Starting phenix.real_space_refine on Wed Jun 18 16:06:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdy_60017/06_2025/8zdy_60017_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdy_60017/06_2025/8zdy_60017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zdy_60017/06_2025/8zdy_60017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdy_60017/06_2025/8zdy_60017.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdy_60017/06_2025/8zdy_60017_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdy_60017/06_2025/8zdy_60017_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.034 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 58 5.49 5 S 91 5.16 5 C 13569 2.51 5 N 3669 2.21 5 O 4177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21564 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2556 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2490 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 15, 'TRANS': 305} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2507 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2520 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 307} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2413 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "F" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2249 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2436 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 152 Chain: "H" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1856 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1288 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "L" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1249 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 10, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 30, 'rna3p': 27} Chain breaks: 1 Time building chain proxies: 13.16, per 1000 atoms: 0.61 Number of scatterers: 21564 At special positions: 0 Unit cell: (119.84, 144.664, 144.664, 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 91 16.00 P 58 15.00 O 4177 8.00 N 3669 7.00 C 13569 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: 4.87 Conformation dependent library (CDL) restraints added in 2.7 seconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5008 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 32 sheets defined 31.6% alpha, 9.3% beta 6 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 6.64 Creating SS restraints... Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.615A pdb=" N ILE A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 312 through 326 removed outlier: 3.618A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 66 through 73 removed outlier: 3.560A pdb=" N ASP B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.734A pdb=" N GLY B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 296 through 305 removed outlier: 5.392A pdb=" N ASP B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.597A pdb=" N MET B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.746A pdb=" N ILE B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 63 through 72 removed outlier: 3.840A pdb=" N GLU C 68 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET C 72 " --> pdb=" O GLU C 68 " (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 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 186 through 202 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 272 removed outlier: 3.539A pdb=" N TYR C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 removed outlier: 4.292A pdb=" N ASP C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.540A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.578A pdb=" N ALA D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.603A pdb=" N THR D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.977A pdb=" N TYR D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 removed outlier: 4.572A pdb=" N ASP D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.646A pdb=" N ALA E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 153 removed outlier: 3.638A pdb=" N LEU E 148 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 202 Processing helix chain 'E' and resid 250 through 260 Processing helix chain 'E' and resid 297 through 306 removed outlier: 3.518A pdb=" N ASP E 302 " --> pdb=" O TYR E 298 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.644A pdb=" N ALA E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 324 " --> pdb=" O MET E 320 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 250 through 259 Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.747A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 302 Processing helix chain 'F' and resid 312 through 324 removed outlier: 3.768A pdb=" N TYR F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 10 removed outlier: 3.787A pdb=" N ILE G 10 " --> pdb=" O ILE G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 31 removed outlier: 3.671A pdb=" N GLU G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'G' and resid 103 through 109 Processing helix chain 'G' and resid 112 through 122 Processing helix chain 'G' and resid 124 through 134 removed outlier: 3.750A pdb=" N ILE G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 181 removed outlier: 3.538A pdb=" N ASN G 170 " --> pdb=" O SER G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 206 removed outlier: 3.592A pdb=" N SER G 204 " --> pdb=" O SER G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.523A pdb=" N ILE G 259 " --> pdb=" O LEU G 255 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY G 263 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 277 Processing helix chain 'G' and resid 281 through 290 removed outlier: 4.220A pdb=" N VAL G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 340 removed outlier: 3.629A pdb=" N PHE G 339 " --> pdb=" O HIS G 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 46 removed outlier: 3.677A pdb=" N PHE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA H 36 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 removed outlier: 4.083A pdb=" N GLU H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 154 Processing helix chain 'H' and resid 163 through 169 removed outlier: 3.744A pdb=" N LEU H 167 " --> pdb=" O ARG H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 184 Processing helix chain 'H' and resid 236 through 240 Processing helix chain 'I' and resid 15 through 23 removed outlier: 3.838A pdb=" N ILE I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 35 removed outlier: 4.124A pdb=" N VAL I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER I 30 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 71 Processing helix chain 'I' and resid 72 through 77 removed outlier: 3.786A pdb=" N LEU I 77 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.680A pdb=" N ARG I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 140 removed outlier: 3.946A pdb=" N GLU I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 45 through 46 current: chain 'A' and resid 167 through 168 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 262 removed outlier: 3.540A pdb=" N ILE A 275 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 45 through 46 current: chain 'B' and resid 172 through 173 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 228 removed outlier: 4.409A pdb=" N LYS B 239 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AB2, 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 167 through 173 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 173 current: chain 'C' and resid 239 through 243 removed outlier: 4.450A pdb=" N PHE C 241 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.224A pdb=" N SER D 20 " --> pdb=" O TYR D 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 172 through 173 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 55 removed outlier: 4.336A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 260 through 262 removed outlier: 3.544A pdb=" N ILE D 275 " --> pdb=" O ASP D 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 21 removed outlier: 6.682A pdb=" N SER E 20 " --> pdb=" O TYR E 107 " (cutoff:3.500A) Processing sheet with id=AB9, 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=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 21 removed outlier: 6.350A pdb=" N SER F 20 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing sheet with id=AC3, 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 172 through 173 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AC6, first strand: chain 'G' and resid 35 through 37 removed outlier: 3.596A pdb=" N ASP G 78 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AC8, first strand: chain 'G' and resid 148 through 154 removed outlier: 4.325A pdb=" N LYS G 148 " --> pdb=" O ILE G 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 157 through 163 current: chain 'H' and resid 215 through 229 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 215 through 229 current: chain 'H' and resid 249 through 253 Processing sheet with id=AC9, first strand: chain 'G' and resid 187 through 188 Processing sheet with id=AD1, first strand: chain 'G' and resid 301 through 305 Processing sheet with id=AD2, first strand: chain 'H' and resid 2 through 17 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 17 current: chain 'H' and resid 101 through 114 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 66 through 68 Processing sheet with id=AD4, first strand: chain 'I' and resid 40 through 42 Processing sheet with id=AD5, first strand: chain 'I' and resid 99 through 101 removed outlier: 4.006A pdb=" N ALA I 142 " --> pdb=" O LEU I 159 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 5.85 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: 5122 1.33 - 1.46: 5281 1.46 - 1.58: 11497 1.58 - 1.70: 118 1.70 - 1.82: 137 Bond restraints: 22155 Sorted by residual: bond pdb=" C PRO G 308 " pdb=" N LEU G 309 " ideal model delta sigma weight residual 1.335 1.434 -0.100 1.25e-02 6.40e+03 6.37e+01 bond pdb=" C SER B 110 " pdb=" N ASP B 111 " ideal model delta sigma weight residual 1.330 1.434 -0.104 1.31e-02 5.83e+03 6.26e+01 bond pdb=" C LEU G 323 " pdb=" N SER G 324 " ideal model delta sigma weight residual 1.330 1.426 -0.096 1.31e-02 5.83e+03 5.34e+01 bond pdb=" C ASP B 198 " pdb=" N THR B 199 " ideal model delta sigma weight residual 1.335 1.431 -0.096 1.38e-02 5.25e+03 4.84e+01 bond pdb=" C GLU F 124 " pdb=" N TYR F 125 " ideal model delta sigma weight residual 1.334 1.238 0.096 1.41e-02 5.03e+03 4.61e+01 ... (remaining 22150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 28260 2.57 - 5.14: 1764 5.14 - 7.71: 261 7.71 - 10.28: 59 10.28 - 12.85: 5 Bond angle restraints: 30349 Sorted by residual: angle pdb=" O ASP B 198 " pdb=" C ASP B 198 " pdb=" N THR B 199 " ideal model delta sigma weight residual 122.15 129.40 -7.25 1.14e+00 7.69e-01 4.04e+01 angle pdb=" N THR E 263 " pdb=" CA THR E 263 " pdb=" C THR E 263 " ideal model delta sigma weight residual 114.31 106.46 7.85 1.29e+00 6.01e-01 3.70e+01 angle pdb=" O LEU G 169 " pdb=" C LEU G 169 " pdb=" N ASN G 170 " ideal model delta sigma weight residual 122.12 128.54 -6.42 1.06e+00 8.90e-01 3.67e+01 angle pdb=" O LYS C 167 " pdb=" C LYS C 167 " pdb=" N GLU C 168 " ideal model delta sigma weight residual 123.27 116.21 7.06 1.17e+00 7.31e-01 3.64e+01 angle pdb=" N THR C 199 " pdb=" CA THR C 199 " pdb=" C THR C 199 " ideal