Starting phenix.real_space_refine on Thu Sep 18 08:32:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9is6_60832/09_2025/9is6_60832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9is6_60832/09_2025/9is6_60832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9is6_60832/09_2025/9is6_60832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9is6_60832/09_2025/9is6_60832.map" model { file = "/net/cci-nas-00/data/ceres_data/9is6_60832/09_2025/9is6_60832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9is6_60832/09_2025/9is6_60832.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 Zn 1 6.06 5 S 69 5.16 5 C 9416 2.51 5 N 2583 2.21 5 O 2843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14912 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1341 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 3, 'ARG:plan': 5, 'PHE:plan': 4, 'ASP:plan': 9, 'ASN:plan1': 6, 'GLN:plan1': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 158 Chain: "H" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1562 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 192} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1747 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain: "F" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2289 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2375 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 287} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2850 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 12, 'TRANS': 381} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'HIS:plan': 2, 'ARG:plan': 2, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "D" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 1975 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 14, 'GLN:plan1': 8, 'ARG:plan': 6, 'TYR:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 215 Chain: "B" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 772 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.34, per 1000 atoms: 0.22 Number of scatterers: 14912 At special positions: 0 Unit cell: (132.6, 150.45, 139.4, 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) Zn 1 29.99 S 69 16.00 O 2843 8.00 N 2583 7.00 C 9416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 690.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 400 " pdb="ZN ZN E 400 " - pdb=" NE2 HIS E 144 " pdb="ZN ZN E 400 " - pdb=" NE2 HIS E 142 " 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3790 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 10 sheets defined 66.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.715A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 282 through 292 removed outlier: 4.461A pdb=" N PHE A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 Processing helix chain 'A' and resid 306 through 322 removed outlier: 4.520A pdb=" N SER A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 4.145A pdb=" N HIS A 330 " --> pdb=" O HIS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.746A pdb=" N ASP A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 379 Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.598A pdb=" N LEU A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 435 " --> pdb=" O HIS A 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 12 Processing helix chain 'H' and resid 17 through 33 removed outlier: 3.633A pdb=" N ASP H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN H 28 " --> pdb=" O THR H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 52 removed outlier: 3.630A pdb=" N TYR H 49 " --> pdb=" O HIS H 45 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL H 52 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 Processing helix chain 'H' and resid 66 through 73 Processing helix chain 'H' and resid 73 through 88 removed outlier: 4.226A pdb=" N VAL H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS H 85 " --> pdb=" O GLY H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 99 removed outlier: 3.965A pdb=" N GLU H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 135 through 143 Processing helix chain 'H' and resid 145 through 156 removed outlier: 3.569A pdb=" N VAL H 154 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 155 " --> pdb=" O THR H 151 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN H 156 " --> pdb=" O TYR H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 196 Processing helix