309 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C GLU G 309 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU G 309 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP G 310 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 200 " -0.024 2.00e-02 2.50e+03 1.82e-02 5.81e+00 pdb=" CG PHE H 200 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE H 200 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE H 200 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 200 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE H 200 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 200 " -0.006 2.00e-02 2.50e+03 ... (remaining 3836 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1138 2.71 - 3.26: 23923 3.26 - 3.80: 41046 3.80 - 4.35: 54078 4.35 - 4.90: 85369 Nonbonded interactions: 205554 Sorted by model distance: nonbonded pdb=" OG SER A 310 " pdb=" OE1 GLN A 311 " model vdw 2.162 3.040 nonbonded pdb=" O2' A J 40 " pdb=" O5' G J 41 " model vdw 2.193 3.040 nonbonded pdb=" O2' G J 27 " pdb=" O5' C J 28 " model vdw 2.207 3.040 nonbonded pdb=" O GLU E 278 " pdb=" OH TYR E 318 " model vdw 2.207 3.040 nonbonded pdb=" NE2 GLN G 34 " pdb=" O PRO G 46 " model vdw 2.215 3.120 ... (remaining 205549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 12 through 52 or resid 79 through 229 or resid 236 through \ 332)) selection = (chain 'D' and (resid 12 through 52 or resid 79 through 229 or resid 236 through \ 332)) selection = (chain 'E' and (resid 12 through 52 or resid 79 through 229 or resid 236 through \ 332)) selection = (chain 'F' and (resid 12 through 52 or resid 79 through 229 or resid 236 through \ 332)) selection = (chain 'G' and (resid 12 through 52 or resid 79 through 229 or resid 236 through \ 332)) selection = (chain 'H' and (resid 12 through 229 or resid 236 through 332)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.430 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.730 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 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 0.060 23873 Z= 0.206 Angle : 0.700 11.881 32669 Z= 0.398 Chirality : 0.045 0.512 3627 Planarity : 0.004 0.073 3839 Dihedral : 20.159 165.677 9460 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.76 % Favored : 94.85 % Rotamer: Outliers : 0.82 % Allowed : 26.71 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2584 helix: 0.40 (0.19), residues: 732 sheet: 0.82 (0.27), residues: 410 loop : -1.05 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 146 TYR 0.026 0.001 TYR D 112 PHE 0.040 0.002 PHE H 200 TRP 0.049 0.002 TRP H 149 HIS 0.012 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00419 (23873) covalent geometry : angle 0.70031 (32669) hydrogen bonds : bond 0.22817 ( 675) hydrogen bonds : angle 8.03783 ( 1849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 570 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.7251 (p0) cc_final: 0.6846 (p0) REVERT: A 52 ILE cc_start: 0.8393 (mp) cc_final: 0.8070 (mp) REVERT: A 55 TYR cc_start: 0.7366 (t80) cc_final: 0.6850 (t80) REVERT: A 172 GLU cc_start: 0.7314 (tp30) cc_final: 0.6946 (tp30) REVERT: A 277 ARG cc_start: 0.8408 (ptp90) cc_final: 0.7939 (ptp90) REVERT: A 307 VAL cc_start: 0.7674 (t) cc_final: 0.7349 (m) REVERT: A 315 ASP cc_start: 0.4851 (t70) cc_final: 0.4382 (t0) REVERT: B 58 GLU cc_start: 0.6510 (tt0) cc_final: 0.6124 (tt0) REVERT: B 65 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7923 (tppt) REVERT: B 77 SER cc_start: 0.8284 (p) cc_final: 0.7480 (p) REVERT: B 80 LEU cc_start: 0.8036 (tp) cc_final: 0.7834 (tt) REVERT: B 90 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8197 (mtmm) REVERT: B 101 TYR cc_start: 0.8238 (m-80) cc_final: 0.7932 (m-80) REVERT: B 103 ASP cc_start: 0.7014 (m-30) cc_final: 0.6131 (m-30) REVERT: B 142 TYR cc_start: 0.8226 (p90) cc_final: 0.7980 (p90) REVERT: B 143 LYS cc_start: 0.7835 (tttp) cc_final: 0.7592 (tptm) REVERT: B 145 ILE cc_start: 0.7697 (mt) cc_final: 0.7369 (tt) REVERT: B 251 LEU cc_start: 0.7243 (tp) cc_final: 0.6956 (tp) REVERT: D 28 THR cc_start: 0.7628 (p) cc_final: 0.7358 (p) REVERT: D 169 TYR cc_start: 0.7502 (m-80) cc_final: 0.7294 (m-80) REVERT: D 208 ASN cc_start: 0.6691 (m-40) cc_final: 0.6413 (m-40) REVERT: D 290 PHE cc_start: 0.7533 (m-80) cc_final: 0.7200 (m-10) REVERT: E 29 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6924 (mm-30) REVERT: E 114 TYR cc_start: 0.8291 (t80) cc_final: 0.7596 (t80) REVERT: E 303 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7568 (ttm-80) REVERT: E 309 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7031 (mt-10) REVERT: F 43 PHE cc_start: 0.8330 (t80) cc_final: 0.8041 (t80) REVERT: F 150 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7589 (ttt90) REVERT: F 216 LYS cc_start: 0.7745 (tttt) cc_final: 0.7470 (tttp) REVERT: F 224 TYR cc_start: 0.7614 (m-80) cc_final: 0.7351 (m-80) REVERT: F 265 TYR cc_start: 0.8241 (p90) cc_final: 0.7644 (p90) REVERT: F 278 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7062 (mm-30) REVERT: F 305 ILE cc_start: 0.8302 (mm) cc_final: 0.8092 (mm) REVERT: F 330 SER cc_start: 0.6751 (p) cc_final: 0.6544 (p) REVERT: C 90 THR cc_start: 0.7760 (m) cc_final: 0.7433 (p) REVERT: C 107 TYR cc_start: 0.8082 (m-10) cc_final: 0.7816 (m-80) REVERT: C 114 TYR cc_start: 0.7872 (t80) cc_final: 0.7413 (t80) REVERT: C 262 ASP cc_start: 0.8009 (t0) cc_final: 0.7737 (t0) REVERT: C 278 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6642 (mm-30) REVERT: G 15 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6691 (mtm-85) REVERT: G 23 ARG cc_start: 0.6870 (mtm-85) cc_final: 0.6629 (mtp85) REVERT: G 203 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8054 (mmtt) REVERT: H 229 MET cc_start: 0.1466 (tmm) cc_final: 0.1061 (tmm) outliers start: 19 outliers final: 5 residues processed: 584 average time/residue: 0.1746 time to fit residues: 154.0687 Evaluate side-chains 524 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 519 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 165 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 311 GLN B 21 ASN I 35 HIS D 173 ASN F 41 HIS ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 195 GLN H 140 ASN ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.183649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.143217 restraints weight = 35068.095| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.54 r_work: 0.3766 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23873 Z= 0.204 Angle : 0.645 11.434 32669 Z= 0.341 Chirality : 0.044 0.197 3627 Planarity : 0.005 0.092 3839 Dihedral : 17.957 172.160 4150 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 3.91 % Allowed : 25.20 % Favored : 70.89 % 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: -0.67 (0.16), residues: 2584 helix: 0.22 (0.18), residues: 769 sheet: 0.43 (0.26), residues: 434 loop : -1.12 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 40 TYR 0.026 0.002 TYR F 114 PHE 0.051 0.002 PHE H 200 TRP 0.026 0.002 TRP H 149 HIS 0.007 0.001 HIS F 41 Details of bonding type rmsd covalent geometry : bond 0.00455 (23873) covalent geometry : angle 0.64455 (32669) hydrogen bonds : bond 0.04953 ( 675) hydrogen bonds : angle 5.99319 ( 1849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 513 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.6273 (t0) cc_final: 0.5254 (m-30) REVERT: A 78 ASP cc_start: 0.7380 (t0) cc_final: 0.7158 (t0) REVERT: A 88 ARG cc_start: 0.8416 (tpp80) cc_final: 0.7966 (tpp80) REVERT: A 118 MET cc_start: 0.5272 (mmp) cc_final: 0.5053 (mmp) REVERT: A 141 TYR cc_start: 0.8196 (p90) cc_final: 0.7963 (p90) REVERT: A 172 GLU cc_start: 0.7789 (tp30) cc_final: 0.7410 (tp30) REVERT: A 307 VAL cc_start: 0.7847 (t) cc_final: 0.7511 (m) REVERT: A 315 ASP cc_start: 0.6341 (t0) cc_final: 0.5838 (t70) REVERT: A 320 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7178 (pmm) REVERT: B 58 GLU cc_start: 0.7249 (tt0) cc_final: 0.6817 (tt0) REVERT: B 80 LEU cc_start: 0.8348 (tp) cc_final: 0.8057 (tt) REVERT: B 90 