model delta sigma weight residual 113.28 106.10 7.18 1.22e+00 6.72e-01 3.47e+01 ... (remaining 30344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 12791 34.43 - 68.87: 536 68.87 - 103.30: 32 103.30 - 137.73: 0 137.73 - 172.17: 5 Dihedral angle restraints: 13364 sinusoidal: 5619 harmonic: 7745 Sorted by residual: dihedral pdb=" O4' C L 38 " pdb=" C1' C L 38 " pdb=" N1 C L 38 " pdb=" C2 C L 38 " ideal model delta sinusoidal sigma weight residual 200.00 35.34 164.66 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' U L 37 " pdb=" C1' U L 37 " pdb=" N1 U L 37 " pdb=" C2 U L 37 " ideal model delta sinusoidal sigma weight residual 200.00 41.16 158.84 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' C L 52 " pdb=" C1' C L 52 " pdb=" N1 C L 52 " pdb=" C2 C L 52 " ideal model delta sinusoidal sigma weight residual -128.00 39.83 -167.83 1 1.70e+01 3.46e-03 6.57e+01 ... (remaining 13361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2916 0.104 - 0.208: 510 0.208 - 0.313: 29 0.313 - 0.417: 2 0.417 - 0.521: 19 Chirality restraints: 3476 Sorted by residual: chirality pdb=" P C L 52 " pdb=" OP1 C L 52 " pdb=" OP2 C L 52 " pdb=" O5' C L 52 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" P G L 25 " pdb=" OP1 G L 25 " pdb=" OP2 G L 25 " pdb=" O5' G L 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" P C L 35 " pdb=" OP1 C L 35 " pdb=" OP2 C L 35 " pdb=" O5' C L 35 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 3473 not shown) Planarity restraints: 3676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 280 " -0.566 9.50e-02 1.11e+02 2.54e-01 3.94e+01 pdb=" NE ARG G 280 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG G 280 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG G 280 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 280 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 272 " 0.475 9.50e-02 1.11e+02 2.13e-01 2.79e+01 pdb=" NE ARG G 272 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG G 272 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG G 272 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 272 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 288 " 0.087 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO D 289 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " 0.068 5.00e-02 4.00e+02 ... (remaining 3673 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4598 2.79 - 3.31: 20074 3.31 - 3.84: 36453 3.84 - 4.37: 43481 4.37 - 4.90: 70470 Nonbonded interactions: 175076 Sorted by model distance: nonbonded pdb=" O GLU B 278 " pdb=" OH TYR B 318 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR D 35 " pdb=" OG1 THR D 90 " model vdw 2.264 3.040 nonbonded pdb=" O LEU D 55 " pdb=" O2' G L 51 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 50 " pdb=" O SER B 81 " model vdw 2.296 3.040 nonbonded pdb=" O GLU E 61 " pdb=" OH TYR F 280 " model vdw 2.305 3.040 ... (remaining 175071 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 'A' and (resid 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or nam \ e CA or name C or name O or name CB )) or resid 18 through 28 or (resid 29 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or r \ esid 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or \ resid 37 or (resid 38 through 39 and (name N or name CA or name C or name O or \ name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 or (resid 81 and (name N or name CA or na \ me C or name O or name CB )) or resid 82 through 86 or (resid 87 through 88 and \ (name N or name CA or name C or name O or name CB )) or resid 89 through 105 or \ (resid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 \ or (resid 108 and (name N or name CA or name C or name O or name CB )) or resid \ 109 through 110 or (resid 111 and (name N or name CA or name C or name O or nam \ e CB )) or resid 112 through 120 or (resid 121 and (name N or name CA or name C \ or name O or name CB )) or resid 122 or (resid 123 through 124 and (name N or na \ me CA or name C or name O or name CB )) or resid 125 through 127 or (resid 128 t \ hrough 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 139 or (resid 140 and (name N or name CA or name C or name O or name CB \ )) or resid 141 through 165 or (resid 166 and (name N or name CA or name C or n \ ame O or name CB )) or resid 167 through 178 or (resid 179 through 180 and (name \ N or name CA or name C or name O or name CB )) or resid 181 through 183 or (res \ id 184 through 185 and (name N or name CA or name C or name O or name CB )) or r \ esid 186 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 197 or (resid 198 through 199 and (name N or na \ me CA or name C or name O or name CB )) or resid 200 through 204 or (resid 205 a \ nd (name N or name CA or name C or name O or name CB )) or resid 206 through 220 \ or (resid 221 through 222 and (name N or name CA or name C or name O or name CB \ )) or resid 223 through 228 or (resid 229 and (name N or name CA or name C or n \ ame O or name CB )) or resid 237 through 238 or (resid 239 and (name N or name C \ A or name C or name O or name CB )) or resid 240 through 241 or (resid 242 and ( \ name N or name CA or name C or name O or name CB )) or resid 243 through 271 or \ (resid 272 and (name N or name CA or name C or name O or name CB )) or resid 273 \ through 277 or (resid 278 and (name N or name CA or name C or name O or name CB \ )) or resid 279 through 283 or (resid 284 and (name N or name CA or name C or n \ ame O or name CB )) or resid 285 or (resid 286 and (name N or name CA or name C \ or name O or name CB )) or resid 287 through 303 or (resid 304 through 305 and ( \ name N or name CA or name C or name O or name CB )) or resid 306 or (resid 307 a \ nd (name N or name CA or name C or name O or name CB )) or resid 308 through 309 \ or (resid 310 and (name N or name CA or name C or name O or name CB )) or resid \ 311 through 314 or (resid 315 and (name N or name CA or name C or name O or nam \ e CB )) or resid 316 through 327 or (resid 328 through 329 and (name N or name C \ A or name C or name O or name CB )) or resid 330)) selection = (chain 'B' and (resid 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or nam \ e CA or name C or name O or name CB )) or resid 18 through 28 or (resid 29 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or r \ esid 35 through 37 or (resid 38 through 39 and (name N or name CA or name C or n \ ame O or name CB )) or resid 40 through 50 or (resid 51 and (name N or name CA o \ r name C or name O or name CB )) or (resid 79 and (name N or name CA or name C o \ r name O or name CB )) or resid 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 87 or (resid 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 105 or (resid 106 and \ (name N or name CA or name C or name O or name CB )) or resid 107 or (resid 108 \ and (name N or name CA or name C or name O or name CB )) or resid 109 through 12 \ 0 or (resid 121 and (name N or name CA or name C or name O or name CB )) or resi \ d 122 or (resid 123 through 124 and (name N or name CA or name C or name O or na \ me CB )) or resid 125 through 149 or (resid 150 and (name N or name CA or name C \ or name O or name CB )) or resid 151 through 155 or (resid 156 and (name N or n \ ame CA or name C or name O or name CB )) or resid 157 through 178 or (resid 179 \ through 180 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 1 through 183 or (resid 184 through 185 and (name N or name CA or name C or name \ O or name CB )) or resid 186 through 190 or (resid 191 and (name N or name CA o \ r name C or name O or name CB )) or resid 192 through 197 or (resid 198 through \ 199 and (name N or name CA or name C or name O or name CB )) or resid 200 throug \ h 204 or (resid 205 and (name N or name CA or name C or name O or name CB )) or \ resid 206 through 220 or (resid 221 through 222 and (name N or name CA or name C \ or name O or name CB )) or resid 223 through 229 or resid 237 through 241 or (r \ esid 242 and (name N or name CA or name C or name O or name CB )) or resid 243 t \ hrough 271 or (resid 272 and (name N or name CA or name C or name O or name CB ) \ ) or resid 273 through 277 or (resid 278 and (name N or name CA or name C or nam \ e O or name CB )) or resid 279 through 283 or (resid 284 and (name N or name CA \ or name C or name O or name CB )) or resid 285 or (resid 286 and (name N or name \ CA or name C or name O or name CB )) or resid 287 through 303 or (resid 304 thr \ ough 305 and (name N or name CA or name C or name O or name CB )) or resid 306 o \ r (resid 307 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 08 through 309 or (resid 310 and (name N or name CA or name C or name O or name \ CB )) or resid 311 through 327 or (resid 328 through 329 and (name N or name CA \ or name C or name O or name CB )) or resid 330)) selection = (chain 'C' and (resid 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 or (resid 36 and (name N or n \ ame CA or name C or name O or name CB )) or resid 37 or (resid 38 through 39 and \ (name N or name CA or name C or name O or name CB )) or resid 40 through 43 or \ (resid 44 and (name N or name CA or name C or name O or name CB )) or resid 45 t \ hrough 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) \ or (resid 79 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 0 or (resid 81 and (name N or name CA or name C or name O or name CB )) or resid \ 82 through 86 or (resid 87 through 88 and (name N or name CA or name C or name \ O or name CB )) or resid 89 through 105 or (resid 106 and (name N or name CA or \ name C or name O or name CB )) or resid 107 or (resid 108 and (name N or name CA \ or name C or name O or name CB )) or resid 109 through 110 or (resid 111 and (n \ ame N or name CA or name C or name O or name CB )) or resid 112 through 120 or ( \ resid 121 and (name N or name CA or name C or name O or name CB )) or resid 122 \ or (resid 123 through 124 and (name N or name CA or name C or name O or name CB \ )) or resid 125 through 127 or (resid 128 through 129 and (name N or name CA or \ name C or name O or name CB )) or resid 130 through 139 or (resid 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 149 or (resi \ d 150 and (name N or name CA or name C or name O or name CB )) or resid 151 thro \ ugh 155 or (resid 156 and (name N or name CA or name C or name O or name CB )) o \ r resid 157 through 165 or (resid 166 and (name N or name CA or name C or name O \ or name CB )) or resid 167 or (resid 168 and (name N or name CA or name C or na \ me O or name CB )) or resid 169 through 178 or (resid 179 through 180 and (name \ N or name CA or name C or name O or name CB )) or resid 181 through 183 or (resi \ d 184 through 185 and (name N or name CA or name C or name O or name CB )) or re \ sid 186 through 197 or (resid 198 through 199 and (name N or name CA or name C o \ r name O or name CB )) or resid 200 through 204 or (resid 205 and (name N or nam \ e CA or name C or name O or name CB )) or resid 206 through 220 or (resid 221 th \ rough 222 and (name N or name CA or name C or name O or name CB )) or resid 223 \ through 228 or (resid 229 and (name N or name CA or name C or name O or name CB \ )) or resid 237 through 238 or (resid 239 and (name N or name CA or name C or na \ me O or name CB )) or resid 240 through 241 or (resid 242 and (name N or name CA \ or name C or name O or name CB )) or resid 243 through 283 or (resid 284 and (n \ ame N or name CA or name C or name O or name CB )) or resid 285 or (resid 286 an \ d (name N or name CA or name C or name O or name CB )) or resid 287 through 292 \ or (resid 293 and (name N or name CA or name C or name O or name CB )) or resid \ 294 through 303 or (resid 304 through 305 and (name N or name CA or name C or na \ me O or name CB )) or resid 306 or (resid 307 and (name N or name CA or name C o \ r name O or name CB )) or resid 308 through 314 or (resid 315 and (name N or nam \ e CA or name C or name O or name CB )) or resid 316 through 327 or (resid 328 th \ rough 329 and (name N or name CA or name C or name O or name CB )) or resid 330) \ ) selection = (chain 'D' and (resid 11 through 28 or (resid 29 through 30 and (name N or name \ CA or name C or name O or name CB )) or resid 31 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 or (resid 38 thr \ ough 39 and (name N or name CA or name C or name O or name CB )) or resid 40 thr \ ough 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or \ resid 45 through 51 or resid 79 through 86 or (resid 87 through 88 and (name N \ or name CA or name C or name O or name CB )) or resid 89 through 105 or (resid 1 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 107 or (res \ id 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ ough 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) \ or resid 112 through 120 or (resid 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 139 or (resid 140 and (name N or name CA or \ name C or name O or name CB )) or resid 141 through 149 or (resid 150 and (name \ N or name CA or name C or name O or name CB )) or resid 151 through 155 or (res \ id 156 and (name N or name CA or name C or name O or name CB )) or resid 157 thr \ ough 164 or (resid 165 through 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 or (resid 168 and (name N or name CA or name C or name \ O or name CB )) or resid 169 through 178 or (resid 179 through 180 and (name N o \ r name CA or name C or name O or name CB )) or resid 181 through 183 or (resid 1 \ 84 through 185 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or nam \ e CB )) or resid 192 through 204 or (resid 205 and (name N or name CA or name C \ or name O or name CB )) or resid 206 through 220 or (resid 221 through 222 and ( \ name N or name CA or name C or name O or name CB )) or resid 223 through 229 or \ resid 237 through 238 or (resid 239 and (name N or name CA or name C or name O o \ r name CB )) or resid 240 through 271 or (resid 272 and (name N or name CA or na \ me C or name O or name CB )) or resid 273 through 277 or (resid 278 and (name N \ or name CA or name C or name O or name CB )) or resid 279 through 285 or (resid \ 286 and (name N or name CA or name C or name O or name CB )) or resid 287 throug \ h 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or \ resid 294 through 303 or (resid 304 through 305 and (name N or name CA or name C \ or name O or name CB )) or resid 306 or (resid 307 and (name N or name CA or na \ me C or name O or name CB )) or resid 308 through 309 or (resid 310 and (name N \ or name CA or name C or name O or name CB )) or resid 311 through 314 or (resid \ 315 and (name N or name CA or name C or name O or name CB )) or resid 316 throug \ h 330)) selection = (chain 'E' and (resid 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or nam \ e CA or name C or name O or name CB )) or resid 18 through 28 or (resid 29 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or r \ esid 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or \ resid 37 or (resid 38 through 39 and (name N or name CA or name C or name O or \ name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 or (resid 81 and (name N or name CA or na \ me C or name O or name CB )) or resid 82 through 87 or (resid 88 and (name N or \ name CA or name C or name O or name CB )) or resid 89 through 107 or (resid 108 \ and (name N or name CA or name C or name O or name CB )) or resid 109 through 11 \ 0 or (resid 111 and (name N or name CA or name C or name O or name CB )) or resi \ d 112 through 120 or (resid 121 and (name N or name CA or name C or name O or na \ me CB )) or resid 122 through 127 or (resid 128 through 129 and (name N or name \ CA or name C or name O or name CB )) or resid 130 through 139 or (resid 140 and \ (name N or name CA or name C or name O or name CB )) or resid 141 through 149 or \ (resid 150 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 1 through 155 or (resid 156 and (name N or name CA or name C or name O or name C \ B )) or resid 157 through 165 or (resid 166 and (name N or name CA or name C or \ name O or name CB )) or resid 167 through 178 or (resid 179 through 180 and (nam \ e N or name CA or name C or name O or name CB )) or resid 181 through 198 or (re \ sid 199 and (name N or name CA or name C or name O or name CB )) or resid 200 th \ rough 220 or (resid 221 through 222 and (name N or name CA or name C or name O o \ r name CB )) or resid 223 through 229 or resid 237 through 238 or (resid 239 and \ (name N or name CA or name C or name O or name CB )) or resid 240 through 241 o \ r (resid 242 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 43 through 283 or (resid 284 and (name N or name CA or name C or name O or name \ CB )) or resid 285 through 303 or (resid 304 through 305 and (name N or name CA \ or name C or name O or name CB )) or resid 306 or (resid 307 and (name N or name \ CA or name C or name O or name CB )) or resid 308 through 309 or (resid 310 and \ (name N or name CA or name C or name O or name CB )) or resid 311 through 314 o \ r (resid 315 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 16 through 327 or (resid 328 through 329 and (name N or name CA or name C or nam \ e O or name CB )) or resid 330)) selection = (chain 'F' and (resid 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or nam \ e CA or name C or name O or name CB )) or resid 18 through 28 or (resid 29 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or r \ esid 37 through 43 or (resid 44 and (name N or name CA or name C or name O or na \ me CB )) or resid 45 through 50 or (resid 51 through 79 and (name N or name CA o \ r name C or name O or name CB )) or resid 80 or (resid 81 and (name N or name CA \ or name C or name O or name CB )) or resid 82 through 87 or (resid 88 and (name \ N or name CA or name C or name O or name CB )) or resid 89 through 105 or (resi \ d 106 and (name N or name CA or name C or name O or name CB )) or resid 107 thro \ ugh 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) o \ r resid 112 through 122 or (resid 123 through 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 127 or (resid 128 through 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 139 \ or (resid 140 and (name N or name CA or name C or name O or name CB )) or resid \ 141 through 149 or (resid 150 and (name N or name CA or name C or name O or name \ CB )) or resid 151 through 165 or (resid 166 and (name N or name CA or name C o \ r name O or name CB )) or resid 167 through 184 or (resid 185 and (name N or nam \ e CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 an \ d (name N or name CA or name C or name O or name CB )) or resid 192 through 198 \ or (resid 199 and (name N or name CA or name C or name O or name CB )) or resid \ 200 through 221 or (resid 222 and (name N or name CA or name C or name O or name \ CB )) or resid 223 through 241 or (resid 242 and (name N or name CA or name C o \ r name O or name CB )) or resid 243 through 277 or (resid 278 and (name N or nam \ e CA or name C or name O or name CB )) or resid 279 through 283 or (resid 284 an \ d (name N or name CA or name C or name O or name CB )) or resid 285 or (resid 28 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 287 through \ 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or re \ sid 294 through 309 or (resid 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 314 or (resid 315 and (name N or name CA or name \ C or name O or name CB )) or resid 316 through 327 or (resid 328 through 329 an \ d (name N or name CA or name C or name O or name CB )) or resid 330)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 51.850 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: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 50.750 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.010 0.104 22155 Z= 0.634 Angle : 1.398 12.851 30349 Z= 0.891 Chirality : 0.082 0.521 3476 Planarity : 0.014 0.254 3676 Dihedral : 18.130 172.166 8356 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.97 % Favored : 92.87 % Rotamer: Outliers : 1.97 % Allowed : 28.51 % Favored : 69.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.14), residues: 2596 helix: -2.07 (0.16), residues: 736 sheet: -0.47 (0.25), residues: 438 loop : -2.56 (0.13), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP C 149 HIS 0.021 0.002 HIS G 328 PHE 0.056 0.004 PHE C 297 TYR 0.048 0.003 TYR A 114 ARG 0.025 0.002 ARG E 150 Details of bonding type rmsd hydrogen bonds : bond 0.19074 ( 595) hydrogen bonds : angle 8.04910 ( 1650) covalent geometry : bond 0.00968 (22155) covalent geometry : angle 1.39793 (30349) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 802 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 THR cc_start: 0.7904 (p) cc_final: 0.7634 (p) REVERT: A 44 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8018 (ttpp) REVERT: A 318 TYR cc_start: 0.7910 (t80) cc_final: 0.7266 (t80) REVERT: A 328 MET cc_start: 0.8089 (mtp) cc_final: 0.7885 (mtp) REVERT: B 39 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7834 (ptpp) REVERT: B 98 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7821 (ttmm) REVERT: B 144 ASN cc_start: 0.8308 (p0) cc_final: 0.8086 (p0) REVERT: B 184 GLU cc_start: 0.7776 (mp0) cc_final: 0.7490 (mp0) REVERT: B 215 VAL cc_start: 0.8343 (p) cc_final: 0.8129 (m) REVERT: B 216 LYS cc_start: 0.8698 (tttt) cc_final: 0.8407 (tttm) REVERT: B 217 ILE cc_start: 0.8471 (pp) cc_final: 0.8187 (pt) REVERT: B 253 LYS cc_start: 0.8105 (tttt) cc_final: 0.7863 (ttmt) REVERT: B 262 ASP cc_start: 0.8095 (t0) cc_final: 0.7841 (t0) REVERT: B 265 TYR cc_start: 0.7566 (p90) cc_final: 0.7182 (p90) REVERT: B 273 PHE cc_start: 0.8380 (p90) cc_final: 0.7900 (p90) REVERT: C 18 ASN cc_start: 0.8081 (m110) cc_final: 0.7844 (m-40) REVERT: C 89 ASP cc_start: 0.7901 (p0) cc_final: 0.7511 (p0) REVERT: C 95 PHE cc_start: 0.8187 (p90) cc_final: 0.7986 (p90) REVERT: C 111 ASP cc_start: 0.8027 (t0) cc_final: 0.7815 (t0) REVERT: C 159 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7044 (tp30) REVERT: C 161 ILE cc_start: 0.8829 (tt) cc_final: 0.8474 (pt) REVERT: C 172 PHE cc_start: 0.7301 (m-10) cc_final: 0.6760 (m-10) REVERT: C 221 MET cc_start: 0.7250 (tpp) cc_final: 0.7046 (mpp) REVERT: C 229 MET cc_start: 0.7608 (ppp) cc_final: 0.7222 (ppp) REVERT: C 242 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8204 (mtpp) REVERT: C 297 PHE cc_start: 0.7248 (t80) cc_final: 0.7042 (t80) REVERT: C 304 MET cc_start: 0.7587 (ttt) cc_final: 0.7273 (ttm) REVERT: C 309 GLU cc_start: 0.7959 (tt0) cc_final: 0.7715 (tm-30) REVERT: D 45 LEU cc_start: 0.8266 (mp) cc_final: 0.8046 (mp) REVERT: D 271 TYR cc_start: 0.7595 (m-10) cc_final: 0.7151 (m-10) REVERT: E 99 VAL cc_start: 0.8553 (t) cc_final: 0.8338 (t) REVERT: E 178 