chain 'G' and resid 2 through 19 removed outlier: 4.038A pdb=" N LYS G 6 " --> pdb=" O ASP G 2 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE G 10 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 36 removed outlier: 3.622A pdb=" N ILE G 31 " --> pdb=" O GLY G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 48 Processing helix chain 'G' and resid 49 through 55 removed outlier: 3.823A pdb=" N GLN G 53 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU G 54 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU G 55 " --> pdb=" O VAL G 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 55' Processing helix chain 'G' and resid 59 through 71 removed outlier: 3.676A pdb=" N LEU G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 88 through 106 removed outlier: 3.732A pdb=" N VAL G 100 " --> pdb=" O LYS G 96 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 101 " --> pdb=" O GLN G 97 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER G 106 " --> pdb=" O THR G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 120 Processing helix chain 'G' and resid 123 through 135 Processing helix chain 'G' and resid 166 through 220 removed outlier: 3.588A pdb=" N LEU G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE G 186 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA G 209 " --> pdb=" O HIS G 205 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU G 210 " --> pdb=" O ARG G 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 216 " --> pdb=" O GLY G 212 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 33 removed outlier: 3.916A pdb=" N MET F 18 " --> pdb=" O HIS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 104 removed outlier: 3.681A pdb=" N LEU F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.831A pdb=" N MET F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA F 129 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET F 131 " --> pdb=" O HIS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 removed outlier: 3.559A pdb=" N SER F 189 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 239 removed outlier: 3.669A pdb=" N ILE F 215 " --> pdb=" O HIS F 211 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG F 225 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS F 232 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.815A pdb=" N LEU F 248 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN F 250 " --> pdb=" O SER F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 304 removed outlier: 3.901A pdb=" N GLU F 295 " --> pdb=" O SER F 291 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 297 " --> pdb=" O MET F 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 removed outlier: 4.123A pdb=" N ARG E 42 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS E 47 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.671A pdb=" N ASP E 115 " --> pdb=" O ASN E 112 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP E 116 " --> pdb=" O ALA E 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 116' Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 152 through 166 removed outlier: 3.570A pdb=" N SER E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.530A pdb=" N THR E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 221 Processing helix chain 'E' and resid 235 through 247 removed outlier: 3.529A pdb=" N ASN E 247 " --> pdb=" O ASP E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 264 through 288 removed outlier: 3.731A pdb=" N GLN E 269 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 336 removed outlier: 4.629A pdb=" N GLU E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN E 321 " --> pdb=" O ILE E 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 16 removed outlier: 3.651A pdb=" N ALA C 10 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 76 through 92 Proline residue: C 84 - end of helix removed outlier: 3.654A pdb=" N ARG C 88 " --> pdb=" O PRO C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.948A pdb=" N VAL C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 124 Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.624A pdb=" N ALA C 132 " --> pdb=" O PRO C 128 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.680A pdb=" N LEU C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.526A pdb=" N PHE C 164 " --> pdb=" O TYR C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 Processing helix