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8103 (mtmm) REVERT: B 97 MET cc_start: 0.7634 (mmm) cc_final: 0.7109 (mmm) REVERT: B 103 ASP cc_start: 0.7638 (m-30) cc_final: 0.7055 (m-30) REVERT: B 142 TYR cc_start: 0.8481 (p90) cc_final: 0.8188 (p90) REVERT: B 143 LYS cc_start: 0.8086 (tttp) cc_final: 0.7674 (tptm) REVERT: B 145 ILE cc_start: 0.7921 (mt) cc_final: 0.7499 (tt) REVERT: B 228 GLU cc_start: 0.7084 (tt0) cc_final: 0.6703 (tt0) REVERT: B 252 CYS cc_start: 0.8142 (p) cc_final: 0.7937 (p) REVERT: I 41 ILE cc_start: -0.0177 (OUTLIER) cc_final: -0.0410 (mp) REVERT: D 44 LYS cc_start: 0.8387 (pttp) cc_final: 0.8132 (pttp) REVERT: D 64 PRO cc_start: 0.6366 (Cg_endo) cc_final: 0.6161 (Cg_exo) REVERT: D 87 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7206 (tp30) REVERT: D 168 GLU cc_start: 0.7839 (tt0) cc_final: 0.7060 (mt-10) REVERT: D 169 TYR cc_start: 0.8257 (m-80) cc_final: 0.7924 (m-80) REVERT: D 208 ASN cc_start: 0.7435 (m-40) cc_final: 0.7095 (m-40) REVERT: D 290 PHE cc_start: 0.8055 (m-80) cc_final: 0.7625 (m-10) REVERT: D 329 PHE cc_start: 0.8103 (m-80) cc_final: 0.7802 (m-10) REVERT: E 29 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7566 (mm-30) REVERT: E 43 PHE cc_start: 0.8032 (t80) cc_final: 0.7760 (t80) REVERT: E 47 LEU cc_start: 0.8100 (tp) cc_final: 0.7796 (tp) REVERT: E 52 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7780 (ttpp) REVERT: E 123 ASP cc_start: 0.7766 (m-30) cc_final: 0.7560 (m-30) REVERT: E 168 GLU cc_start: 0.8112 (tt0) cc_final: 0.7414 (mt-10) REVERT: E 222 GLU cc_start: 0.7925 (tt0) cc_final: 0.7640 (tt0) REVERT: E 239 LYS cc_start: 0.7839 (mmmm) cc_final: 0.7619 (mtpp) REVERT: E 244 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7771 (mt-10) REVERT: E 253 LYS cc_start: 0.7890 (tptt) cc_final: 0.7567 (tttp) REVERT: E 269 THR cc_start: 0.8270 (t) cc_final: 0.8062 (p) REVERT: E 303 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7852 (ttm-80) REVERT: E 309 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7594 (mt-10) REVERT: F 17 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5819 (pt0) REVERT: F 29 GLU cc_start: 0.8160 (mp0) cc_final: 0.7905 (mp0) REVERT: F 216 LYS cc_start: 0.8063 (tttt) cc_final: 0.7744 (tttp) REVERT: F 224 TYR cc_start: 0.8150 (m-80) cc_final: 0.7936 (m-80) REVERT: F 239 LYS cc_start: 0.8226 (mptt) cc_final: 0.7802 (mptt) REVERT: F 253 LYS cc_start: 0.7904 (tptm) cc_final: 0.7617 (tptm) REVERT: F 265 TYR cc_start: 0.8346 (p90) cc_final: 0.7926 (p90) REVERT: F 272 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: F 278 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7595 (mm-30) REVERT: F 299 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7646 (mtmm) REVERT: F 315 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7383 (t0) REVERT: F 330 SER cc_start: 0.7179 (p) cc_final: 0.6903 (p) REVERT: C 29 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: C 75 ASN cc_start: 0.8373 (t0) cc_final: 0.8069 (t0) REVERT: C 90 THR cc_start: 0.8221 (m) cc_final: 0.7689 (p) REVERT: C 140 ASN cc_start: 0.7463 (m-40) cc_final: 0.7207 (m-40) REVERT: C 239 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7655 (mmtt) REVERT: C 267 ASP cc_start: 0.7601 (m-30) cc_final: 0.7371 (m-30) REVERT: C 331 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7981 (pttm) REVERT: G 15 ARG cc_start: 0.7172 (mtm-85) cc_final: 0.6861 (mtm-85) REVERT: G 29 GLU cc_start: 0.7536 (mp0) cc_final: 0.7251 (mp0) REVERT: G 45 LEU cc_start: 0.7427 (tt) cc_final: 0.7174 (tt) REVERT: G 103 LYS cc_start: 0.8511 (mttt) cc_final: 0.8226 (tttm) REVERT: G 203 LYS cc_start: 0.8413 (mmtt) cc_final: 0.8174 (mmtt) REVERT: H 179 LEU cc_start: 0.3315 (OUTLIER) cc_final: 0.2947 (mm) REVERT: H 229 MET cc_start: 0.1323 (tmm) cc_final: 0.0944 (tmm) REVERT: H 304 MET cc_start: 0.4982 (tpp) cc_final: 0.4726 (tpp) REVERT: H 320 MET cc_start: 0.2678 (mmt) cc_final: 0.2473 (mmm) outliers start: 91 outliers final: 37 residues processed: 576 average time/residue: 0.1604 time to fit residues: 142.0104 Evaluate side-chains 544 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 499 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 254 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 240 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 206 ASN B 20 ASN B 21 ASN B 184 GLN D 256 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN F 144 ASN ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 ASN ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.176509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.135925 restraints weight = 35239.250| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.58 r_work: 0.3693 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23873 Z= 0.157 Angle : 0.583 9.076 32669 Z= 0.307 Chirality : 0.042 0.198 3627 Planarity : 0.005 0.065 3839 Dihedral : 17.861 171.785 4146 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.30 % Favored : 95.55 % Rotamer: Outliers : 3.95 % Allowed : 25.81 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2584 helix: 0.29 (0.18), residues: 774 sheet: 0.42 (0.26), residues: 413 loop : -1.08 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 284 TYR 0.017 0.001 TYR F 125 PHE 0.032 0.002 PHE H 200 TRP 0.022 0.001 TRP G 149 HIS 0.006 0.001 HIS H 317 Details of bonding type rmsd covalent geometry : bond 0.00353 (23873) covalent geometry : angle 0.58286 (32669) hydrogen bonds : bond 0.04528 ( 675) hydrogen bonds : angle 5.52908 ( 1849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 508 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.6314 (t0) cc_final: 0.5384 (m-30) REVERT: A 88 ARG cc_start: 0.8456 (tpp80) cc_final: 0.7820 (tpp80) REVERT: A 141 TYR cc_start: 0.8347 (p90) cc_final: 0.8023 (p90) REVERT: A 172 GLU cc_start: 0.7852 (tp30) cc_final: 0.7569 (tp30) REVERT: A 178 TYR cc_start: 0.8031 (t80) cc_final: 0.7581 (t80) REVERT: A 277 ARG cc_start: 0.8450 (ptp90) cc_final: 0.8222 (ptp90) REVERT: A 307 VAL cc_start: 0.7883 (t) cc_final: 0.7593 (m) REVERT: A 315 ASP cc_start: 0.6613 (OUTLIER) cc_final: 0.5989 (t70) REVERT: A 316 SER cc_start: 0.6860 (OUTLIER) cc_final: 0.6655 (p) REVERT: B 58 GLU cc_start: 0.7200 (tt0) cc_final: 0.6804 (tt0) REVERT: B 65 LYS cc_start: 0.8646 (tppt) cc_final: 0.8359 (tppt) REVERT: B 97 MET cc_start: 0.7702 (mmm) cc_final: 0.7230 (mmm) REVERT: B 103 ASP cc_start: 0.7543 (m-30) cc_final: 0.7074 (m-30) REVERT: B 143 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7894 (tmtt) REVERT: B 145 ILE cc_start: 0.7923 (mt) cc_final: 0.7483 (tt) REVERT: B 219 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6735 (tt0) REVERT: B 228 GLU cc_start: 0.7278 (tt0) cc_final: 0.6907 (tt0) REVERT: B 244 LYS cc_start: 0.8629 (ttpp) cc_final: 0.8218 (ttpp) REVERT: I 98 LEU cc_start: -0.2735 (OUTLIER) cc_final: -0.4416 (mt) REVERT: D 44 LYS cc_start: 0.8465 (pttp) cc_final: 0.8163 (pttp) REVERT: D 54 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.7182 (p) REVERT: D 107 TYR cc_start: 0.8384 (t80) cc_final: 0.8073 (t80) REVERT: D 290 PHE cc_start: 0.8017 (m-80) cc_final: 0.7683 (m-10) REVERT: D 329 PHE cc_start: 0.8137 (m-80) cc_final: 0.7919 (m-10) REVERT: E 28 THR cc_start: 0.8334 (p) cc_final: 0.8077 (p) REVERT: E 29 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7436 (mm-30) REVERT: E 52 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7934 (ttpp) REVERT: E 109 CYS cc_start: 0.6711 (t) cc_final: 0.6464 (t) REVERT: E 123 ASP cc_start: 0.7828 (m-30) cc_final: 0.7598 (m-30) REVERT: E 168 GLU cc_start: 0.7957 (tt0) cc_final: 0.7340 (mt-10) REVERT: E 222 GLU cc_start: 0.7910 (tt0) cc_final: 0.7604 (tt0) REVERT: E 239 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7685 (mtpp) REVERT: E 253 LYS cc_start: 0.7991 (tptt) cc_final: 0.7691 (tttt) REVERT: E 273 PHE cc_start: 0.8006 (p90) cc_final: 0.7730 (p90) REVERT: E 303 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7801 (ttm-80) REVERT: E 309 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7623 (mt-10) REVERT: F 17 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5931 (pt0) REVERT: F 29 GLU cc_start: 0.8117 (mp0) cc_final: 0.7879 (mp0) REVERT: F 43 PHE cc_start: 0.8731 (t80) cc_final: 0.8353 (t80) REVERT: F 157 ILE cc_start: 0.8344 (mt) cc_final: 0.8012 (tt) REVERT: F 239 LYS cc_start: 0.8247 (mptt) cc_final: 0.7836 (mptt) REVERT: F 253 LYS cc_start: 0.7908 (tptm) cc_final: 0.7640 (tptm) REVERT: F 265 TYR cc_start: 0.8259 (p90) cc_final: 0.8012 (p90) REVERT: F 272 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: F 278 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7551 (mm-30) REVERT: F 305 ILE cc_start: 0.8321 (mm) cc_final: 0.8061 (mm) REVERT: F 315 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7372 (t0) REVERT: F 330 SER cc_start: 0.7205 (p) cc_final: 0.6560 (m) REVERT: C 29 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: C 75 ASN cc_start: 0.8273 (t0) cc_final: 0.7945 (t0) REVERT: C 140 ASN cc_start: 0.7414 (m-40) cc_final: 0.7190 (m-40) REVERT: C 160 THR cc_start: 0.8423 (m) cc_final: 0.8034 (p) REVERT: C 229 MET cc_start: 0.7501 (tmm) cc_final: 0.7243 (tmm) REVERT: C 267 ASP cc_start: 0.7609 (m-30) cc_final: 0.7359 (m-30) REVERT: C 331 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8091 (pttm) REVERT: G 15 ARG cc_start: 0.7055 (mtm-85) cc_final: 0.6780 (mtm-85) REVERT: G 29 GLU cc_start: 0.7629 (mp0) cc_final: 0.7326 (mp0) REVERT: G 45 LEU cc_start: 0.7619 (tt) cc_final: 0.7401 (tt) REVERT: G 103 LYS cc_start: 0.8522 (mttt) cc_final: 0.8196 (mttt) REVERT: G 186 ASN cc_start: 0.6389 (t0) cc_final: 0.6032 (t0) REVERT: G 203 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8188 (mmtt) REVERT: G 212 THR cc_start: 0.7866 (m) cc_final: 0.7629 (t) REVERT: G 253 LYS cc_start: 0.7453 (tptt) cc_final: 0.6625 (mmmm) REVERT: H 94 ASP cc_start: 0.5054 (m-30) cc_final: 0.4729 (m-30) REVERT: H 97 ILE cc_start: 0.5600 (mp) cc_final: 0.5135 (tp) REVERT: H 229 MET cc_start: 0.1355 (tmm) cc_final: 0.0987 (tmm) REVERT: H 304 MET cc_start: 0.5106 (tpp) cc_final: 0.4807 (tpp) outliers start: 92 outliers final: 43 residues processed: 572 average time/residue: 0.1626 time to fit residues: 143.8158 Evaluate side-chains 550 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 495 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 275 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 57 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 327 HIS B 21 ASN B 44 ASN B 184 GLN B 237 ASN D 194 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 113 ASN F 144 ASN C 113 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.175054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134592 restraints weight = 35164.629| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.58 r_work: 0.3674 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23873 Z= 0.186 Angle : 0.590 8.228 32669 Z= 0.312 Chirality : 0.043 0.215 3627 Planarity : 0.005 0.056 3839 Dihedral : 17.697 172.056 4143 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 3.86 % Allowed : 26.19 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2584 helix: 0.30 (0.18), residues: 782 sheet: 0.31 (0.25), residues: 428 loop : -1.13 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 40 TYR 0.018 0.002 TYR C 265 PHE 0.024 0.002 PHE H 200 TRP 0.023 0.002 TRP G 149 HIS 0.006 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00418 (23873) covalent geometry : angle 0.58988 (32669) hydrogen bonds : bond 0.04246 ( 675) hydrogen bonds : angle 5.28611 ( 1849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 526 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7894 (tpp80) REVERT: A 171 TYR cc_start: 0.7381 (t80) cc_final: 0.7066 (t80) REVERT: A 172 GLU cc_start: 0.7846 (tp30) cc_final: 0.7545 (mm-30) REVERT: A 178 TYR cc_start: 0.8074 (t80) cc_final: 0.7609 (t80) REVERT: A 218 LYS cc_start: 0.7705 (tppt) cc_final: 0.7360 (tppt) REVERT: A 226 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7619 (ttmt) REVERT: A 281 LYS cc_start: 0.7046 (mmmt) cc_final: 0.6839 (mmmt) REVERT: A 307 VAL cc_start: 0.8012 (t) cc_final: 0.7753 (m) REVERT: A 315 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6160 (t70) REVERT: A 316 SER cc_start: 0.6903 (OUTLIER) cc_final: 0.6703 (p) REVERT: B 58 GLU cc_start: 0.7241 (tt0) cc_final: 0.6786 (tt0) REVERT: B 61 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7009 (mm-30) REVERT: B 65 LYS cc_start: 0.8657 (tppt) cc_final: 0.8437 (tppt) REVERT: B 97 MET cc_start: 0.7760 (mmm) cc_final: 0.7306 (mmm) REVERT: B 103 ASP cc_start: 0.7514 (m-30) cc_final: 0.7173 (m-30) REVERT: B 143 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7872 (tmtt) REVERT: B 145 ILE cc_start: 0.7980 (mt) cc_final: 0.7501 (tt) REVERT: B 153 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7022 (t0) REVERT: B 219 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: B 228 GLU cc_start: 0.7400 (tt0) cc_final: 0.6997 (tt0) REVERT: B 244 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8209 (ttpp) REVERT: B 246 GLU cc_start: 0.7597 (mp0) cc_final: 0.7381 (mp0) REVERT: D 44 LYS cc_start: 0.8472 (pttp) cc_final: 0.8170 (pttp) REVERT: D 54 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7128 (p) REVERT: D 87 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7436 (mp0) REVERT: D 168 GLU cc_start: 0.7920 (tt0) cc_final: 0.7670 (tt0) REVERT: D 222 GLU cc_start: 0.6280 (tt0) cc_final: 0.5907 (tt0) REVERT: D 229 MET cc_start: 0.7782 (tpp) cc_final: 0.7330 (tpp) REVERT: D 265 TYR cc_start: 0.8114 (p90) cc_final: 0.7674 (p90) REVERT: D 284 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7400 (ttp80) REVERT: D 290 PHE cc_start: 0.8086 (m-80) cc_final: 0.7776 (m-10) REVERT: D 303 ARG cc_start: 0.7779 (mtp180) cc_final: 0.7578 (ttp80) REVERT: D 328 MET cc_start: 0.7326 (ptm) cc_final: 0.6979 (ptm) REVERT: E 28 THR cc_start: 0.8349 (p) cc_final: 0.8102 (p) REVERT: E 29 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7392 (mm-30) REVERT: E 33 TRP cc_start: 0.8600 (m-90) cc_final: 0.8332 (m-90) REVERT: E 43 PHE cc_start: 0.8052 (t80) cc_final: 0.7815 (t80) REVERT: E 109 CYS cc_start: 0.6829 (t) cc_final: 0.6625 (t) REVERT: E 123 ASP cc_start: 0.7794 (m-30) cc_final: 0.7579 (m-30) REVERT: E 222 GLU cc_start: 0.7922 (tt0) cc_final: 0.7615 (tt0) REVERT: E 239 LYS cc_start: 0.7937 (mmmm) cc_final: 0.7731 (mtpp) REVERT: E 253 LYS cc_start: 0.7985 (tptt) cc_final: 0.7670 (tttt) REVERT: E 303 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7790 (ttm-80) REVERT: E 309 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7625 (mt-10) REVERT: F 23 ARG cc_start: 0.8378 (ptp90) cc_final: 0.7446 (ptt-90) REVERT: F 29 GLU cc_start: 0.8130 (mp0) cc_final: 0.7896 (mp0) REVERT: F 123 ASP cc_start: 0.7164 (m-30) cc_final: 0.6873 (m-30) REVERT: F 126 ILE cc_start: 0.8456 (mt) cc_final: 0.8207 (mp) REVERT: F 144 ASN cc_start: 0.8289 (m-40) cc_final: 0.8078 (m-40) REVERT: F 157 ILE cc_start: 0.8407 (mt) cc_final: 0.8115 (tt) REVERT: F 222 GLU cc_start: 0.7501 (tt0) cc_final: 0.7161 (tt0) REVERT: F 224 TYR cc_start: 0.8229 (m-80) cc_final: 0.7762 (m-10) REVERT: F 230 THR cc_start: 0.7727 (m) cc_final: 0.7274 (t) REVERT: F 239 LYS cc_start: 0.8291 (mptt) cc_final: 0.7844 (mptt) REVERT: F 253 LYS cc_start: 0.7957 (tptm) cc_final: 0.7621 (tptt) REVERT: F 272 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: F 284 ARG cc_start: 0.8080 (ttm170) cc_final: 0.7680 (mtp180) REVERT: F 305 ILE cc_start: 0.8318 (mm) cc_final: 0.8095 (mm) REVERT: F 315 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7366 (t0) REVERT: F 330 SER cc_start: 0.7299 (p) cc_final: 0.7024 (p) REVERT: C 29 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: C 38 LEU cc_start: 0.8173 (mp) cc_final: 0.7926 (mp) REVERT: C 75 ASN cc_start: 0.8249 (t0) cc_final: 0.7988 (t0) REVERT: C 90 THR cc_start: 0.8236 (m) cc_final: 0.8026 (m) REVERT: C 104 GLU cc_start: 0.8152 (mp0) cc_final: 0.7902 (mp0) REVERT: C 331 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8133 (pttm) REVERT: G 15 ARG cc_start: 0.7054 (mtm-85) cc_final: 0.6801 (mtm-85) REVERT: G 21 PHE cc_start: 0.7754 (m-80) cc_final: 0.7443 (m-10) REVERT: G 29 