ASN cc_start: 0.8370 (t0) cc_final: 0.8096 (t0) REVERT: E 224 TYR cc_start: 0.7705 (m-10) cc_final: 0.7465 (m-10) REVERT: E 244 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7468 (mt-10) REVERT: E 290 PHE cc_start: 0.8014 (m-10) cc_final: 0.7778 (m-80) REVERT: E 299 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7944 (mtmt) REVERT: E 318 TYR cc_start: 0.7343 (t80) cc_final: 0.6791 (t80) REVERT: E 322 ILE cc_start: 0.8394 (tp) cc_final: 0.8069 (tt) REVERT: F 36 ASP cc_start: 0.8007 (t0) cc_final: 0.7696 (t0) REVERT: F 48 LEU cc_start: 0.8824 (mm) cc_final: 0.8620 (mp) REVERT: F 111 ASP cc_start: 0.7733 (t0) cc_final: 0.7293 (t0) REVERT: F 206 TYR cc_start: 0.7927 (p90) cc_final: 0.7726 (p90) REVERT: G 51 ASN cc_start: 0.7757 (t0) cc_final: 0.7499 (t0) REVERT: G 129 ARG cc_start: 0.6710 (ttt90) cc_final: 0.6302 (ttt90) REVERT: G 172 GLU cc_start: 0.7426 (tp30) cc_final: 0.7192 (tp30) REVERT: G 176 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7551 (ttm170) REVERT: G 190 LEU cc_start: 0.7237 (mp) cc_final: 0.6869 (tt) REVERT: G 224 LEU cc_start: 0.8882 (tp) cc_final: 0.8556 (tt) REVERT: G 229 ASP cc_start: 0.7740 (m-30) cc_final: 0.7414 (m-30) REVERT: G 262 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6800 (tm-30) REVERT: G 265 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7476 (ttp-110) REVERT: H 80 LEU cc_start: 0.8392 (tm) cc_final: 0.8071 (tt) REVERT: H 126 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7999 (ttmm) REVERT: H 240 LEU cc_start: 0.8110 (tp) cc_final: 0.7714 (tp) REVERT: I 83 TYR cc_start: 0.7472 (m-80) cc_final: 0.6923 (m-80) REVERT: I 132 LYS cc_start: 0.8141 (tptm) cc_final: 0.7889 (tptm) outliers start: 41 outliers final: 15 residues processed: 820 average time/residue: 0.4034 time to fit residues: 502.9241 Evaluate side-chains 741 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 725 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain I residue 155 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 0.0070 chunk 68 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 239 optimal weight: 0.6980 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 26 ASN C 113 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 195 GLN C 208 ASN C 308 ASN D 140 ASN E 18 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 140 ASN G 170 ASN G 270 ASN G 327 HIS H 12 ASN H 17 ASN I 29 HIS I 106 ASN I 137 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097994 restraints weight = 39789.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100965 restraints weight = 17113.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102805 restraints weight = 9302.531| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22155 Z= 0.152 Angle : 0.658 8.778 30349 Z= 0.350 Chirality : 0.043 0.241 3476 Planarity : 0.006 0.082 3676 Dihedral : 15.724 178.395 3798 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.10 % Allowed : 24.04 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.15), residues: 2596 helix: -0.92 (0.17), residues: 766 sheet: -0.21 (0.26), residues: 415 loop : -2.14 (0.14), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 149 HIS 0.007 0.001 HIS G 328 PHE 0.027 0.002 PHE B 243 TYR 0.028 0.002 TYR E 224 ARG 0.009 0.001 ARG F 291 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 595) hydrogen bonds : angle 5.53894 ( 1650) covalent geometry : bond 0.00336 (22155) covalent geometry : angle 0.65787 (30349) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 743 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7642 (tp) REVERT: A 253 LYS cc_start: 0.7803 (tttt) cc_final: 0.7444 (ttmt) REVERT: A 318 TYR cc_start: 0.7960 (t80) cc_final: 0.7642 (t80) REVERT: B 39 LYS cc_start: 0.8002 (ptpt) cc_final: 0.7730 (ptpp) REVERT: B 55 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7441 (tp) REVERT: B 98 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7604 (ttmm) REVERT: B 106 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7718 (mtp) REVERT: B 142 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7693 (mt) REVERT: B 216 LYS cc_start: 0.8576 (tttt) cc_final: 0.8287 (tttm) REVERT: B 217 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8115 (pt) REVERT: B 241 PHE cc_start: 0.8762 (t80) cc_final: 0.8427 (t80) REVERT: B 242 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8257 (ttpp) REVERT: B 265 TYR cc_start: 0.7436 (p90) cc_final: 0.7083 (p90) REVERT: B 270 THR cc_start: 0.8285 (p) cc_final: 0.7956 (p) REVERT: B 273 PHE cc_start: 0.8325 (p90) cc_final: 0.7951 (p90) REVERT: B 278 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6533 (mt-10) REVERT: C 21 PHE cc_start: 0.8091 (m-80) cc_final: 0.6930 (m-10) REVERT: C 89 ASP cc_start: 0.7841 (p0) cc_final: 0.7440 (p0) REVERT: C 95 PHE cc_start: 0.8105 (p90) cc_final: 0.7767 (p90) REVERT: C 106 MET cc_start: 0.7703 (tpp) cc_final: 0.7357 (tpp) REVERT: C 111 ASP cc_start: 0.7438 (t0) cc_final: 0.7051 (t0) REVERT: C 159 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: C 179 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8434 (mp) REVERT: C 221 MET cc_start: 0.7047 (tpp) cc_final: 0.6840 (mpp) REVERT: C 229 MET cc_start: 0.7303 (ppp) cc_final: 0.7035 (ppp) REVERT: C 253 LYS cc_start: 0.7960 (tptt) cc_final: 0.7635 (tttt) REVERT: D 43 PHE cc_start: 0.8491 (t80) cc_final: 0.8277 (t80) REVERT: D 253 LYS cc_start: 0.7567 (tptt) cc_final: 0.7139 (tppt) REVERT: D 262 ASP cc_start: 0.7279 (t0) cc_final: 0.7007 (t0) REVERT: D 290 PHE cc_start: 0.8325 (m-80) cc_final: 0.8025 (m-80) REVERT: E 40 ARG cc_start: 0.7852 (ptt90) cc_final: 0.7305 (ptt90) REVERT: E 99 VAL cc_start: 0.8289 (t) cc_final: 0.8071 (t) REVERT: E 159 GLU cc_start: 0.7527 (tp30) cc_final: 0.7128 (tp30) REVERT: E 255 ASN cc_start: 0.8179 (t0) cc_final: 0.7975 (t0) REVERT: E 290 PHE cc_start: 0.8066 (m-10) cc_final: 0.7655 (m-80) REVERT: E 309 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5499 (tm-30) REVERT: F 36 ASP cc_start: 0.7773 (t0) cc_final: 0.7477 (t0) REVERT: F 48 LEU cc_start: 0.8629 (mm) cc_final: 0.8352 (mp) REVERT: F 153 LYS cc_start: 0.7863 (tppt) cc_final: 0.7377 (mptt) REVERT: F 191 GLU cc_start: 0.7765 (tp30) cc_final: 0.7487 (tp30) REVERT: F 203 LYS cc_start: 0.8519 (tppt) cc_final: 0.8316 (mmtp) REVERT: F 206 TYR cc_start: 0.7773 (p90) cc_final: 0.7552 (p90) REVERT: F 228 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6872 (tm-30) REVERT: F 318 TYR cc_start: 0.8102 (t80) cc_final: 0.7546 (t80) REVERT: G 47 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.6936 (p0) REVERT: G 63 ASN cc_start: 0.7446 (t0) cc_final: 0.7088 (t0) REVERT: G 172 GLU cc_start: 0.7160 (tp30) cc_final: 0.6885 (tp30) REVERT: G 190 LEU cc_start: 0.6919 (mp) cc_final: 0.6701 (tt) REVERT: G 210 LEU cc_start: 0.8346 (mt) cc_final: 0.8142 (tp) REVERT: G 224 LEU cc_start: 0.8668 (tp) cc_final: 0.8356 (tt) REVERT: G 229 ASP cc_start: 0.7650 (m-30) cc_final: 0.7431 (m-30) REVERT: G 234 LEU cc_start: 0.8231 (mp) cc_final: 0.7978 (mp) REVERT: G 262 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6787 (tm-30) REVERT: G 265 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7651 (ttp-110) REVERT: G 272 ARG cc_start: 0.8166 (ttm110) cc_final: 0.7929 (ttm170) REVERT: G 277 ARG cc_start: 0.7399 (mtt180) cc_final: 0.7103 (mtt180) REVERT: G 307 VAL cc_start: 0.8700 (m) cc_final: 0.8477 (p) REVERT: G 322 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6657 (mtm) REVERT: H 1 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6233 (mpp) REVERT: H 80 LEU cc_start: 0.8310 (tm) cc_final: 0.7895 (tt) REVERT: H 126 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7852 (ttmm) REVERT: I 132 LYS cc_start: 0.8093 (tptm) cc_final: 0.7792 (tptm) REVERT: I 165 LYS cc_start: 0.7854 (mmmt) cc_final: 0.7620 (mmmt) outliers start: 106 outliers final: 47 residues processed: 794 average time/residue: 0.3469 time to fit residues: 417.7615 Evaluate side-chains 787 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 729 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 322 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 164 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 49 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 230 optimal weight: 0.0570 chunk 98 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 chunk 74 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN C 140 ASN E 18 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN F 140 ASN F 190 ASN I 53 HIS I 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098002 restraints weight = 39713.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.101012 restraints weight = 17038.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.102890 restraints weight = 9203.275| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22155 Z= 0.126 Angle : 0.601 7.281 30349 Z= 0.316 Chirality : 0.042 0.197 3476 Planarity : 0.005 0.065 3676 Dihedral : 15.492 178.018 3784 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.71 % Allowed : 24.66 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.15), residues: 2596 helix: -0.21 (0.18), residues: 750 sheet: -0.14 (0.26), residues: 415 loop : -1.97 (0.14), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 149 HIS 0.009 0.001 HIS G 304 PHE 0.025 0.002 PHE B 243 TYR 0.026 0.001 TYR E 318 ARG 0.006 0.001 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 595) hydrogen bonds : angle 5.12584 ( 1650) covalent geometry : bond 0.00276 (22155) covalent geometry : angle 0.60105 (30349) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 736 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7750 (tt) REVERT: A 253 LYS cc_start: 0.7854 (tttt) cc_final: 0.7509 (ttmt) REVERT: A 318 TYR cc_start: 0.7927 (t80) cc_final: 0.7334 (t80) REVERT: B 55 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7484 (tt) REVERT: B 142 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7736 (mt) REVERT: B 144 ASN cc_start: 0.8258 (p0) cc_final: 0.8048 (p0) REVERT: B 184 GLU cc_start: 0.7609 (mp0) cc_final: 0.7402 (mp0) REVERT: B 216 LYS cc_start: 0.8508 (tttt) cc_final: 0.8203 (tttm) REVERT: B 217 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8045 (pt) REVERT: B 222 GLU cc_start: 0.7728 (tt0) cc_final: 0.7479 (tt0) REVERT: B 241 PHE cc_start: 0.8752 (t80) cc_final: 0.8472 (t80) REVERT: B 242 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8287 (ttpp) REVERT: B 265 TYR cc_start: 0.7390 (p90) cc_final: 0.6885 (p90) REVERT: B 267 ASP cc_start: 0.6663 (p0) cc_final: 0.5926 (p0) REVERT: B 271 TYR cc_start: 0.8221 (m-10) cc_final: 0.7966 (m-10) REVERT: B 273 PHE cc_start: 0.8268 (p90) cc_final: 0.7714 (p90) REVERT: B 278 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6535 (mt-10) REVERT: C 43 PHE cc_start: 0.8140 (t80) cc_final: 0.7635 (t80) REVERT: C 82 CYS cc_start: 0.8323 (t) cc_final: 0.7906 (p) REVERT: C 89 ASP cc_start: 0.7849 (p0) cc_final: 0.7412 (p0) REVERT: C 90 THR cc_start: 0.8173 (m) cc_final: 0.7859 (m) REVERT: C 95 PHE cc_start: 0.8318 (p90) cc_final: 0.7987 (p90) REVERT: C 111 ASP cc_start: 0.7397 (t0) cc_final: 0.6995 (t0) REVERT: C 159 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: C 179 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8427 (mp) REVERT: C 221 MET cc_start: 0.7067 (tpp) cc_final: 0.6841 (mpp) REVERT: C 229 MET cc_start: 0.7247 (ppp) cc_final: 0.7015 (ppp) REVERT: C 252 GLN cc_start: 0.8273 (pm20) cc_final: 0.7878 (pm20) REVERT: D 77 GLN