chain 'C' and resid 196 through 209 removed outlier: 3.915A pdb=" N GLU C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 removed outlier: 3.552A pdb=" N LYS C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 257 through 270 removed outlier: 3.641A pdb=" N LEU C 263 " --> pdb=" O PRO C 259 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 264 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 removed outlier: 4.250A pdb=" N VAL C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.598A pdb=" N PHE C 286 " --> pdb=" O ARG C 282 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 3.849A pdb=" N GLN C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 300 " --> pdb=" O LYS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.870A pdb=" N LYS C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 330 through 345 removed outlier: 3.582A pdb=" N ALA C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 399 removed outlier: 3.642A pdb=" N ILE C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 389 " --> pdb=" O GLY C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'D' and resid 93 through 109 Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 135 through 150 Processing helix chain 'D' and resid 156 through 165 removed outlier: 3.703A pdb=" N PHE D 165 " --> pdb=" O ASN D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 190 removed outlier: 4.004A pdb=" N MET D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 203 removed outlier: 3.768A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.527A pdb=" N GLN D 208 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 235 removed outlier: 3.666A pdb=" N GLU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 removed outlier: 3.601A pdb=" N THR D 247 " --> pdb=" O ARG D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 268 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.502A pdb=" N ALA D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 315 removed outlier: 4.142A pdb=" N LYS D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.942A pdb=" N THR D 325 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 326' Processing helix chain 'D' and resid 330 through 344 Processing helix chain 'D' and resid 365 through 392 removed outlier: 3.580A pdb=" N LEU D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 359 removed outlier: 3.573A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 375 Processing helix chain 'B' and resid 377 through 391 Processing helix chain 'B' and resid 414 through 436 removed outlier: 3.705A pdb=" N ASP B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 352 through 354 removed outlier: 3.566A pdb=" N VAL A 353 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.911A pdb=" N THR H 159 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET H 166 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 109 through 111 removed outlier: 3.624A pdb=" N CYS G 151 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG G 142 " --> pdb=" O PRO G 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 66 through 67 removed outlier: 6.317A pdb=" N THR F 10 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 75 through 78 removed outlier: 3.838A pdb=" N ASN F 75 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY F 60 " --> pdb=" O TRP F 112 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP F 112 " --> pdb=" O GLY F 60 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL F 62 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR F 108 " --> pdb=" O GLY F 64 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N VAL F 138 " --> pdb=" O TYR F 108 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU F 110 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL F 140 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP F 112 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU F 142 " --> pdb=" O TRP F 112 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER F 114 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'E' and resid 59 through 62 removed outlier: 7.165A pdb=" N VAL E 59 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE E 233 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE E 61 " --> pdb=" O PHE E 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 98 through 101 removed outlier: 6.714A pdb=" N GLY E 83 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP E 140 