GLU cc_start: 0.7622 (mp0) cc_final: 0.7260 (mt-10) REVERT: G 45 LEU cc_start: 0.7763 (tt) cc_final: 0.7549 (tt) REVERT: G 103 LYS cc_start: 0.8508 (mttt) cc_final: 0.8179 (mttt) REVERT: G 106 MET cc_start: 0.8172 (ttt) cc_final: 0.7760 (tpp) REVERT: G 186 ASN cc_start: 0.6483 (t0) cc_final: 0.6080 (t0) REVERT: G 203 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8140 (mmtt) REVERT: G 212 THR cc_start: 0.7950 (m) cc_final: 0.7707 (t) REVERT: H 21 PHE cc_start: 0.7371 (m-80) cc_final: 0.6846 (m-80) REVERT: H 94 ASP cc_start: 0.5141 (m-30) cc_final: 0.4744 (m-30) REVERT: H 191 GLU cc_start: 0.6200 (mt-10) cc_final: 0.5996 (mp0) REVERT: H 229 MET cc_start: 0.1567 (tmm) cc_final: 0.1159 (tmm) REVERT: H 304 MET cc_start: 0.5204 (tpp) cc_final: 0.4899 (tpp) outliers start: 90 outliers final: 59 residues processed: 584 average time/residue: 0.1646 time to fit residues: 146.1216 Evaluate side-chains 572 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 503 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 275 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 78 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 230 optimal weight: 20.0000 chunk 118 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 192 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 44 ASN B 237 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 113 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.176234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.135675 restraints weight = 34895.117| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.58 r_work: 0.3681 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23873 Z= 0.149 Angle : 0.563 10.988 32669 Z= 0.298 Chirality : 0.042 0.198 3627 Planarity : 0.004 0.055 3839 Dihedral : 17.632 171.850 4141 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.37 % Favored : 95.47 % Rotamer: Outliers : 4.34 % Allowed : 26.92 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2584 helix: 0.44 (0.18), residues: 780 sheet: 0.41 (0.27), residues: 396 loop : -1.10 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 303 TYR 0.027 0.001 TYR D 125 PHE 0.027 0.002 PHE D 329 TRP 0.017 0.001 TRP G 149 HIS 0.004 0.001 HIS H 317 Details of bonding type rmsd covalent geometry : bond 0.00334 (23873) covalent geometry : angle 0.56328 (32669) hydrogen bonds : bond 0.04022 ( 675) hydrogen bonds : angle 5.09593 ( 1849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 499 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.6052 (ttp80) cc_final: 0.5738 (tmm-80) REVERT: A 171 TYR cc_start: 0.7359 (t80) cc_final: 0.7038 (t80) REVERT: A 172 GLU cc_start: 0.7799 (tp30) cc_final: 0.7515 (mm-30) REVERT: A 178 TYR cc_start: 0.8068 (t80) cc_final: 0.7666 (t80) REVERT: A 218 LYS cc_start: 0.7710 (tppt) cc_final: 0.7349 (tppt) REVERT: A 281 LYS cc_start: 0.7040 (mmmt) cc_final: 0.6830 (mmmt) REVERT: A 315 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6188 (t70) REVERT: A 316 SER cc_start: 0.6944 (OUTLIER) cc_final: 0.6679 (p) REVERT: A 319 ASN cc_start: 0.7381 (t0) cc_final: 0.6688 (t0) REVERT: B 9 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 58 GLU cc_start: 0.7186 (tt0) cc_final: 0.6762 (tt0) REVERT: B 61 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7164 (mm-30) REVERT: B 65 LYS cc_start: 0.8660 (tppt) cc_final: 0.8429 (tppt) REVERT: B 90 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8178 (mtmm) REVERT: B 103 ASP cc_start: 0.7501 (m-30) cc_final: 0.7149 (m-30) REVERT: B 126 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7934 (ttmm) REVERT: B 143 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7977 (tmtt) REVERT: B 145 ILE cc_start: 0.7967 (mt) cc_final: 0.7511 (tt) REVERT: B 153 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7019 (t0) REVERT: B 219 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6696 (tt0) REVERT: B 228 GLU cc_start: 0.7395 (tt0) cc_final: 0.6989 (tt0) REVERT: B 244 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8158 (ttpp) REVERT: B 246 GLU cc_start: 0.7603 (mp0) cc_final: 0.7367 (mp0) REVERT: D 54 VAL cc_start: 0.7564 (OUTLIER) cc_final: 0.7065 (p) REVERT: D 200 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8389 (m-10) REVERT: D 229 MET cc_start: 0.7859 (tpp) cc_final: 0.7611 (tpp) REVERT: D 278 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7337 (mm-30) REVERT: D 284 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7422 (ttp80) REVERT: D 290 PHE cc_start: 0.8153 (m-80) cc_final: 0.7782 (m-10) REVERT: D 328 MET cc_start: 0.7289 (ptm) cc_final: 0.6910 (ptm) REVERT: D 329 PHE cc_start: 0.7996 (m-80) cc_final: 0.7586 (m-10) REVERT: E 28 THR cc_start: 0.8343 (p) cc_final: 0.8094 (p) REVERT: E 29 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7384 (mm-30) REVERT: E 43 PHE cc_start: 0.7993 (t80) cc_final: 0.7680 (t80) REVERT: E 123 ASP cc_start: 0.7807 (m-30) cc_final: 0.7596 (m-30) REVERT: E 200 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: E 222 GLU cc_start: 0.7899 (tt0) cc_final: 0.7559 (tt0) REVERT: E 253 LYS cc_start: 0.8015 (tptt) cc_final: 0.7685 (tttt) REVERT: E 303 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7775 (ttm-80) REVERT: E 309 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7634 (mt-10) REVERT: F 17 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5896 (pt0) REVERT: F 23 ARG cc_start: 0.8341 (ptp90) cc_final: 0.7431 (ptt-90) REVERT: F 29 GLU cc_start: 0.8051 (mp0) cc_final: 0.7814 (mp0) REVERT: F 144 ASN cc_start: 0.8323 (m-40) cc_final: 0.7842 (m110) REVERT: F 157 ILE cc_start: 0.8398 (mt) cc_final: 0.8117 (tt) REVERT: F 222 GLU cc_start: 0.7403 (tt0) cc_final: 0.7030 (tt0) REVERT: F 224 TYR cc_start: 0.8220 (m-80) cc_final: 0.7663 (m-10) REVERT: F 230 THR cc_start: 0.7841 (m) cc_final: 0.7358 (t) REVERT: F 239 LYS cc_start: 0.8326 (mptt) cc_final: 0.7906 (mptt) REVERT: F 253 LYS cc_start: 0.7952 (tptm) cc_final: 0.7672 (tttt) REVERT: F 272 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: F 284 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7692 (mtp180) REVERT: F 290 PHE cc_start: 0.8064 (m-80) cc_final: 0.7723 (m-80) REVERT: F 299 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7701 (mtmm) REVERT: F 305 ILE cc_start: 0.8310 (mm) cc_final: 0.8086 (mm) REVERT: F 315 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7390 (t0) REVERT: F 330 SER cc_start: 0.7197 (p) cc_final: 0.6931 (p) REVERT: C 29 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: C 38 LEU cc_start: 0.8152 (mp) cc_final: 0.7919 (mm) REVERT: C 77 GLN cc_start: 0.7510 (mm-40) cc_final: 0.6834 (mm-40) REVERT: C 90 THR cc_start: 0.8205 (m) cc_final: 0.7977 (m) REVERT: C 104 GLU cc_start: 0.8174 (mp0) cc_final: 0.7832 (mp0) REVERT: C 331 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8152 (pttm) REVERT: G 15 ARG cc_start: 0.6946 (mtm-85) cc_final: 0.6726 (mtm-85) REVERT: G 29 GLU cc_start: 0.7633 (mp0) cc_final: 0.7240 (mt-10) REVERT: G 45 LEU cc_start: 0.7772 (tt) cc_final: 0.7560 (tt) REVERT: G 103 LYS cc_start: 0.8510 (mttt) cc_final: 0.8199 (mttt) REVERT: G 186 ASN cc_start: 0.6473 (t0) cc_final: 0.6065 (t0) REVERT: H 21 PHE cc_start: 0.7367 (m-80) cc_final: 0.6876 (m-80) REVERT: H 94 ASP cc_start: 0.5051 (m-30) cc_final: 0.4671 (m-30) REVERT: H 229 MET cc_start: 0.1620 (tmm) cc_final: 0.1202 (tmm) REVERT: H 304 MET cc_start: 0.5303 (tpp) cc_final: 0.4971 (tpp) outliers start: 101 outliers final: 59 residues processed: 559 average time/residue: 0.1658 time to fit residues: 141.7872 Evaluate side-chains 559 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 486 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 275 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 169 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 203 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 44 ASN E 77 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.174944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134637 restraints weight = 35087.375| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.57 r_work: 0.3675 