cc_start: 0.7255 (tt0) cc_final: 0.7034 (tt0) REVERT: D 153 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8540 (mmtm) REVERT: D 253 LYS cc_start: 0.7667 (tptt) cc_final: 0.7220 (tppt) REVERT: D 262 ASP cc_start: 0.7138 (t0) cc_final: 0.6834 (t0) REVERT: D 272 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6193 (mp0) REVERT: E 26 ASN cc_start: 0.8004 (t0) cc_final: 0.7701 (t0) REVERT: E 40 ARG cc_start: 0.8022 (ptt90) cc_final: 0.7617 (ptt90) REVERT: E 99 VAL cc_start: 0.8350 (t) cc_final: 0.8147 (t) REVERT: E 131 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: E 159 GLU cc_start: 0.7394 (tp30) cc_final: 0.7154 (tp30) REVERT: E 309 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5583 (tm-30) REVERT: E 318 TYR cc_start: 0.7655 (t80) cc_final: 0.7411 (t80) REVERT: F 36 ASP cc_start: 0.7799 (t0) cc_final: 0.7482 (t0) REVERT: F 48 LEU cc_start: 0.8609 (mm) cc_final: 0.8338 (mp) REVERT: F 111 ASP cc_start: 0.7122 (t0) cc_final: 0.6771 (t0) REVERT: F 114 TYR cc_start: 0.8251 (t80) cc_final: 0.7948 (t80) REVERT: F 140 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7817 (t0) REVERT: F 153 LYS cc_start: 0.7869 (tppt) cc_final: 0.7300 (mptt) REVERT: F 191 GLU cc_start: 0.7771 (tp30) cc_final: 0.7535 (tp30) REVERT: F 204 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7848 (mtt-85) REVERT: F 228 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6953 (tm-30) REVERT: F 318 TYR cc_start: 0.8130 (t80) cc_final: 0.7857 (t80) REVERT: G 63 ASN cc_start: 0.7535 (t0) cc_final: 0.7140 (t0) REVERT: G 172 GLU cc_start: 0.7179 (tp30) cc_final: 0.6944 (tp30) REVERT: G 190 LEU cc_start: 0.6917 (mp) cc_final: 0.6645 (tt) REVERT: G 224 LEU cc_start: 0.8601 (tp) cc_final: 0.8337 (tt) REVERT: G 234 LEU cc_start: 0.8258 (mp) cc_final: 0.8037 (mp) REVERT: G 262 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6968 (tm-30) REVERT: G 265 ARG cc_start: 0.8028 (ttp-110) cc_final: 0.7765 (ttp-110) REVERT: G 277 ARG cc_start: 0.7401 (mtt180) cc_final: 0.7097 (mtt180) REVERT: G 307 VAL cc_start: 0.8712 (m) cc_final: 0.8491 (p) REVERT: H 17 ASN cc_start: 0.8102 (t0) cc_final: 0.7896 (t0) REVERT: H 80 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8146 (tp) REVERT: H 126 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7924 (ttmm) REVERT: H 150 THR cc_start: 0.8867 (t) cc_final: 0.8641 (m) outliers start: 98 outliers final: 43 residues processed: 782 average time/residue: 0.3593 time to fit residues: 426.3785 Evaluate side-chains 767 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 714 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 138 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 198 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 256 ASN E 18 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 ASN H 12 ASN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 237 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.107759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094282 restraints weight = 40109.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097247 restraints weight = 17082.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099102 restraints weight = 9234.346| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22155 Z= 0.196 Angle : 0.632 8.635 30349 Z= 0.333 Chirality : 0.043 0.199 3476 Planarity : 0.005 0.073 3676 Dihedral : 15.428 177.906 3782 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.38 % Allowed : 24.71 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 2596 helix: -0.06 (0.19), residues: 762 sheet: -0.09 (0.26), residues: 420 loop : -1.91 (0.14), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 149 HIS 0.006 0.001 HIS G 328 PHE 0.027 0.002 PHE B 243 TYR 0.025 0.002 TYR E 224 ARG 0.013 0.001 ARG D 303 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 595) hydrogen bonds : angle 5.01771 ( 1650) covalent geometry : bond 0.00437 (22155) covalent geometry : angle 0.63208 (30349) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 760 time to evaluate : 3.951 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 89 ASP cc_start: 0.7917 (p0) cc_final: 0.7624 (p0) REVERT: A 253 LYS cc_start: 0.7971 (tttt) cc_final: 0.7584 (ttmt) REVERT: A 318 TYR cc_start: 0.8010 (t80) cc_final: 0.7399 (t80) REVERT: B 55 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7461 (tp) REVERT: B 109 CYS cc_start: 0.7477 (t) cc_final: 0.7194 (t) REVERT: B 139 VAL cc_start: 0.8156 (t) cc_final: 0.7915 (p) REVERT: B 184 GLU cc_start: 0.7626 (mp0) cc_final: 0.7407 (mp0) REVERT: B 216 LYS cc_start: 0.8556 (tttt) cc_final: 0.8266 (tttm) REVERT: B 217 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8183 (pt) REVERT: B 265 TYR cc_start: 0.7495 (p90) cc_final: 0.7181 (p90) REVERT: B 272 GLU cc_start: 0.6619 (mp0) cc_final: 0.6371 (mp0) REVERT: B 273 PHE cc_start: 0.8321 (p90) cc_final: 0.7803 (p90) REVERT: B 278 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6600 (mt-10) REVERT: B 290 PHE cc_start: 0.7965 (m-80) cc_final: 0.7647 (m-80) REVERT: B 291 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7306 (mtp180) REVERT: B 325 ARG cc_start: 0.6937 (ttt90) cc_final: 0.6621 (ttt90) REVERT: C 43 PHE cc_start: 0.8299 (t80) cc_final: 0.7786 (t80) REVERT: C 89 ASP cc_start: 0.7888 (p0) cc_final: 0.7412 (p0) REVERT: C 90 THR cc_start: 0.8113 (m) cc_final: 0.7895 (m) REVERT: C 95 PHE cc_start: 0.8466 (p90) cc_final: 0.8116 (p90) REVERT: C 111 ASP cc_start: 0.7485 (t0) cc_final: 0.7210 (t0) REVERT: C 120 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: C 151 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8200 (m110) REVERT: C 159 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6431 (tm-30) REVERT: C 179 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8540 (mp) REVERT: C 183 VAL cc_start: 0.8114 (m) cc_final: 0.7905 (p) REVERT: C 229 MET cc_start: 0.7301 (ppp) cc_final: 0.7071 (ppp) REVERT: C 253 LYS cc_start: 0.8026 (tttt) cc_final: 0.7729 (tttt) REVERT: C 265 TYR cc_start: 0.7246 (p90) cc_final: 0.6606 (p90) REVERT: C 270 THR cc_start: 0.8212 (p) cc_final: 0.7818 (t) REVERT: C 284 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.8183 (mtt90) REVERT: D 153 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8515 (mmtm) REVERT: D 262 ASP cc_start: 0.7124 (t0) cc_final: 0.6886 (t70) REVERT: D 265 TYR cc_start: 0.7930 (p90) cc_final: 0.7622 (p90) REVERT: D 272 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6502 (mp0) REVERT: E 40 ARG cc_start: 0.8273 (ptt90) cc_final: 0.7686 (ptt90) REVERT: E 99 VAL cc_start: 0.8366 (t) cc_final: 0.8153 (t) REVERT: E 131 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: E 159 GLU cc_start: 0.7280 (tp30) cc_final: 0.7012 (tp30) REVERT: E 309 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5615 (tm-30) REVERT: E 318 TYR cc_start: 0.7664 (t80) cc_final: 0.7409 (t80) REVERT: F 17 GLU cc_start: 0.6885 (tp30) cc_final: 0.6675 (tp30) REVERT: F 48 LEU cc_start: 0.8654 (mm) cc_final: 0.8377 (mp) REVERT: F 89 ASP cc_start: 0.7979 (p0) cc_final: 0.7293 (p0) REVERT: F 104 GLU cc_start: 0.7170 (mp0) cc_final: 0.6892 (mp0) REVERT: F 106 MET cc_start: 0.7253 (mmm) cc_final: 0.6712 (mmm) REVERT: F 191 GLU cc_start: 0.7757 (tp30) cc_final: 0.7536 (tp30) REVERT: F 228 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6998 (tm-30) REVERT: G 63 ASN cc_start: 0.7606 (t0) cc_final: 0.7291 (t0) REVERT: G 172 GLU cc_start: 0.7231 (tp30) cc_final: 0.6974 (tp30) REVERT: G 234 LEU cc_start: 0.8317 (mp) cc_final: 0.8107 (mp) REVERT: G 262 GLU cc_start: 0.7613 (mm-30) cc_final: 0.6971 (tm-30) REVERT: G 265 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7853 (ttp-110) REVERT: G 277 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7124 (mtt180) REVERT: G 307 VAL cc_start: 0.8780 (m) cc_final: 0.8527 (p) REVERT: G 322 MET cc_start: 0.7010 (mtm) cc_final: 0.6809 (mtm) REVERT: H 126 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7950 (ttmm) REVERT: H 150 THR cc_start: 0.8905 (t) cc_final: 0.8658 (m) REVERT: I 128 GLU cc_start: 0.7615 (tt0) cc_final: 0.7408 (tm-30) outliers start: 112 outliers final: 64 residues processed: 812 average time/residue: 0.3752 time to fit residues: 468.9407 Evaluate side-chains 800 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 729 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 68 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 217 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN C 140 ASN E 18 ASN E 140 ASN F 140 ASN G 35 HIS ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.091614 restraints weight = 40285.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094530 restraints weight = 17000.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096344 restraints weight = 9122.554| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 22155 Z= 0.249 Angle : 0.668 9.071 30349 Z= 0.352 Chirality : 0.045 0.221 3476 Planarity : 0.005 0.082 3676 Dihedral : 15.439 178.745 3779 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.55 % Favored : 94.41 % Rotamer: Outliers : 6.11 % Allowed : 25.72 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 2596 helix: 0.00 (0.19), residues: 764 sheet: -0.11 (0.26), residues: 424 loop : -1.93 (0.14), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 149 HIS 0.009 0.001 HIS G 304 PHE 0.030 0.002 PHE B 243 TYR 0.024 0.002 TYR D 125 ARG 0.009 0.001 ARG E 150 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 595) hydrogen bonds : angle 5.10128 ( 1650) covalent geometry : bond 0.00556 (22155) covalent geometry : angle 0.66764 (30349) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 755 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.7987 (p0) cc_final: 0.7676 (p0) REVERT: A 104 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 159 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7346 (mt-10) REVERT: A 175 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8289 (tttm) REVERT: A 242 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7697 (tttt) REVERT: A 253 LYS cc_start: 0.8018 (tttt) cc_final: 0.7644 (ttmt) REVERT: A 318 TYR cc_start: 0.8021 (t80) cc_final: 0.7632 (t80) REVERT: B 35 THR cc_start: 0.7831 (t) cc_final: 0.7265 (p) REVERT: B 52 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8453 (ttmm) REVERT: B 55 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7508 (tp) REVERT: B 90 THR cc_start: 0.8440 (m) cc_final: 0.7960 (p) REVERT: B 109 CYS cc_start: 0.7379 (t) cc_final: 0.7079 (t) REVERT: B 139 VAL cc_start: 0.8201 (t) cc_final: 0.7922 (p) REVERT: B 184 GLU cc_start: 0.7594 (mp0) cc_final: 0.7377 (mp0) REVERT: B 216 LYS cc_start: 0.8592 (tttt) cc_final: 0.8292 (tttm) REVERT: B 217 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8318 (pt) REVERT: B 242 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8112 (ttmm) REVERT: B 272 GLU cc_start: 0.6707 (mp0) cc_final: 0.6401 (mp0) REVERT: B 278 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6707 (mt-10) REVERT: B 291 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7502 (mtp180) REVERT: C 43 PHE cc_start: 0.8457 (t80) cc_final: 0.7944 (t80) REVERT: C 89 ASP cc_start: 0.7887 (p0) cc_final: 0.7356 (p0) REVERT: C 90 THR cc_start: 0.8193 (m) cc_final: 0.7947 (m) REVERT: C 95 PHE cc_start: 0.8570 (p90) cc_final: 0.8235 (p90) REVERT: C 111 ASP cc_start: 0.7490 (t0) cc_final: 0.7121 (t0) REVERT: C 120 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: C 140 