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET E 85 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 174 " --> pdb=" O HIS E 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 318 through 319 Processing sheet with id=AB1, first strand: chain 'B' and resid 364 through 366 removed outlier: 3.778A pdb=" N ILE B 365 " --> pdb=" O LEU B 405 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4999 1.34 - 1.46: 3085 1.46 - 1.58: 6958 1.58 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 15158 Sorted by residual: bond pdb=" N ILE D 259 " pdb=" CA ILE D 259 " ideal model delta sigma weight residual 1.462 1.494 -0.031 1.06e-02 8.90e+03 8.81e+00 bond pdb=" N ILE H 34 " pdb=" CA ILE H 34 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.36e+00 bond pdb=" N ILE D 203 " pdb=" CA ILE D 203 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.81e+00 bond pdb=" N VAL D 266 " pdb=" CA VAL D 266 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.22e-02 6.72e+03 7.54e+00 bond pdb=" N LEU D 257 " pdb=" CA LEU D 257 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.25e-02 6.40e+03 7.07e+00 ... (remaining 15153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 20073 1.70 - 3.41: 399 3.41 - 5.11: 66 5.11 - 6.81: 14 6.81 - 8.52: 4 Bond angle restraints: 20556 Sorted by residual: angle pdb=" CB LYS C 141 " pdb=" CG LYS C 141 " pdb=" CD LYS C 141 " ideal model delta sigma weight residual 111.30 119.71 -8.41 2.30e+00 1.89e-01 1.34e+01 angle pdb=" CA LEU F 52 " pdb=" C LEU F 52 " pdb=" O LEU F 52 " ideal model delta sigma weight residual 122.64 118.08 4.56 1.25e+00 6.40e-01 1.33e+01 angle pdb=" CA LEU D 284 " pdb=" C LEU D 284 " pdb=" O LEU D 284 " ideal model delta sigma weight residual 122.36 117.99 4.37 1.21e+00 6.83e-01 1.30e+01 angle pdb=" N TYR D 201 " pdb=" CA TYR D 201 " pdb=" C TYR D 201 " ideal model delta sigma weight residual 111.28 107.42 3.86 1.09e+00 8.42e-01 1.26e+01 angle pdb=" N VAL D 174 " pdb=" CA VAL D 174 " pdb=" C VAL D 174 " ideal model delta sigma weight residual 112.29 108.98 3.31 9.40e-01 1.13e+00 1.24e+01 ... (remaining 20551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7886 17.94 - 35.88: 963 35.88 - 53.82: 269 53.82 - 71.76: 51 71.76 - 89.70: 26 Dihedral angle restraints: 9195 sinusoidal: 3361 harmonic: 5834 Sorted by residual: dihedral pdb=" CA ASP E 238 " pdb=" CB ASP E 238 " pdb=" CG ASP E 238 " pdb=" OD1 ASP E 238 " ideal model delta sinusoidal sigma weight residual -30.00 -86.11 56.11 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU D 269 " pdb=" CG GLU D 269 " pdb=" CD GLU D 269 " pdb=" OE1 GLU D 269 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA THR D 325 " pdb=" C THR D 325 " pdb=" N LEU D 326 " pdb=" CA LEU D 326 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 9192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1951 0.047 - 0.094: 353 0.094 - 0.141: 68 0.141 - 0.188: 13 0.188 - 0.236: 4 Chirality restraints: 2389 Sorted by residual: chirality pdb=" CG LEU A 343 " pdb=" CB LEU A 343 " pdb=" CD1 LEU A 343 " pdb=" CD2 LEU A 343 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE H 34 " pdb=" N ILE H 34 " pdb=" C ILE H 34 " pdb=" CB ILE H 34 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE D 203 " pdb=" N ILE D 203 " pdb=" C ILE D 203 " pdb=" CB ILE D 203 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 2386 not shown) Planarity restraints: 2657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 255 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C SER D 255 " 0.043 2.00e-02 2.50e+03 pdb=" O SER D 255 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS D 256 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 67 " 0.135 9.50e-02 1.11e+02 6.10e-02 2.94e+00 pdb=" NE ARG F 67 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 67 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG F 67 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 67 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 154 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO G 155 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 155 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 155 " -0.019 5.00e-02 4.00e+02 ... (remaining 2654 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 112 2.57 - 3.15: 12341 3.15 - 3.73: 23867 3.73 - 4.32: 29520 4.32 - 4.90: 48294 Nonbonded interactions: 114134 Sorted by model distance: nonbonded pdb=" OD2 