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23873 Z= 0.178 Angle : 0.583 9.482 32669 Z= 0.307 Chirality : 0.042 0.194 3627 Planarity : 0.004 0.055 3839 Dihedral : 17.524 172.023 4139 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.01 % Rotamer: Outliers : 4.98 % Allowed : 26.84 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2584 helix: 0.46 (0.18), residues: 781 sheet: 0.37 (0.28), residues: 365 loop : -1.15 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 204 TYR 0.029 0.001 TYR D 125 PHE 0.029 0.002 PHE E 172 TRP 0.025 0.001 TRP G 149 HIS 0.004 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00405 (23873) covalent geometry : angle 0.58325 (32669) hydrogen bonds : bond 0.04057 ( 675) hydrogen bonds : angle 5.03064 ( 1849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 496 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.5466 (mmt) cc_final: 0.5266 (mmt) REVERT: A 142 ARG cc_start: 0.6152 (ttp80) cc_final: 0.5834 (tmm-80) REVERT: A 171 TYR cc_start: 0.7436 (t80) cc_final: 0.7124 (t80) REVERT: A 172 GLU cc_start: 0.7808 (tp30) cc_final: 0.7527 (mm-30) REVERT: A 178 TYR cc_start: 0.8071 (t80) cc_final: 0.7694 (t80) REVERT: A 218 LYS cc_start: 0.7787 (tppt) cc_final: 0.7404 (tppt) REVERT: A 226 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7743 (ttmt) REVERT: A 281 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6845 (mmmt) REVERT: A 315 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6302 (t70) REVERT: A 316 SER cc_start: 0.7013 (OUTLIER) cc_final: 0.6752 (p) REVERT: A 319 ASN cc_start: 0.7449 (t0) cc_final: 0.6835 (t0) REVERT: B 58 GLU cc_start: 0.7208 (tt0) cc_final: 0.6814 (tt0) REVERT: B 61 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7239 (mm-30) REVERT: B 65 LYS cc_start: 0.8684 (tppt) cc_final: 0.8431 (tppt) REVERT: B 90 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8244 (mtmm) REVERT: B 103 ASP cc_start: 0.7559 (m-30) cc_final: 0.7219 (m-30) REVERT: B 143 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8000 (tttp) REVERT: B 145 ILE cc_start: 0.8018 (mt) cc_final: 0.7554 (tt) REVERT: B 153 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7030 (t0) REVERT: B 219 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6798 (tt0) REVERT: B 228 GLU cc_start: 0.7447 (tt0) cc_final: 0.7064 (tt0) REVERT: B 244 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8175 (ttpp) REVERT: B 246 GLU cc_start: 0.7657 (mp0) cc_final: 0.7386 (mp0) REVERT: D 29 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7458 (mm-30) REVERT: D 87 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7510 (mp0) REVERT: D 168 GLU cc_start: 0.7829 (tt0) cc_final: 0.7171 (mt-10) REVERT: D 200 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8425 (m-10) REVERT: D 222 GLU cc_start: 0.6263 (tt0) cc_final: 0.5911 (tt0) REVERT: D 229 MET cc_start: 0.7838 (tpp) cc_final: 0.7598 (tpp) REVERT: D 284 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7479 (ttp80) REVERT: D 290 PHE cc_start: 0.8150 (m-80) cc_final: 0.7800 (m-10) REVERT: D 328 MET cc_start: 0.7198 (ptm) cc_final: 0.6843 (ptm) REVERT: D 329 PHE cc_start: 0.8052 (m-80) cc_final: 0.7588 (m-10) REVERT: E 28 THR cc_start: 0.8384 (p) cc_final: 0.8154 (p) REVERT: E 29 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7366 (mm-30) REVERT: E 123 ASP cc_start: 0.7789 (m-30) cc_final: 0.7568 (m-30) REVERT: E 200 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8399 (m-10) REVERT: E 253 LYS cc_start: 0.8018 (tptt) cc_final: 0.7680 (tttt) REVERT: E 303 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7784 (ttm-80) REVERT: E 309 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7612 (mt-10) REVERT: F 23 ARG cc_start: 0.8404 (ptp90) cc_final: 0.7463 (ptt-90) REVERT: F 29 GLU cc_start: 0.8066 (mp0) cc_final: 0.7827 (mp0) REVERT: F 125 TYR cc_start: 0.7476 (t80) cc_final: 0.7160 (t80) REVERT: F 144 ASN cc_start: 0.8321 (m-40) cc_final: 0.7850 (m110) REVERT: F 157 ILE cc_start: 0.8393 (mt) cc_final: 0.8139 (tt) REVERT: F 222 GLU cc_start: 0.7458 (tt0) cc_final: 0.7042 (tt0) REVERT: F 224 TYR cc_start: 0.8188 (m-80) cc_final: 0.7534 (m-10) REVERT: F 272 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: F 278 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7571 (mm-30) REVERT: F 284 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7665 (mtp180) REVERT: F 304 MET cc_start: 0.7819 (mmm) cc_final: 0.7592 (tmm) REVERT: F 305 ILE cc_start: 0.8299 (mm) cc_final: 0.8040 (mm) REVERT: F 315 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7417 (t0) REVERT: F 330 SER cc_start: 0.7287 (p) cc_final: 0.7022 (p) REVERT: C 29 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: C 77 GLN cc_start: 0.7399 (mm-40) cc_final: 0.6877 (mm-40) REVERT: C 90 THR cc_start: 0.8202 (m) cc_final: 0.7968 (m) REVERT: C 104 GLU cc_start: 0.8197 (mp0) cc_final: 0.7859 (mp0) REVERT: C 181 THR cc_start: 0.8645 (t) cc_final: 0.8315 (p) REVERT: C 262 ASP cc_start: 0.8414 (t0) cc_final: 0.8202 (t0) REVERT: C 331 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8261 (pttp) REVERT: G 15 ARG cc_start: 0.6969 (mtm-85) cc_final: 0.6700 (mtm180) REVERT: G 29 GLU cc_start: 0.7623 (mp0) cc_final: 0.7190 (mt-10) REVERT: G 45 LEU cc_start: 0.7847 (tt) cc_final: 0.7641 (tt) REVERT: G 126 ILE cc_start: 0.6792 (mt) cc_final: 0.6459 (tt) REVERT: G 186 ASN cc_start: 0.6537 (t0) cc_final: 0.6147 (t0) REVERT: G 203 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7987 (mmtt) REVERT: H 21 PHE cc_start: 0.7443 (m-80) cc_final: 0.6947 (m-80) REVERT: H 94 ASP cc_start: 0.5105 (m-30) cc_final: 0.4700 (m-30) REVERT: H 184 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5542 (mp0) REVERT: H 229 MET cc_start: 0.1642 (tmm) cc_final: 0.1142 (tmm) REVERT: H 304 MET cc_start: 0.5359 (tpp) cc_final: 0.4885 (tpp) outliers start: 116 outliers final: 68 residues processed: 567 average time/residue: 0.1649 time to fit residues: 143.1549 Evaluate side-chains 570 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 490 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 275 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 147 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 265 optimal weight: 20.0000 chunk 255 optimal weight: 0.0770 chunk 170 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 238 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.177159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137243 restraints weight = 34997.699| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.58 r_work: 0.3687 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23873 Z= 0.143 Angle : 0.571 10.097 32669 Z= 0.298 Chirality : 0.042 0.182 3627 Planarity : 0.004 0.054 3839 Dihedral : 17.475 172.000 4139 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.26 % Favored : 95.63 % Rotamer: Outliers : 4.04 % Allowed : 27.74 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2584 helix: 0.58 (0.18), residues: 780 sheet: 0.38 (0.27), residues: 386 loop : -1.14 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 204 TYR 0.031 0.001 TYR A 294 PHE 0.027 0.002 PHE E 172 TRP 0.016 0.001 TRP G 149 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00327 (23873) covalent geometry : angle 0.57076 (32669) hydrogen bonds : bond 0.03858 ( 675) hydrogen bonds : angle 4.93574 ( 1849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 495 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7786 (tp30) cc_final: 0.7457 (mm-30) REVERT: A 178 TYR cc_start: 0.8026 (t80) cc_final: 0.7652 (t80) REVERT: A 218 LYS cc_start: 0.7835 (tppt) cc_final: 0.7455 (tppt) REVERT: A 226 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7635 (ttmt) REVERT: A 281 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6842 (mmmt) REVERT: A 315 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6312 (t70) REVERT: A 316 SER cc_start: 0.7035 (OUTLIER) cc_final: 0.6767 (p) REVERT: A 319 ASN cc_start: 0.7556 (t0) cc_final: 0.6893 (t0) REVERT: B 58 GLU cc_start: 0.7212 (tt0) cc_final: 0.6834 (tt0) REVERT: B 61 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 65 LYS