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7466 (t0) REVERT: C 156 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6950 (mt-10) REVERT: C 159 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6405 (tm-30) REVERT: C 229 MET cc_start: 0.7349 (ppp) cc_final: 0.7081 (ppp) REVERT: C 252 GLN cc_start: 0.8440 (pm20) cc_final: 0.7998 (pm20) REVERT: C 253 LYS cc_start: 0.8076 (tttt) cc_final: 0.7761 (tttt) REVERT: C 265 TYR cc_start: 0.7346 (p90) cc_final: 0.6863 (p90) REVERT: C 270 THR cc_start: 0.8362 (p) cc_final: 0.7952 (t) REVERT: C 320 MET cc_start: 0.7623 (mmm) cc_final: 0.6992 (mmm) REVERT: D 253 LYS cc_start: 0.7793 (tppt) cc_final: 0.7195 (tppt) REVERT: D 262 ASP cc_start: 0.7146 (t0) cc_final: 0.6928 (t70) REVERT: E 37 PHE cc_start: 0.8097 (t80) cc_final: 0.7779 (t80) REVERT: E 131 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: E 159 GLU cc_start: 0.7269 (tp30) cc_final: 0.6881 (tp30) REVERT: E 173 ASN cc_start: 0.8298 (t0) cc_final: 0.8066 (t0) REVERT: E 180 ASP cc_start: 0.8053 (m-30) cc_final: 0.7759 (t0) REVERT: E 309 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5658 (tm-30) REVERT: E 318 TYR cc_start: 0.7682 (t80) cc_final: 0.7325 (t80) REVERT: F 21 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: F 48 LEU cc_start: 0.8666 (mm) cc_final: 0.8405 (mp) REVERT: F 89 ASP cc_start: 0.7988 (p0) cc_final: 0.7270 (p0) REVERT: F 104 GLU cc_start: 0.7305 (mp0) cc_final: 0.7008 (mp0) REVERT: F 106 MET cc_start: 0.7324 (mmm) cc_final: 0.6755 (mmm) REVERT: F 140 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7727 (t0) REVERT: F 144 ASN cc_start: 0.8031 (p0) cc_final: 0.7779 (p0) REVERT: F 191 GLU cc_start: 0.7849 (tp30) cc_final: 0.7568 (tp30) REVERT: F 228 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7019 (tm-30) REVERT: F 315 ASP cc_start: 0.7726 (m-30) cc_final: 0.7324 (t0) REVERT: G 87 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7200 (pptt) REVERT: G 89 PRO cc_start: 0.8641 (Cg_endo) cc_final: 0.8394 (Cg_exo) REVERT: G 172 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: G 175 ASP cc_start: 0.7840 (m-30) cc_final: 0.7614 (t0) REVERT: G 262 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7027 (tm-30) REVERT: G 265 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7899 (ttp-110) REVERT: G 277 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7216 (mtt180) REVERT: G 307 VAL cc_start: 0.8814 (m) cc_final: 0.8573 (p) REVERT: H 20 ASN cc_start: 0.7696 (m-40) cc_final: 0.7455 (m110) REVERT: H 126 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7949 (ttmm) REVERT: H 166 ASN cc_start: 0.8200 (m110) cc_final: 0.7982 (t0) REVERT: H 177 ASP cc_start: 0.7455 (m-30) cc_final: 0.7170 (m-30) REVERT: H 183 LEU cc_start: 0.8808 (mt) cc_final: 0.8472 (mp) REVERT: H 221 ILE cc_start: 0.8514 (pt) cc_final: 0.8155 (pt) REVERT: H 222 PHE cc_start: 0.8636 (m-80) cc_final: 0.8266 (m-80) REVERT: I 113 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7650 (mtm110) REVERT: I 128 GLU cc_start: 0.7671 (tt0) cc_final: 0.7466 (tm-30) outliers start: 127 outliers final: 85 residues processed: 808 average time/residue: 0.3393 time to fit residues: 417.1172 Evaluate side-chains 814 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 719 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 169 TYR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 155 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 231 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 29 optimal weight: 0.0030 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 234 optimal weight: 0.0170 chunk 248 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.4830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN E 140 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 HIS H 12 ASN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094131 restraints weight = 39832.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097060 restraints weight = 16689.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098862 restraints weight = 8924.740| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22155 Z= 0.134 Angle : 0.621 9.158 30349 Z= 0.325 Chirality : 0.042 0.207 3476 Planarity : 0.005 0.052 3676 Dihedral : 15.332 178.747 3775 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.76 % Allowed : 28.32 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.16), residues: 2596 helix: 0.19 (0.19), residues: 761 sheet: 0.06 (0.26), residues: 422 loop : -1.87 (0.14), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 149 HIS 0.009 0.001 HIS G 304 PHE 0.031 0.002 PHE B 243 TYR 0.031 0.001 TYR D 224 ARG 0.009 0.001 ARG E 150 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 595) hydrogen bonds : angle 4.93130 ( 1650) covalent geometry : bond 0.00303 (22155) covalent geometry : angle 0.62085 (30349) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 738 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7283 (mm-30) REVERT: A 159 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 175 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8274 (tttm) REVERT: A 242 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7674 (tttt) REVERT: A 309 GLU cc_start: 0.7177 (pt0) cc_final: 0.6924 (pm20) REVERT: A 318 TYR cc_start: 0.7934 (t80) cc_final: 0.7412 (t80) REVERT: A 320 MET cc_start: 0.7741 (tpp) cc_final: 0.6992 (mpp) REVERT: B 35 THR cc_start: 0.7790 (t) cc_final: 0.7311 (p) REVERT: B 55 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (tt) REVERT: B 90 THR cc_start: 0.8394 (m) cc_final: 0.7941 (p) REVERT: B 109 CYS cc_start: 0.7357 (t) cc_final: 0.7062 (t) REVERT: B 216 LYS cc_start: 0.8499 (tttt) cc_final: 0.8222 (tttm) REVERT: B 217 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8230 (pt) REVERT: B 242 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8108 (ttmm) REVERT: B 253 LYS cc_start: 0.8277 (tttt) cc_final: 0.8027 (tppt) REVERT: B 278 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6699 (mt-10) REVERT: C 26 ASN cc_start: 0.7961 (t0) cc_final: 0.7731 (t0) REVERT: C 43 PHE cc_start: 0.8404 (t80) cc_final: 0.7878 (t80) REVERT: C 89 ASP cc_start: 0.7902 (p0) cc_final: 0.7364 (p0) REVERT: C 90 THR cc_start: 0.8199 (m) cc_final: 0.7945 (m) REVERT: C 107 TYR cc_start: 0.7825 (t80) cc_final: 0.7387 (t80) REVERT: C 111 ASP cc_start: 0.7402 (t0) cc_final: 0.7159 (t0) REVERT: C 120 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: C 156 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6864 (mt-10) REVERT: C 159 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6397 (tm-30) REVERT: C 229 MET cc_start: 0.7304 (ppp) cc_final: 0.7052 (ppp) REVERT: C 252 GLN cc_start: 0.8427 (pm20) cc_final: 0.7979 (pm20) REVERT: C 253 LYS cc_start: 0.8060 (tttt) cc_final: 0.7743 (tttt) REVERT: C 270 THR cc_start: 0.8268 (p) cc_final: 0.7908 (t) REVERT: C 320 MET cc_start: 0.7637 (mmm) cc_final: 0.7266 (mmm) REVERT: D 253 LYS cc_start: 0.7755 (tppt) cc_final: 0.7466 (tppt) REVERT: D 262 ASP cc_start: 0.7067 (t0) cc_final: 0.6800 (t70) REVERT: D 272 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6363 (mp0) REVERT: E 18 ASN cc_start: 0.7691 (t0) cc_final: 0.7369 (t0) REVERT: E 131 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: E 159 GLU cc_start: 0.7299 (tp30) cc_final: 0.6963 (tp30) REVERT: E 180 ASP cc_start: 0.8048 (m-30) cc_final: 0.7714 (t0) REVERT: E 309 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5620 (tm-30) REVERT: F 21 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: F 40 ARG cc_start: 0.7624 (ptp-170) cc_final: 0.7422 (ptp90) REVERT: F 48 LEU cc_start: 0.8627 (mm) cc_final: 0.8372 (mp) REVERT: F 104 GLU cc_start: 0.7241 (mp0) cc_final: 0.6945 (mp0) REVERT: F 106 MET cc_start: 0.7264 (mmm) cc_final: 0.6712 (mmm) REVERT: F 144 ASN cc_start: 0.8068 (p0) cc_final: 0.7799 (p0) REVERT: F 153 LYS cc_start: 0.8288 (mmmm) cc_final: 0.8073 (mtpp) REVERT: F 191 GLU cc_start: 0.7766 (tp30) cc_final: 0.7496 (tp30) REVERT: F 228 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7050 (tm-30) REVERT: G 17 GLU cc_start: 0.8213 (pp20) cc_final: 0.7891 (pp20) REVERT: G 87 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7212 (pptt) REVERT: G 172 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: G 175 ASP cc_start: 0.7827 (m-30) cc_final: 0.7601 (t0) REVERT: G 262 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7034 (tm-30) REVERT: G 265 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7912 (ttp-110) REVERT: G 277 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7147 (mtt180) REVERT: G 307 VAL cc_start: 0.8812 (m) cc_final: 0.8579 (p) REVERT: H 53 ASN cc_start: 0.7794 (t0) cc_final: 0.7576 (m-40) REVERT: H 126 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8042 (ttmm) REVERT: H 177 ASP cc_start: 0.7400 (m-30) cc_final: 0.7118 (m-30) REVERT: H 221 ILE cc_start: 0.8479 (pt) cc_final: 0.8187 (pt) REVERT: I 113 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7552 (mtm110) outliers start: 99 outliers final: 66 residues processed: 778 average time/residue: 0.3383 time to fit residues: 402.4158 Evaluate side-chains 798 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 724 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 169 TYR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 151 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS G 170 ASN G 304 HIS ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 99 GLN H 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.091847 restraints weight = 40097.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094739 restraints weight = 16940.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096520 restraints weight = 9164.884| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 22155 Z= 0.219 Angle : 0.665 9.393 30349 Z= 0.348 Chirality : 0.044 0.221 3476 Planarity : 0.005 0.053 3676 Dihedral : 15.351 178.335 3775 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.29 % Allowed : 28.41 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.16), residues: 2596 helix: 0.21 (0.19), residues: 765 sheet: -0.05 (0.26), residues: 435 loop : -1.83 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 149 HIS 0.010 0.001 HIS G 304 PHE 0.032 0.002 PHE B 243 TYR 0.028 0.002 TYR D 224 ARG 0.010 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 595) hydrogen bonds : angle 4.96336 ( 1650) covalent geometry : bond 0.00499 (22155) covalent geometry : angle 0.66488 (30349) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 741 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8249 (ptt-90) cc_final: 0.7912 (ptt90) REVERT: A 89 ASP cc_start: 0.8000 (p0) cc_final: 0.7759 (p0) REVERT: A 104 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 175 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8282 (tttm) REVERT: A 242 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7713 (tttt) REVERT: A 308 ASN cc_start: 0.8134 (m-40) cc_final: 0.7861 (t0) REVERT: A 309 GLU cc_start: 0.7276 (pt0) cc_final: 0.6993 (pm20) REVERT: A 320 MET cc_start: 0.7759 (tpp) cc_final: 0.7002 (mpp) REVERT: B 35 THR cc_start: 0.7826 (t) cc_final: 0.7342 (p) REVERT: B 52 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8398 (ttmm) REVERT: B 55 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7512 (tp) REVERT: B 90 THR cc_start: 0.8439 (m) cc_final: 0.7947 (p) REVERT: B 126 ILE cc_start: 0.8595 (mm) cc_final: 0.8357 (mt) REVERT: B 144 ASN cc_start: 0.8225 (p0) cc_final: 0.7868 (p0) REVERT: B 156 GLU cc_start: 0.6832 (tt0) cc_final: 0.6522 (tt0) REVERT: B 183 VAL cc_start: 0.8209 (p) cc_final: 0.7955 (t) REVERT: B 184 GLU cc_start: 0.7419 (mp0) cc_final: 0.7091 (mp0) REVERT: B 216 LYS cc_start: 0.8554 (tttt) cc_final: 0.8183 (tttt) REVERT: B 242 LYS cc_start: 0.8527 (ttpp) cc_final: 0.8113 (ttmm) REVERT: B 253 LYS cc_start: 0.8326 (tttt) cc_final: 0.8103 (tppt) REVERT: B 278 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6762 (mt-10) REVERT: C 21 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7819 (m-10) REVERT: C 26 ASN cc_start: 0.7906 (t0) cc_final: 0.7554 (t0) REVERT: C 43 PHE cc_start: 0.8502 (t80) cc_final: 0.7989 (t80) REVERT: C 89 ASP cc_start: 0.7908 (p0) cc_final: 0.7385 (p0) REVERT: C 90 THR cc_start: 0.8206 (m) cc_final: 0.7971 (m) REVERT: C 111 ASP cc_start: 0.7405 (t0) cc_final: 0.7175 (t0) REVERT: C 120 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: C 156 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6971 (mt-10) REVERT: C 159 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6425 (tm-30) REVERT: C 179 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8353 (mp) REVERT: C 229 MET cc_start: 0.7376 (ppp) cc_final: 0.7099 (ppp) REVERT: C 252 GLN cc_start: 0.8418 (pm20) cc_final: 0.7959 (pm20) REVERT: C 253 LYS cc_start: 0.8108 (tttt) cc_final: 0.7780 (tttt) REVERT: C 270 THR cc_start: 0.8362 (p) cc_final: 0.7995 (t) REVERT: C 320 MET cc_start: 0.7632 (mmm) cc_final: 0.7016 (mmm) REVERT: D 253 LYS cc_start: 0.7769 (tppt) cc_final: 0.7481 (tppt) REVERT: D 262 ASP cc_start: 0.7087 (t0) cc_final: 0.6867 (t0) REVERT: D 272 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6454 (mp0) REVERT: E 18 ASN cc_start: 0.7705 (t0) cc_final: 0.7328 (t0) REVERT: E 131 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: E 159 GLU cc_start: 0.7224 (tp30) cc_final: 0.6858 (tp30) REVERT: E 180 ASP cc_start: 0.8075 (m-30) cc_final: 0.7734 (t0) REVERT: E 309 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5693 (tm-30) REVERT: F 21 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: F 40 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7576 (mtm-85) REVERT: F 48 LEU cc_start: 0.8668 (mm) cc_final: 0.8405 (mp) REVERT: F 89 ASP cc_start: 0.7982 (p0) cc_final: 0.7289 (p0) REVERT: F 104 GLU cc_start: 0.7272 (mp0) cc_final: 0.6966 (mp0) REVERT: F 106 MET cc_start: 0.7333 (mmm) cc_final: 0.6773 (mmm) REVERT: F 144 ASN cc_start: 0.8094 (p0) cc_final: 0.7861 (p0) REVERT: F 191 GLU cc_start: 0.7775 (tp30) cc_final: 0.7480 (tp30) REVERT: F 228 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7056 (tm-30) REVERT: F 315 ASP cc_start: 0.7729 (m-30) cc_final: 0.7331 (t0) REVERT: G 17 GLU cc_start: 0.8230 (pp20) cc_final: 0.7909 (pp20) REVERT: G 87 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7230 (pptt) REVERT: G 89 PRO cc_start: 0.8718 (Cg_endo) cc_final: 0.8513 (Cg_exo) REVERT: G 175 ASP cc_start: 0.7841 (m-30) cc_final: 0.7634 (t0) REVERT: G 201 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7477 (ttp80) REVERT: G 262 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7041 (tm-30) REVERT: G 277 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7246 (mtt180) REVERT: G 307 VAL cc_start: 0.8827 (m) cc_final: 0.8597 (p) REVERT: H 126 LYS cc_start: 0.8420 (ttmm) cc_final: 0.7928 (ttmm) REVERT: H 177 ASP cc_start: 0.7444 (m-30) cc_final: 0.7196 (m-30) REVERT: H 183 LEU cc_start: 0.8789 (mt) cc_final: 0.8443 (mp) REVERT: I 113 ARG cc_start: 0.7778 (mtt90) cc_final: 0.7514 (mtm110) outliers start: 110 outliers final: 73 residues processed: 787 average time/residue: 0.3446 time to fit residues: 412.0884 Evaluate side-chains 822 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 741 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 169 TYR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 304 HIS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 155 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 99 optimal weight: 5.9990 chunk 101 optimal weight: 0.0040 chunk 82 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN G 35 HIS ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.093146 restraints weight = 40089.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096085 restraints weight = 16796.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097881 restraints weight = 8963.437| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22155 Z= 0.159 Angle : 0.646 9.162 30349 Z= 0.337 Chirality : 0.043 0.223 3476 Planarity : 0.005 0.053 3676 Dihedral : 15.311 178.551 3773 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.10 % Allowed : 29.18 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.16), residues: 2596 helix: 0.31 (0.19), residues: 764 sheet: 0.08 (0.27), residues: 405 loop : -1.80 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 149 HIS 0.016 0.001 HIS G 304 PHE 0.034 0.002 PHE B 243 TYR 0.026 0.001 TYR D 125 ARG 0.010 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 595) hydrogen bonds : angle 4.89604 ( 1650) covalent geometry : bond 0.00365 (22155) covalent geometry : angle 0.64590 (30349) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 734 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7354 (mm-30) REVERT: A 175 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8297 (tttm) REVERT: A 253 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7653 (ttmt) REVERT: A 308 ASN cc_start: 0.8114 (m-40) cc_final: 0.7835 (t0) REVERT: A 309 GLU cc_start: 0.7213 (pt0) cc_final: 0.6976 (pm20) REVERT: A 320 MET cc_start: 0.7708 (tpp) cc_final: 0.6951 (mpp) REVERT: B 35 THR cc_start: 0.7826 (t) cc_final: 0.7358 (p) REVERT: B 52 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8384 (ttmm) REVERT: B 55 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7529 (tp) REVERT: B 90 THR cc_start: 0.8471 (m) cc_final: 0.7930 (p) REVERT: B 144 ASN cc_start: 0.8242 (p0) cc_final: 0.7948 (p0) REVERT: B 156 GLU cc_start: 0.6794 (tt0) cc_final: 0.6466 (tt0) REVERT: B 184 GLU cc_start: 0.7410 (mp0) cc_final: 0.7036 (mp0) REVERT: B 216 LYS cc_start: 0.8536 (tttt) cc_final: 0.8163 (tttt) REVERT: B 242 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8107 (ttmm) REVERT: B 253 LYS cc_start: 0.8291 (tttt) cc_final: 0.8070 (tppt) REVERT: B 278 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6747 (mt-10) REVERT: C 43 PHE cc_start: 0.8493 (t80) cc_final: 0.7976 (t80) REVERT: C 89 ASP cc_start: 0.7901 (p0) cc_final: 0.7367 (p0) REVERT: C 90 THR cc_start: 0.8199 (m) cc_final: 0.7970 (m) REVERT: C 111 ASP cc_start: 0.7350 (t0) cc_final: 0.7124 (t0) REVERT: C 120 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: C 156 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: C 159 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6369 (tm-30) REVERT: C 179 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8346 (mp) REVERT: C 229 MET cc_start: 0.7362 (ppp) cc_final: 0.7088 (ppp) REVERT: C 252 GLN cc_start: 0.8409 (pm20) cc_final: 0.7961 (pm20) REVERT: C 253 LYS cc_start: 0.8085 (tttt) cc_final: 0.7779 (tttt) REVERT: C 270 THR cc_start: 0.8327 (p) cc_final: 0.7943 (t) REVERT: C 320 MET cc_start: 0.7636 (mmm) cc_final: 0.7043 (mmm) REVERT: D 20 SER cc_start: 0.7615 (p) cc_final: 0.7398 (p) REVERT: D 153 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8420 (mmtm) REVERT: D 253 LYS cc_start: 0.7777 (tppt) cc_final: 0.7460 (tppt) REVERT: D 262 ASP cc_start: 0.7098 (t0) cc_final: 0.6874 (t0) REVERT: D 272 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6556 (mp0) REVERT: E 18 ASN cc_start: 0.7692 (t0) cc_final: 0.7381 (t0) REVERT: E 159 GLU cc_start: 0.7184 (tp30) cc_final: 0.6947 (tp30) REVERT: E 180 ASP cc_start: 0.8067 (m-30) cc_final: 0.7716 (t0) REVERT: E 309 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5613 (tm-30) REVERT: F 21 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: F 48 LEU cc_start: 0.8647 (mm) cc_final: 0.8383 (mp) REVERT: F 89 ASP cc_start: 0.7989 (p0) cc_final: 0.7274 (p0) REVERT: F 104 GLU cc_start: 0.7231 (mp0) cc_final: 0.6946 (mp0) REVERT: F 111 ASP cc_start: 0.7482 (t0) cc_final: 0.7232 (t0) REVERT: F 144 ASN cc_start: 0.8133 (p0) cc_final: 0.7831 (p0) REVERT: F 191 GLU cc_start: 0.7784 (tp30) cc_final: 0.7511 (tp30) REVERT: F 228 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7050 (tm-30) REVERT: G 17 GLU cc_start: 0.8208 (pp20) cc_final: 0.7876 (pp20) REVERT: G 87 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7244 (pptt) REVERT: G 89 PRO cc_start: 0.8704 (Cg_endo) cc_final: 0.8473 (Cg_exo) REVERT: G 172 GLU cc_start: 0.7152 (tp30) cc_final: 0.6816 (tp30) REVERT: G 175 ASP cc_start: 0.7852 (m-30) cc_final: 0.7621 (t0) REVERT: G 201 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7468 (ttp80) REVERT: G 262 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7038 (tm-30) REVERT: G 277 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7186 (mtt180) REVERT: G 307 VAL cc_start: 0.8801 (m) cc_final: 0.8598 (p) REVERT: H 33 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7602 (mt) REVERT: H 126 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8038 (ttmm) REVERT: H 183 LEU cc_start: 0.8793 (mt) cc_final: 0.8450 (mp) REVERT: H 222 PHE cc_start: 0.8621 (m-80) cc_final: 0.8278 (m-10) REVERT: I 113 ARG cc_start: 0.7753 (mtt90) cc_final: 0.7466 (mtm110) outliers start: 106 outliers final: 74 residues processed: 773 average time/residue: 0.3342 time to fit residues: 392.7608 Evaluate side-chains 810 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 728 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 169 TYR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 151 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 103 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 237 optimal weight: 0.0970 chunk 226 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS G 304 HIS ** G 327 HIS ** 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 = 0.3412 r_free = 0.3412 target = 0.106322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.092935 restraints weight = 40104.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095852 restraints weight = 16934.