ASP E 155 " pdb="ZN ZN E 400 " model vdw 1.987 2.230 nonbonded pdb=" OE2 GLU E 108 " pdb="ZN ZN E 400 " model vdw 1.987 2.230 nonbonded pdb=" OE2 GLU A 374 " pdb=" OH TYR C 314 " model vdw 2.180 3.040 nonbonded pdb=" ND2 ASN A 427 " pdb=" O VAL C 172 " model vdw 2.197 3.120 nonbonded pdb=" OH TYR H 191 " pdb=" OD1 ASP C 377 " model vdw 2.200 3.040 ... (remaining 114129 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15160 Z= 0.193 Angle : 0.567 8.517 20556 Z= 0.329 Chirality : 0.040 0.236 2389 Planarity : 0.003 0.061 2657 Dihedral : 17.782 89.696 5405 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.54 % Allowed : 30.34 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.19), residues: 1959 helix: 1.09 (0.15), residues: 1191 sheet: -1.35 (0.45), residues: 142 loop : -2.02 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 67 TYR 0.011 0.001 TYR G 77 PHE 0.014 0.001 PHE E 43 TRP 0.007 0.001 TRP H 158 HIS 0.008 0.001 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.00308 (15158) covalent geometry : angle 0.56677 (20556) hydrogen bonds : bond 0.27004 ( 885) hydrogen bonds : angle 6.66658 ( 2613) metal coordination : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 250 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLN cc_start: 0.8152 (tp40) cc_final: 0.7886 (tp40) REVERT: H 87 TRP cc_start: 0.7931 (t-100) cc_final: 0.6985 (t-100) REVERT: H 91 TYR cc_start: 0.8629 (m-80) cc_final: 0.8188 (m-80) REVERT: H 110 MET cc_start: 0.6228 (ttt) cc_final: 0.5405 (ttp) REVERT: H 127 LEU cc_start: 0.8502 (tt) cc_final: 0.8211 (tp) REVERT: H 156 ASN cc_start: 0.7146 (t0) cc_final: 0.6879 (t0) REVERT: G 54 LEU cc_start: 0.7319 (tp) cc_final: 0.7090 (tp) REVERT: F 124 MET cc_start: 0.8252 (tpt) cc_final: 0.7904 (tpt) REVERT: F 170 GLN cc_start: 0.8107 (mt0) cc_final: 0.7774 (mt0) REVERT: F 236 MET cc_start: 0.7307 (tpp) cc_final: 0.6639 (ttt) REVERT: E 169 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: C 243 LYS cc_start: 0.7781 (tptt) cc_final: 0.7259 (tttt) REVERT: C 253 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6444 (t80) REVERT: D 256 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7506 (ttpp) REVERT: B 378 GLU cc_start: 0.7631 (tm-30) cc_final: 0.6273 (mt-10) outliers start: 8 outliers final: 1 residues processed: 256 average time/residue: 0.1257 time to fit residues: 47.5275 Evaluate side-chains 191 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 256 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN G 7 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN E 128 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN C 306 ASN B 402 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.132745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.099833 restraints weight = 33092.366| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.35 r_work: 0.3426 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15160 Z= 0.179 Angle : 0.598 7.871 20556 Z= 0.324 Chirality : 0.041 0.223 2389 Planarity : 0.004 0.044 2657 Dihedral : 4.813 75.641 2131 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 3.99 % Allowed : 27.57 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.19), residues: 1959 helix: 1.51 (0.15), residues: 1234 sheet: -1.53 (0.44), residues: 145 loop : -2.12 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 67 TYR 0.016 0.002 TYR H 51 PHE 0.017 0.002 PHE G 152 TRP 0.008 0.001 TRP D 370 HIS 0.007 0.001 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.00394 (15158) covalent geometry : angle 0.59846 (20556) hydrogen bonds : bond 0.06589 ( 885) hydrogen bonds : angle 4.80241 ( 2613) metal coordination : bond 0.00689 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ILE cc_start: 0.8525 (pt) cc_final: 0.8319 (mm) REVERT: A 432 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8179 (tm-30) REVERT: H 1 MET cc_start: 0.6882 (mpp) cc_final: 0.6570 (mpp) REVERT: H 46 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5848 (tt) REVERT: H 49 TYR cc_start: 0.7063 (m-80) cc_final: 0.6817 (m-10) REVERT: H 54 ASP cc_start: 0.7580 (t0) cc_final: 0.7096 (t0) REVERT: H 85 LYS cc_start: 0.7691 (mmtp) cc_final: 0.7482 (mttm) REVERT: H 91 TYR cc_start: 0.8590 (m-80) cc_final: 0.8203 (m-80) REVERT: H 127 LEU cc_start: 0.8757 (tt) cc_final: 0.8546 (tp) REVERT: H 156 ASN cc_start: 0.7545 (t0) cc_final: 0.7185 (t0) REVERT: H 170 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7395 (pptt) REVERT: G 24 GLU cc_start: 0.8795 (pm20) cc_final: 0.8594 (mm-30) REVERT: G 107 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8107 (m110) REVERT: F 170 GLN cc_start: 0.8252 (mt0) cc_final: 0.7862 (mt0) REVERT: F 236 MET cc_start: 0.7157 (tpp) cc_final: 0.6775 (ttt) REVERT: E 82 MET cc_start: 0.8640 (tmm) cc_final: 0.8283 (ttm) REVERT: E 112 ASN cc_start: 0.7984 (t0) cc_final: 0.7783 (t0) REVERT: E 169 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: E 272 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8307 (t0) REVERT: C 142 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7876 (tpp-160) REVERT: C 243 LYS cc_start: 0.7962 (tptt) cc_final: 0.7282 (tttt) REVERT: D 248 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9085 (mm) REVERT: D 283 GLU cc_start: 0.8030 (tp30) cc_final: 0.7648 (tp30) REVERT: D 362 ASP cc_start: 0.8062 (p0) cc_final: 0.7220 (m-30) REVERT: B 400 GLU cc_start: 0.8667 (tp30) cc_final: 0.8116 (tm-30) outliers start: 59 outliers final: 29 residues processed: 256 average time/residue: 0.1181 time to fit residues: 45.5575 Evaluate side-chains 226 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 86 HIS Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 272 ASP Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 178 optimal weight: 3.9990 chunk 167 optimal weight: 0.0770 chunk 131 optimal weight: 0.6980 chunk 163 optimal weight: 40.0000 chunk 191 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN E 221 HIS E 336 ASN C 115 HIS C 147 HIS ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.135470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.102781 restraints weight = 33277.600| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.40 r_work: 0.3474 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15160 Z= 0.116 Angle : 0.507 6.672 20556 Z= 0.269 Chirality : 0.038 0.159 2389 Planarity : 0.003 0.035 2657 Dihedral : 4.512 76.764 2127 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.58 % Allowed : 27.03 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.20), residues: 1959 helix: 1.77 (0.15), residues: 1239 sheet: -1.32 (0.44), residues: 144 loop : -2.13 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 285 TYR 0.013 0.001 TYR F 108 PHE 0.012 0.001 PHE G 152 TRP 0.009 0.001 TRP H 62 HIS 0.006 0.001 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.00230 (15158) covalent geometry : angle 0.50737 (20556) hydrogen bonds : bond 0.04830 ( 885) hydrogen bonds : angle 4.22608 ( 2613) metal coordination : bond 0.00251 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 54 ASP cc_start: 0.7537 (t0) cc_final: 0.6952 (t0) REVERT: H 85 LYS cc_start: 0.7519 (mmtp) cc_final: 0.7130 (mttt) REVERT: H 170 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7420 (pptt) REVERT: G 24 GLU cc_start: 0.8803 (pm20) cc_final: 0.8540 (mm-30) REVERT: F 170 GLN cc_start: 0.8237 (mt0) cc_final: 0.7843 (mt0) REVERT: F 236 MET cc_start: 0.6894 (tpp) cc_final: 0.6596 (ttt) REVERT: F 302 THR cc_start: 0.7880 (t) cc_final: 0.7580 (t) REVERT: E 112 ASN cc_start: 0.8017 (t0) cc_final: 0.7744 (t0) REVERT: E 169 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: C 243 LYS cc_start: 0.7997 (tptt) cc_final: 0.7379 (tttt) REVERT: C 309 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6465 (mpt180) REVERT: D 219 ASN cc_start: 0.7852 (t0) cc_final: 0.7456 (t0) REVERT: D 223 GLN cc_start: 0.7646 (mt0) cc_final: 0.7180 (mt0) REVERT: D 232 THR cc_start: 0.8883 (m) cc_final: 0.8421 (p) REVERT: D 248 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9041 (mm) REVERT: D 283 GLU cc_start: 0.7820 (tp30) cc_final: 0.7448 (tp30) REVERT: D 288 GLN cc_start: 0.6772 (mm-40) cc_final: 0.5192 (tp40) REVERT: D 362 ASP cc_start: 0.8012 (p0) cc_final: 0.7298 (m-30) REVERT: B 400 GLU cc_start: 0.8608 (tp30) cc_final: 0.8135 (tm-30) REVERT: B 406 LEU cc_start: 0.8137 (mm) cc_final: 0.7554 (tt) outliers start: 53 outliers final: 24 residues processed: 265 average time/residue: 0.1212 time to fit residues: 47.8723 Evaluate side-chains 212 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 86 HIS Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 117 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.133626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100518 restraints weight = 33108.316| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.38 r_work: 0.3437 