cc_start: 0.8662 (tppt) cc_final: 0.8450 (tppt) REVERT: B 90 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8223 (mtmm) REVERT: B 103 ASP cc_start: 0.7562 (m-30) cc_final: 0.7249 (m-30) REVERT: B 143 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8043 (tmtt) REVERT: B 145 ILE cc_start: 0.7980 (mt) cc_final: 0.7774 (mm) REVERT: B 153 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7007 (t0) REVERT: B 219 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6698 (tt0) REVERT: B 228 GLU cc_start: 0.7459 (tt0) cc_final: 0.7084 (tt0) REVERT: B 244 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8195 (ttpp) REVERT: B 246 GLU cc_start: 0.7643 (mp0) cc_final: 0.7374 (mp0) REVERT: D 87 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7515 (mp0) REVERT: D 168 GLU cc_start: 0.7773 (tt0) cc_final: 0.7118 (mt-10) REVERT: D 200 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8347 (m-10) REVERT: D 222 GLU cc_start: 0.6161 (tt0) cc_final: 0.5876 (tt0) REVERT: D 241 PHE cc_start: 0.8446 (t80) cc_final: 0.8220 (t80) REVERT: D 278 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7432 (mm-30) REVERT: D 284 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7526 (ttp80) REVERT: D 290 PHE cc_start: 0.8113 (m-80) cc_final: 0.7805 (m-10) REVERT: D 328 MET cc_start: 0.7232 (ptm) cc_final: 0.6891 (ptm) REVERT: D 329 PHE cc_start: 0.8055 (m-80) cc_final: 0.7539 (m-10) REVERT: E 28 THR cc_start: 0.8332 (p) cc_final: 0.8074 (p) REVERT: E 29 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7377 (mm-30) REVERT: E 43 PHE cc_start: 0.8083 (t80) cc_final: 0.7718 (t80) REVERT: E 123 ASP cc_start: 0.7787 (m-30) cc_final: 0.7562 (m-30) REVERT: E 200 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8410 (m-10) REVERT: E 253 LYS cc_start: 0.8020 (tptt) cc_final: 0.7645 (tttp) REVERT: E 258 LEU cc_start: 0.8462 (mt) cc_final: 0.8256 (mp) REVERT: E 303 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7759 (ttm-80) REVERT: E 309 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7585 (mt-10) REVERT: F 23 ARG cc_start: 0.8357 (ptp90) cc_final: 0.7438 (ptt-90) REVERT: F 29 GLU cc_start: 0.8005 (mp0) cc_final: 0.7794 (mp0) REVERT: F 39 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7454 (mtmm) REVERT: F 125 TYR cc_start: 0.7451 (t80) cc_final: 0.7129 (t80) REVERT: F 157 ILE cc_start: 0.8421 (mt) cc_final: 0.8188 (tt) REVERT: F 222 GLU cc_start: 0.7403 (tt0) cc_final: 0.6990 (tt0) REVERT: F 224 TYR cc_start: 0.8173 (m-80) cc_final: 0.7515 (m-10) REVERT: F 272 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: F 278 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7511 (mm-30) REVERT: F 284 ARG cc_start: 0.7974 (ttm170) cc_final: 0.7683 (mtp180) REVERT: F 304 MET cc_start: 0.7803 (mmm) cc_final: 0.7558 (tmm) REVERT: F 305 ILE cc_start: 0.8284 (mm) cc_final: 0.8022 (mm) REVERT: F 315 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7426 (t0) REVERT: F 330 SER cc_start: 0.7214 (p) cc_final: 0.6951 (p) REVERT: C 29 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: C 77 GLN cc_start: 0.7337 (mm-40) cc_final: 0.6849 (mm-40) REVERT: C 90 THR cc_start: 0.8188 (m) cc_final: 0.7972 (m) REVERT: C 104 GLU cc_start: 0.8192 (mp0) cc_final: 0.7826 (mp0) REVERT: C 156 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7529 (mt-10) REVERT: C 163 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8195 (p) REVERT: C 181 THR cc_start: 0.8665 (t) cc_final: 0.8299 (p) REVERT: C 262 ASP cc_start: 0.8388 (t0) cc_final: 0.8156 (t0) REVERT: C 331 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8245 (pttp) REVERT: G 29 GLU cc_start: 0.7606 (mp0) cc_final: 0.7163 (mt-10) REVERT: G 45 LEU cc_start: 0.7867 (tt) cc_final: 0.7665 (tt) REVERT: G 121 LYS cc_start: 0.7348 (mmtt) cc_final: 0.7065 (mmmm) REVERT: G 186 ASN cc_start: 0.6537 (t0) cc_final: 0.6151 (t0) REVERT: H 21 PHE cc_start: 0.7427 (m-80) cc_final: 0.6943 (m-80) REVERT: H 94 ASP cc_start: 0.5065 (m-30) cc_final: 0.4662 (m-30) REVERT: H 191 GLU cc_start: 0.6393 (mt-10) cc_final: 0.6079 (mp0) REVERT: H 229 MET cc_start: 0.1694 (tmm) cc_final: 0.1204 (tmm) REVERT: H 304 MET cc_start: 0.5385 (tpp) cc_final: 0.4891 (tpp) outliers start: 94 outliers final: 60 residues processed: 554 average time/residue: 0.1633 time to fit residues: 139.3525 Evaluate side-chains 555 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 483 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 275 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 6 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 170 optimal weight: 0.0170 chunk 136 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.177329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137713 restraints weight = 34809.488| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.54 r_work: 0.3697 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23873 Z= 0.139 Angle : 0.569 10.445 32669 Z= 0.298 Chirality : 0.041 0.178 3627 Planarity : 0.004 0.055 3839 Dihedral : 17.429 172.176 4139 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.41 % Favored : 95.47 % Rotamer: Outliers : 4.04 % Allowed : 27.91 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2584 helix: 0.56 (0.18), residues: 782 sheet: 0.30 (0.26), residues: 423 loop : -1.06 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 204 TYR 0.017 0.001 TYR D 125 PHE 0.025 0.002 PHE E 172 TRP 0.017 0.001 TRP G 149 HIS 0.004 0.001 HIS H 317 Details of bonding type rmsd covalent geometry : bond 0.00316 (23873) covalent geometry : angle 0.56868 (32669) hydrogen bonds : bond 0.03788 ( 675) hydrogen bonds : angle 4.91462 ( 1849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 493 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8474 (tpp80) cc_final: 0.7872 (tpp80) REVERT: A 118 MET cc_start: 0.5549 (mmt) cc_final: 0.5340 (mtt) REVERT: A 171 TYR cc_start: 0.7318 (t80) cc_final: 0.6943 (t80) REVERT: A 172 GLU cc_start: 0.7768 (tp30) cc_final: 0.7451 (mm-30) REVERT: A 178 TYR cc_start: 0.8010 (t80) cc_final: 0.7671 (t80) REVERT: A 218 LYS cc_start: 0.7863 (tppt) cc_final: 0.7470 (tppt) REVERT: A 226 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7675 (ttmt) REVERT: A 281 LYS cc_start: 0.7128 (mmmt) cc_final: 0.6847 (mmmt) REVERT: A 315 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6287 (t70) REVERT: A 316 SER cc_start: 0.7063 (OUTLIER) cc_final: 0.6807 (p) REVERT: A 322 MET cc_start: 0.5441 (ptp) cc_final: 0.5003 (tmm) REVERT: B 58 GLU cc_start: 0.7231 (tt0) cc_final: 0.6842 (tt0) REVERT: B 61 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7048 (mm-30) REVERT: B 90 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8284 (mtmm) REVERT: B 143 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8012 (tmtt) REVERT: B 145 ILE cc_start: 0.7931 (mt) cc_final: 0.7707 (mm) REVERT: B 153 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7072 (t0) REVERT: B 219 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6692 (tt0) REVERT: B 228 GLU cc_start: 0.7464 (tt0) cc_final: 0.7088 (tt0) REVERT: B 244 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8156 (ttpp) REVERT: B 246 GLU cc_start: 0.7620 (mp0) cc_final: 0.7340 (mp0) REVERT: D 43 PHE cc_start: 0.8511 (t80) cc_final: 0.8158 (t80) REVERT: D 87 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7542 (mp0) REVERT: D 168 GLU cc_start: 0.7758 (tt0) cc_final: 0.7146 (mt-10) REVERT: D 191 GLU cc_start: 0.7540 (tt0) cc_final: 0.7150 (tt0) REVERT: D 200 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8315 (m-10) REVERT: D 222 GLU cc_start: 0.6113 (tt0) cc_final: 0.5853 (tt0) REVERT: D 278 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7391 (mm-30) REVERT: D 284 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7495 (ttp80) REVERT: D 290 PHE cc_start: 0.8091 (m-80) cc_final: 0.7739 (m-10) REVERT: D 328 MET cc_start: 0.7214 (ptm) cc_final: 0.6883 (ptm) REVERT: D 329 PHE cc_start: 0.8062 (m-80) cc_final: 0.7617 (m-10) REVERT: E 28 THR cc_start: 0.8309 (p) cc_final: 0.8042 (p) REVERT: E 29 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7350 (mm-30) REVERT: E 43 PHE cc_start: 0.8051 (t80) cc_final: 0.7766 (t80) REVERT: E 123 ASP cc_start: 0.7772 (m-30) cc_final: 0.7549 (m-30) REVERT: E 200 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8412 (m-10) REVERT: E 253 LYS cc_start: 0.8037 (tptt) cc_final: 0.7654 (tttp) REVERT: E 258 LEU cc_start: 0.8439 (mt) cc_final: 0.8090 (mp) REVERT: E 273 PHE cc_start: 0.7962 (p90) cc_final: 0.7638 (p90) REVERT: E 303 ARG cc_start: 0.8029 (mtp180) cc_final: 0.7701 (ttm-80) REVERT: E 309 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7559 (mt-10) REVERT: F 23 ARG cc_start: 0.8357 (ptp90) cc_final: 0.7428 (ptt-90) REVERT: F 29 GLU cc_start: 0.8023 (mp0) cc_final: 0.7801 (mp0) REVERT: F 125 TYR cc_start: 0.7487 (t80) cc_final: 0.7156 (t80) REVERT: F 157 ILE cc_start: 0.8440 (mt) cc_final: 0.8202 (tt) REVERT: F 222 GLU cc_start: 0.7362 (tt0) cc_final: 0.6933 (tt0) REVERT: F 224 TYR cc_start: 0.8155 (m-80) cc_final: 0.7475 (m-10) REVERT: F 272 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: F 278 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7553 (mm-30) REVERT: F 284 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7683 (mtp180) REVERT: F 305 ILE cc_start: 0.8304 (mm) cc_final: 0.8050 (mm) REVERT: F 315 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7435 (t0) REVERT: F 330 SER cc_start: 0.7206 (p) cc_final: 0.6956 (p) REVERT: C 29 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: C 77 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6825 (mm-40) REVERT: C 90 THR cc_start: 0.8201 (m) cc_final: 0.7982 (m) REVERT: C 104 GLU cc_start: 0.8203 (mp0) cc_final: 0.7827 (mp0) REVERT: C 144 ASN cc_start: 0.8245 (p0) cc_final: 0.8027 (p0) REVERT: C 156 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7535 (mt-10) REVERT: C 163 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8167 (p) REVERT: C 181 THR cc_start: 0.8681 (t) cc_final: 0.8329 (p) REVERT: C 262 ASP cc_start: 0.8404 (t0) cc_final: 0.8158 (t0) REVERT: C 331 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8233 (pttp) REVERT: G 29 GLU cc_start: 0.7581 (mp0) cc_final: 0.7044 (mp0) REVERT: G 121 LYS cc_start: 0.7305 (mmtt) cc_final: 0.7057 (mmmm) REVERT: G 186 ASN cc_start: 0.6571 (t0) cc_final: 0.6142 (t0) REVERT: G 311 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5194 (tp) REVERT: H 21 PHE cc_start: 0.7445 (m-80) cc_final: 0.6951 (m-80) REVERT: H 94 ASP cc_start: 0.5072 (m-30) cc_final: 0.4670 (m-30) REVERT: H 191 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6123 (mp0) REVERT: H 229 MET cc_start: 0.1742 (tmm) cc_final: 0.1246 (tmm) REVERT: H 277 VAL cc_start: -0.0964 (OUTLIER) cc_final: -0.1206 (p) outliers start: 94 outliers final: 64 residues processed: 555 average time/residue: 0.1601 time to fit residues: 137.8029 Evaluate side-chains 566 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 488 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 277 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 123 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 254 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 44 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** G 34 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 = 0.4259 r_free = 0.4259 target = 0.173627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.133740 restraints weight = 34997.468| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.52 r_work: 0.3666 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23873 Z= 0.222 Angle : 0.614 10.440 32669 Z= 0.321 Chirality : 0.044 0.183 3627 Planarity : 0.004 0.053 3839 Dihedral : 17.397 172.228 4139 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 3.86 % Allowed : 28.51 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2584 helix: 0.52 (0.19), residues: 770 sheet: 0.25 (0.28), residues: 378 loop : -1.21 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 204 TYR 0.021 0.002 TYR G 125 PHE 0.033 0.002 PHE E 95 TRP 0.025 0.002 TRP G 149 HIS 0.005 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00504 (23873) covalent geometry : angle 0.61403 (32669) hydrogen bonds : bond 0.04172 ( 675) hydrogen bonds : angle 5.04413 ( 1849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 506 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7414 (m-40) cc_final: 0.7013 (m110) REVERT: A 171 TYR cc_start: 0.7361 (t80) cc_final: 0.7046 (t80) REVERT: A 172 GLU cc_start: 0.7792 (tp30) cc_final: 0.7510 (mm-30) REVERT: A 178 TYR cc_start: 0.8031 (t80) cc_final: 0.7644 (t80) REVERT: A 218 LYS cc_start: 0.7899 (tppt) cc_final: 0.7524 (tppt) REVERT: A 226 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7646 (ttmt) REVERT: A 281 LYS cc_start: 0.7158 (mmmt) cc_final: 0.6896 (mmmt) REVERT: A 316 SER cc_start: 0.7079 (OUTLIER) cc_final: 0.6821 (p) REVERT: A 322 MET cc_start: 0.5251 (ptp) cc_final: 0.4768 (tmm) REVERT: B 58 GLU cc_start: 0.7275 (tt0) cc_final: 0.6884 (tt0) REVERT: B 61 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7057 (mm-30) REVERT: B 90 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8259 (mtmm) REVERT: B 103 ASP cc_start: 0.7555 (m-30) cc_final: 0.7313 (m-30) REVERT: B 143 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7881 (tmtt) REVERT: B 153 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7127 (t0) REVERT: B 206 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 213 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6808 (mptt) REVERT: B 219 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: B 228 GLU cc_start: 0.7479 (tt0) cc_final: 0.7130 (tt0) REVERT: B 246 GLU cc_start: 0.7642 (mp0) cc_final: 0.7361 (mp0) REVERT: D 200 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8293 (m-10) REVERT: D 222 GLU cc_start: 0.6401 (tt0) cc_final: 0.6033 (tt0) REVERT: D 290 PHE cc_start: 0.8168 (m-80) cc_final: 0.7835 (m-10) REVERT: D 328 MET cc_start: 0.7154 (ptm) cc_final: 0.6841 (ptm) REVERT: D 329 PHE cc_start: 0.8090 (m-80) cc_final: 0.7702 (m-10) REVERT: E 28 THR cc_start: 0.8373 (p) cc_final: 0.8157 (p) REVERT: E 29 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7556 (mm-30) REVERT: E 43 PHE cc_start: 0.8097 (t80) cc_final: 0.7893 (t80) REVERT: E 123 ASP cc_start: 0.7778 (m-30) cc_final: 0.7552 (m-30) REVERT: E 253 LYS cc_start: 0.8033 (tptt) cc_final: 0.7677 (tttt) REVERT: E 273 PHE cc_start: 0.8008 (p90) cc_final: 0.7678 (p90) REVERT: E 303 ARG cc_start: 0.8082 (mtp180) cc_final: 0.7744 (ttm-80) REVERT: E 309 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7557 (mt-10) REVERT: F 23 ARG cc_start: 0.8370 (ptp90) cc_final: 0.7387 (ptt-90) REVERT: F 29 GLU cc_start: 0.8075 (mp0) cc_final: 0.7832 (mp0) REVERT: F 125 TYR cc_start: 0.7495 (t80) cc_final: 0.7186 (t80) REVERT: F 157 ILE cc_start: 0.8426 (mt) cc_final: 0.8177 (tt) REVERT: F 222 GLU cc_start: 0.7444 (tt0) cc_final: 0.7010 (tt0) REVERT: F 224 TYR cc_start: 0.8202 (m-80) cc_final: 0.7524 (m-10) REVERT: F 272 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: F 278 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7571 (mm-30) REVERT: F 284 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7694 (mtp180) REVERT: F 305 ILE cc_start: 0.8332 (mm) cc_final: 0.8096 (mm) REVERT: F 315 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7506 (t0) REVERT: F 330 SER cc_start: 0.7339 (p) cc_final: 0.7107 (p) REVERT: C 77 GLN cc_start: 0.7399 (mm-40) cc_final: 0.6927 (mm-40) REVERT: C 90 THR cc_start: 0.8236 (m) cc_final: 0.8032 (m) REVERT: C 104 GLU cc_start: 0.8225 (mp0) cc_final: 0.7824 (mp0) REVERT: C 144 ASN cc_start: 0.8260 (p0) cc_final: 0.8060 (p0) REVERT: C 156 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7532 (mt-10) REVERT: C 163 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8171 (p) REVERT: C 181 THR cc_start: 0.8727 (t) cc_final: 0.8397 (p) REVERT: C 262 ASP cc_start: 0.8462 (t0) cc_final: 0.8201 (t0) REVERT: G 15 ARG cc_start: 0.6896 (mtm-85) cc_final: 0.6678 (mtm180) REVERT: G 29 GLU cc_start: 0.7605 (mp0) cc_final: 0.7178 (mt-10) REVERT: G 137 ARG cc_start: 0.6566 (ttm170) cc_final: 0.6056 (ttm170) REVERT: G 311 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.4999 (tp) REVERT: H 21 PHE cc_start: 0.7483 (m-80) cc_final: 0.6960 (m-80) REVERT: H 94 ASP cc_start: 0.5222 (m-30) cc_final: 0.4765 (m-30) REVERT: H 184 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5759 (mp0) REVERT: H 191 GLU cc_start: 0.6460 (mt-10) cc_final: 0.6134 (mp0) REVERT: H 229 MET cc_start: 0.1679 (tmm) cc_final: 0.1171 (tmm) outliers start: 90 outliers final: 60 residues processed: 565 average time/residue: 0.1629 time to fit residues: 141.5605 Evaluate side-chains 563 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 492 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 167 optimal weight: 0.0770 chunk 196 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 51 optimal weight: 0.0980 chunk 264 optimal weight: 7.