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097672 restraints weight = 9119.132| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22155 Z= 0.173 Angle : 0.659 9.212 30349 Z= 0.343 Chirality : 0.043 0.297 3476 Planarity : 0.005 0.052 3676 Dihedral : 15.285 178.724 3773 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 4.57 % Allowed : 30.05 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2596 helix: 0.33 (0.19), residues: 764 sheet: 0.06 (0.27), residues: 405 loop : -1.78 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 149 HIS 0.010 0.001 HIS G 304 PHE 0.036 0.002 PHE B 243 TYR 0.032 0.002 TYR C 318 ARG 0.013 0.001 ARG E 150 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 595) hydrogen bonds : angle 4.87779 ( 1650) covalent geometry : bond 0.00397 (22155) covalent geometry : angle 0.65906 (30349) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 731 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.7002 (t0) cc_final: 0.6756 (t0) REVERT: A 40 ARG cc_start: 0.8220 (ptt-90) cc_final: 0.7889 (ptt90) REVERT: A 104 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7331 (mm-30) REVERT: A 175 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8265 (tttm) REVERT: A 253 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7647 (ttmt) REVERT: A 308 ASN cc_start: 0.8093 (m-40) cc_final: 0.7850 (t0) REVERT: A 309 GLU cc_start: 0.7218 (pt0) cc_final: 0.6982 (pm20) REVERT: A 320 MET cc_start: 0.7723 (tpp) cc_final: 0.6953 (mpp) REVERT: B 35 THR cc_start: 0.7799 (t) cc_final: 0.7373 (p) REVERT: B 52 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8471 (ttmm) REVERT: B 55 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7513 (tp) REVERT: B 90 THR cc_start: 0.8452 (m) cc_final: 0.7947 (p) REVERT: B 156 GLU cc_start: 0.6808 (tt0) cc_final: 0.6485 (tt0) REVERT: B 184 GLU cc_start: 0.7402 (mp0) cc_final: 0.7022 (mp0) REVERT: B 216 LYS cc_start: 0.8537 (tttt) cc_final: 0.8145 (tttt) REVERT: B 242 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8079 (ttmm) REVERT: B 253 LYS cc_start: 0.8287 (tttt) cc_final: 0.8077 (tppt) REVERT: B 278 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6745 (mt-10) REVERT: C 43 PHE cc_start: 0.8508 (t80) cc_final: 0.8014 (t80) REVERT: C 89 ASP cc_start: 0.7892 (p0) cc_final: 0.7350 (p0) REVERT: C 90 THR cc_start: 0.8209 (m) cc_final: 0.7980 (m) REVERT: C 111 ASP cc_start: 0.7367 (t0) cc_final: 0.7130 (t0) REVERT: C 120 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: C 156 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: C 159 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6377 (tm-30) REVERT: C 179 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8350 (mp) REVERT: C 185 ASP cc_start: 0.7221 (p0) cc_final: 0.6754 (p0) REVERT: C 229 MET cc_start: 0.7357 (ppp) cc_final: 0.7027 (ppp) REVERT: C 252 GLN cc_start: 0.8399 (pm20) cc_final: 0.7944 (pm20) REVERT: C 253 LYS cc_start: 0.8113 (tttt) cc_final: 0.7794 (tttt) REVERT: C 265 TYR cc_start: 0.7389 (p90) cc_final: 0.6904 (p90) REVERT: C 270 THR cc_start: 0.8346 (p) cc_final: 0.7907 (t) REVERT: C 320 MET cc_start: 0.7639 (mmm) cc_final: 0.7075 (mmm) REVERT: D 20 SER cc_start: 0.7609 (p) cc_final: 0.7398 (p) REVERT: D 153 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8405 (mmtm) REVERT: D 262 ASP cc_start: 0.7112 (t0) cc_final: 0.6876 (t0) REVERT: D 272 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6553 (mm-30) REVERT: D 278 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6736 (mt-10) REVERT: E 18 ASN cc_start: 0.7683 (t0) cc_final: 0.7321 (t0) REVERT: E 159 GLU cc_start: 0.7192 (tp30) cc_final: 0.6951 (tp30) REVERT: E 180 ASP cc_start: 0.8063 (m-30) cc_final: 0.7704 (t0) REVERT: E 309 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5645 (tm-30) REVERT: F 21 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: F 89 ASP cc_start: 0.7994 (p0) cc_final: 0.7286 (p0) REVERT: F 104 GLU cc_start: 0.7218 (mp0) cc_final: 0.6919 (mp0) REVERT: F 144 ASN cc_start: 0.8144 (p0) cc_final: 0.7832 (p0) REVERT: F 191 GLU cc_start: 0.7759 (tp30) cc_final: 0.7496 (tp30) REVERT: F 228 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7054 (tm-30) REVERT: F 315 ASP cc_start: 0.7653 (m-30) cc_final: 0.7248 (t0) REVERT: G 17 GLU cc_start: 0.8177 (pp20) cc_final: 0.7862 (pp20) REVERT: G 87 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7257 (pptt) REVERT: G 89 PRO cc_start: 0.8725 (Cg_endo) cc_final: 0.8508 (Cg_exo) REVERT: G 175 ASP cc_start: 0.7856 (m-30) cc_final: 0.7632 (t0) REVERT: G 176 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7950 (ttm170) REVERT: G 201 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7463 (ttp80) REVERT: G 262 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7050 (tm-30) REVERT: G 277 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7202 (mtt180) REVERT: G 322 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6900 (mtm) REVERT: H 10 LYS cc_start: 0.7543 (mmtm) cc_final: 0.7331 (mmtt) REVERT: H 33 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7621 (mt) REVERT: H 126 LYS cc_start: 0.8423 (ttmm) cc_final: 0.7906 (ttmm) REVERT: H 222 PHE cc_start: 0.8618 (m-80) cc_final: 0.8236 (m-80) REVERT: I 113 ARG cc_start: 0.7744 (mtt90) cc_final: 0.7454 (mtm110) REVERT: I 132 LYS cc_start: 0.8218 (tptp) cc_final: 0.7822 (tptp) outliers start: 95 outliers final: 73 residues processed: 763 average time/residue: 0.3345 time to fit residues: 388.8900 Evaluate side-chains 813 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 731 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 304 HIS Chi-restraints excluded: chain G residue 322 MET Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.106072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092639 restraints weight = 39535.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095568 restraints weight = 16675.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097389 restraints weight = 8956.916| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22155 Z= 0.207 Angle : 0.679 10.125 30349 Z= 0.354 Chirality : 0.044 0.294 3476 Planarity : 0.005 0.064 3676 Dihedral : 15.300 178.502 3773 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.28 % Allowed : 30.72 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2596 helix: 0.34 (0.19), residues: 762 sheet: 0.02 (0.27), residues: 410 loop : -1.75 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 149 HIS 0.011 0.001 HIS G 304 PHE 0.038 0.002 PHE B 243 TYR 0.034 0.002 TYR D 224 ARG 0.013 0.001 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 595) hydrogen bonds : angle 4.90798 ( 1650) covalent geometry : bond 0.00472 (22155) covalent geometry : angle 0.67909 (30349) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 719 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.7023 (t0) cc_final: 0.6764 (t0) REVERT: A 104 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7354 (mm-30) REVERT: A 159 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 175 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8242 (tttp) REVERT: A 253 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7653 (ttmt) REVERT: A 308 ASN cc_start: 0.8092 (m-40) cc_final: 0.7836 (t0) REVERT: A 309 GLU cc_start: 0.7210 (pt0) cc_final: 0.6980 (pm20) REVERT: A 320 MET cc_start: 0.7723 (tpp) cc_final: 0.6944 (mpp) REVERT: B 35 THR cc_start: 0.7835 (t) cc_final: 0.7421 (p) REVERT: B 55 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7530 (tp) REVERT: B 81 SER cc_start: 0.8115 (t) cc_final: 0.7579 (p) REVERT: B 90 THR cc_start: 0.8477 (m) cc_final: 0.7940 (p) REVERT: B 156 GLU cc_start: 0.6873 (tt0) cc_final: 0.6554 (tt0) REVERT: B 184 GLU cc_start: 0.7400 (mp0) cc_final: 0.7026 (mp0) REVERT: B 216 LYS cc_start: 0.8521 (tttt) cc_final: 0.8158 (tttt) REVERT: B 253 LYS cc_start: 0.8289 (tttt) cc_final: 0.8075 (tppt) REVERT: B 278 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6782 (mt-10) REVERT: B 318 TYR cc_start: 0.7950 (t80) cc_final: 0.7637 (t80) REVERT: B 324 ILE cc_start: 0.8013 (mp) cc_final: 0.7731 (mt) REVERT: C 43 PHE cc_start: 0.8534 (t80) cc_final: 0.8070 (t80) REVERT: C 89 ASP cc_start: 0.7869 (p0) cc_final: 0.7332 (p0) REVERT: C 90 THR cc_start: 0.8219 (m) cc_final: 0.7988 (m) REVERT: C 95 PHE cc_start: 0.8676 (p90) cc_final: 0.8414 (p90) REVERT: C 111 ASP cc_start: 0.7373 (t0) cc_final: 0.7158 (t0) REVERT: C 120 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: C 156 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: C 159 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6389 (tm-30) REVERT: C 179 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8340 (mp) REVERT: C 185 ASP cc_start: 0.7240 (p0) cc_final: 0.6781 (p0) REVERT: C 229 MET cc_start: 0.7373 (ppp) cc_final: 0.7127 (ppp) REVERT: C 252 GLN cc_start: 0.8405 (pm20) cc_final: 0.7958 (pm20) REVERT: C 253 LYS cc_start: 0.8108 (tttt) cc_final: 0.7778 (tttt) REVERT: C 265 TYR cc_start: 0.7415 (p90) cc_final: 0.6912 (p90) REVERT: C 270 THR cc_start: 0.8379 (p) cc_final: 0.7942 (t) REVERT: C 306 LEU cc_start: 0.8132 (mt) cc_final: 0.7923 (tp) REVERT: C 320 MET cc_start: 0.7653 (mmm) cc_final: 0.7087 (mmm) REVERT: D 153 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8407 (mmtm) REVERT: D 262 ASP cc_start: 0.7136 (t0) cc_final: 0.6930 (t0) REVERT: D 272 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6745 (mm-30) REVERT: D 278 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6699 (mt-10) REVERT: E 18 ASN cc_start: 0.7675 (t0) cc_final: 0.7312 (t0) REVERT: E 159 GLU cc_start: 0.7199 (tp30) cc_final: 0.6944 (tp30) REVERT: E 180 ASP cc_start: 0.8063 (m-30) cc_final: 0.7695 (t0) REVERT: E 290 PHE cc_start: 0.7987 (m-80) cc_final: 0.7579 (t80) REVERT: F 21 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: F 89 ASP cc_start: 0.8007 (p0) cc_final: 0.7687 (p0) REVERT: F 104 GLU cc_start: 0.7201 (mp0) cc_final: 0.6915 (mp0) REVERT: F 144 ASN cc_start: 0.8153 (p0) cc_final: 0.7827 (p0) REVERT: F 191 GLU cc_start: 0.7768 (tp30) cc_final: 0.7509 (tp30) REVERT: F 228 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7065 (tm-30) REVERT: F 315 ASP cc_start: 0.7661 (m-30) cc_final: 0.7264 (t0) REVERT: G 17 GLU cc_start: 0.8198 (pp20) cc_final: 0.7888 (pp20) REVERT: G 87 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7260 (pptt) REVERT: G 132 ILE cc_start: 0.8433 (pp) cc_final: 0.8154 (pp) REVERT: G 175 ASP cc_start: 0.7787 (m-30) cc_final: 0.7574 (t0) REVERT: G 176 ARG cc_start: 0.8256 (ttm170) cc_final: 0.7993 (ttm170) REVERT: G 266 LYS cc_start: 0.8644 (mttm) cc_final: 0.8418 (mttm) REVERT: G 277 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7224 (mtt180) REVERT: H 33 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7675 (mt) REVERT: H 126 LYS cc_start: 0.8429 (ttmm) cc_final: 0.7957 (ttmm) REVERT: H 183 LEU cc_start: 0.8811 (mt) cc_final: 0.8481 (mp) REVERT: H 222 PHE cc_start: 0.8639 (m-80) cc_final: 0.8261 (m-80) REVERT: I 113 ARG cc_start: 0.7735 (mtt90) cc_final: 0.7427 (mtm110) REVERT: I 132 LYS cc_start: 0.8253 (tptp) cc_final: 0.7889 (tptp) outliers start: 89 outliers final: 76 residues processed: 751 average time/residue: 0.3295 time to fit residues: 378.1562 Evaluate side-chains 795 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 712 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 164 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 220 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS G 304 HIS ** G 327 HIS ** 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 = 0.3418 r_free = 0.3418 target = 0.106601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093215 restraints weight = 39231.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096144 restraints weight = 16540.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097959 restraints weight = 8880.076| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22155 Z= 0.183 Angle : 0.671 9.401 30349 Z= 0.349 Chirality : 0.044 0.279 3476 Planarity : 0.005 0.092 3676 Dihedral : 15.267 178.679 3771 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.28 % Allowed : 31.06 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2596 helix: 0.35 (0.19), residues: 760 sheet: 0.05 (0.27), residues: 399 loop : -1.73 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 149 HIS 0.013 0.001 HIS G 304 PHE 0.037 0.002 PHE B 243 TYR 0.034 0.002 TYR D 224 ARG 0.012 0.001 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 595) hydrogen bonds : angle 4.88296 ( 1650) covalent geometry : bond 0.00420 (22155) covalent geometry : angle 0.67068 (30349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9790.27 seconds wall clock time: 172 minutes 41.13 seconds (10361.13 seconds total)