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 44 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.137509 restraints weight = 34803.829| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.53 r_work: 0.3707 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23873 Z= 0.120 Angle : 0.584 12.456 32669 Z= 0.303 Chirality : 0.041 0.177 3627 Planarity : 0.004 0.052 3839 Dihedral : 17.316 172.086 4139 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 2.71 % Allowed : 30.10 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2584 helix: 0.55 (0.19), residues: 776 sheet: 0.30 (0.26), residues: 422 loop : -1.09 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 204 TYR 0.024 0.001 TYR C 224 PHE 0.026 0.002 PHE D 43 TRP 0.023 0.001 TRP G 264 HIS 0.011 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00271 (23873) covalent geometry : angle 0.58399 (32669) hydrogen bonds : bond 0.03815 ( 675) hydrogen bonds : angle 4.93966 ( 1849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 502 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7343 (m-40) cc_final: 0.6920 (m110) REVERT: A 55 TYR cc_start: 0.8048 (t80) cc_final: 0.7675 (t80) REVERT: A 88 ARG cc_start: 0.8462 (tpp80) cc_final: 0.7792 (tpp80) REVERT: A 118 MET cc_start: 0.5548 (mmt) cc_final: 0.5311 (mtt) REVERT: A 172 GLU cc_start: 0.7726 (tp30) cc_final: 0.7450 (mm-30) REVERT: A 178 TYR cc_start: 0.8006 (t80) cc_final: 0.7704 (t80) REVERT: A 218 LYS cc_start: 0.7890 (tppt) cc_final: 0.7491 (tppt) REVERT: A 226 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7894 (ttmt) REVERT: A 281 LYS cc_start: 0.7138 (mmmt) cc_final: 0.6829 (mmmt) REVERT: A 315 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6318 (t70) REVERT: A 316 SER cc_start: 0.7104 (OUTLIER) cc_final: 0.6843 (p) REVERT: A 322 MET cc_start: 0.5177 (ptp) cc_final: 0.4741 (tmm) REVERT: B 58 GLU cc_start: 0.7162 (tt0) cc_final: 0.6821 (tt0) REVERT: B 61 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 90 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8285 (mtmm) REVERT: B 97 MET cc_start: 0.7776 (mmm) cc_final: 0.7372 (mmm) REVERT: B 103 ASP cc_start: 0.7531 (m-30) cc_final: 0.7257 (m-30) REVERT: B 143 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8106 (tttm) REVERT: B 153 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.7006 (t0) REVERT: B 206 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7471 (mt-10) REVERT: B 219 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6700 (tt0) REVERT: B 228 GLU cc_start: 0.7475 (tt0) cc_final: 0.7103 (tt0) REVERT: B 244 LYS cc_start: 0.8385 (ttpp) cc_final: 0.7847 (ptpp) REVERT: B 246 GLU cc_start: 0.7560 (mp0) cc_final: 0.7302 (mp0) REVERT: D 191 GLU cc_start: 0.7536 (tt0) cc_final: 0.7150 (tt0) REVERT: D 200 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8246 (m-10) REVERT: D 222 GLU cc_start: 0.6140 (tt0) cc_final: 0.5914 (tt0) REVERT: D 242 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8102 (tttm) REVERT: D 284 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7469 (ttp80) REVERT: D 290 PHE cc_start: 0.8137 (m-80) cc_final: 0.7783 (m-80) REVERT: D 328 MET cc_start: 0.7223 (ptm) cc_final: 0.6901 (ptm) REVERT: D 329 PHE cc_start: 0.8070 (m-80) cc_final: 0.7600 (m-10) REVERT: E 28 THR cc_start: 0.8296 (p) cc_final: 0.7994 (p) REVERT: E 29 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7406 (mm-30) REVERT: E 123 ASP cc_start: 0.7762 (m-30) cc_final: 0.7539 (m-30) REVERT: E 253 LYS cc_start: 0.8027 (tptt) cc_final: 0.7624 (tttp) REVERT: E 284 ARG cc_start: 0.8097 (ptp-170) cc_final: 0.7563 (ptt180) REVERT: E 303 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7650 (ttm-80) REVERT: E 309 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7550 (mt-10) REVERT: F 23 ARG cc_start: 0.8295 (ptp90) cc_final: 0.7436 (ptt-90) REVERT: F 29 GLU cc_start: 0.8006 (mp0) cc_final: 0.7786 (mp0) REVERT: F 121 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8094 (mmtt) REVERT: F 125 TYR cc_start: 0.7469 (t80) cc_final: 0.7225 (t80) REVERT: F 144 ASN cc_start: 0.8342 (m-40) cc_final: 0.7930 (m110) REVERT: F 157 ILE cc_start: 0.8446 (mt) cc_final: 0.8217 (tt) REVERT: F 222 GLU cc_start: 0.7337 (tt0) cc_final: 0.6909 (tt0) REVERT: F 224 TYR cc_start: 0.8148 (m-80) cc_final: 0.7509 (m-10) REVERT: F 272 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: F 278 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7477 (mm-30) REVERT: F 284 ARG cc_start: 0.7906 (ttm170) cc_final: 0.7655 (mtp180) REVERT: F 304 MET cc_start: 0.7950 (tmm) cc_final: 0.6267 (tmm) REVERT: F 315 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7461 (t0) REVERT: F 330 SER cc_start: 0.7174 (p) cc_final: 0.6926 (p) REVERT: C 77 GLN cc_start: 0.7261 (mm-40) cc_final: 0.6813 (mm-40) REVERT: C 90 THR cc_start: 0.8190 (m) cc_final: 0.7973 (m) REVERT: C 104 GLU cc_start: 0.8189 (mp0) cc_final: 0.7747 (mp0) REVERT: C 144 ASN cc_start: 0.8208 (p0) cc_final: 0.7816 (p0) REVERT: C 156 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7563 (mt-10) REVERT: C 163 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8125 (p) REVERT: C 181 THR cc_start: 0.8645 (t) cc_final: 0.8312 (p) REVERT: G 15 ARG cc_start: 0.6756 (mtm-85) cc_final: 0.6554 (mtm180) REVERT: G 29 GLU cc_start: 0.7588 (mp0) cc_final: 0.7058 (mp0) REVERT: G 264 TRP cc_start: 0.7524 (m-90) cc_final: 0.7246 (m-90) REVERT: H 20 SER cc_start: 0.6218 (m) cc_final: 0.5438 (t) REVERT: H 21 PHE cc_start: 0.7402 (m-80) cc_final: 0.6823 (m-80) REVERT: H 94 ASP cc_start: 0.5038 (m-30) cc_final: 0.4650 (m-30) REVERT: H 191 GLU cc_start: 0.6563 (mt-10) cc_final: 0.6249 (mp0) REVERT: H 229 MET cc_start: 0.1628 (tmm) cc_final: 0.1126 (tmm) REVERT: H 277 VAL cc_start: -0.1065 (OUTLIER) cc_final: -0.1317 (p) outliers start: 63 outliers final: 44 residues processed: 541 average time/residue: 0.1654 time to fit residues: 137.1466 Evaluate side-chains 545 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 491 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 93 optimal weight: 0.7980 chunk 233 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 44 ASN E 77 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN C 80 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.175550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135802 restraints weight = 34876.114| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.52 r_work: 0.3689 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23873 Z= 0.159 Angle : 0.591 11.581 32669 Z= 0.306 Chirality : 0.042 0.208 3627 Planarity : 0.004 0.052 3839 Dihedral : 17.258 172.338 4139 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 3.01 % Allowed : 29.54 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2584 helix: 0.58 (0.19), residues: 782 sheet: 0.30 (0.27), residues: 410 loop : -1.12 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 137 TYR 0.024 0.001 TYR C 224 PHE 0.034 0.002 PHE D 43 TRP 0.020 0.001 TRP G 149 HIS 0.004 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00368 (23873) covalent geometry : angle 0.59058 (32669) hydrogen bonds : bond 0.03825 ( 675) hydrogen bonds : angle 4.90404 ( 1849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6884.97 seconds wall clock time: 118 minutes 33.03 seconds (7113.03 seconds total)