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15160 Z= 0.136 Angle : 0.525 10.712 20556 Z= 0.275 Chirality : 0.039 0.169 2389 Planarity : 0.003 0.040 2657 Dihedral : 4.483 74.554 2127 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.12 % Allowed : 26.89 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.20), residues: 1959 helix: 1.82 (0.15), residues: 1246 sheet: -1.25 (0.44), residues: 144 loop : -2.20 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 206 TYR 0.016 0.001 TYR G 77 PHE 0.015 0.001 PHE C 237 TRP 0.009 0.001 TRP D 370 HIS 0.005 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00310 (15158) covalent geometry : angle 0.52544 (20556) hydrogen bonds : bond 0.04638 ( 885) hydrogen bonds : angle 4.14711 ( 2613) metal coordination : bond 0.00418 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6719 (m-70) REVERT: H 2 ASP cc_start: 0.5978 (p0) cc_final: 0.5765 (p0) REVERT: H 54 ASP cc_start: 0.7582 (t0) cc_final: 0.7151 (t0) REVERT: H 85 LYS cc_start: 0.7636 (mmtp) cc_final: 0.7425 (mttm) REVERT: H 91 TYR cc_start: 0.8506 (m-80) cc_final: 0.8134 (m-80) REVERT: H 110 MET cc_start: 0.7741 (ttt) cc_final: 0.7018 (ttp) REVERT: H 170 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7231 (pptt) REVERT: G 24 GLU cc_start: 0.8809 (pm20) cc_final: 0.8514 (mm-30) REVERT: G 206 ARG cc_start: 0.8405 (ttp-110) cc_final: 0.7506 (ptm160) REVERT: F 170 GLN cc_start: 0.8217 (mt0) cc_final: 0.7839 (mt0) REVERT: E 57 LYS cc_start: 0.8414 (mmtp) cc_final: 0.7943 (tptt) REVERT: E 58 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8109 (mpp80) REVERT: E 82 MET cc_start: 0.8713 (tmm) cc_final: 0.8329 (ttm) REVERT: E 112 ASN cc_start: 0.8094 (t0) cc_final: 0.7842 (t0) REVERT: E 154 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7282 (mp) REVERT: E 169 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: C 243 LYS cc_start: 0.7998 (tptt) cc_final: 0.7374 (tttt) REVERT: C 309 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6396 (mpt180) REVERT: D 219 ASN cc_start: 0.7913 (t0) cc_final: 0.7446 (t0) REVERT: D 223 GLN cc_start: 0.7756 (mt0) cc_final: 0.7220 (mt0) REVERT: D 232 THR cc_start: 0.8760 (m) cc_final: 0.8360 (p) REVERT: D 283 GLU cc_start: 0.7761 (tp30) cc_final: 0.7403 (tp30) REVERT: D 362 ASP cc_start: 0.8016 (p0) cc_final: 0.7361 (m-30) REVERT: B 400 GLU cc_start: 0.8631 (tp30) cc_final: 0.7976 (tm-30) outliers start: 61 outliers final: 31 residues processed: 244 average time/residue: 0.1229 time to fit residues: 44.9629 Evaluate side-chains 223 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 86 HIS Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 175 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 1 optimal weight: 40.0000 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.135128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.102151 restraints weight = 33024.989| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.39 r_work: 0.3418 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15160 Z= 0.108 Angle : 0.506 8.703 20556 Z= 0.263 Chirality : 0.038 0.161 2389 Planarity : 0.003 0.036 2657 Dihedral : 4.429 74.979 2127 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.45 % Allowed : 26.96 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1959 helix: 1.92 (0.15), residues: 1248 sheet: -1.10 (0.45), residues: 144 loop : -2.15 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 437 TYR 0.012 0.001 TYR E 147 PHE 0.012 0.001 PHE E 218 TRP 0.008 0.001 TRP H 62 HIS 0.005 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00231 (15158) covalent geometry : angle 0.50565 (20556) hydrogen bonds : bond 0.04144 ( 885) hydrogen bonds : angle 3.98940 ( 2613) metal coordination : bond 0.00195 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6737 (m-70) REVERT: H 54 ASP cc_start: 0.7549 (t0) cc_final: 0.7123 (t0) REVERT: H 85 LYS cc_start: 0.7582 (mmtp) cc_final: 0.7368 (mttm) REVERT: H 110 MET cc_start: 0.7855 (ttt) cc_final: 0.7246 (ttp) REVERT: H 170 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7510 (pptt) REVERT: G 24 GLU cc_start: 0.8781 (pm20) cc_final: 0.8465 (mm-30) REVERT: F 170 GLN cc_start: 0.8198 (mt0) cc_final: 0.7829 (mt0) REVERT: F 302 THR cc_start: 0.7851 (t) cc_final: 0.7592 (t) REVERT: E 58 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8075 (mpp80) REVERT: E 82 MET cc_start: 0.8735 (tmm) cc_final: 0.8359 (ttm) REVERT: E 112 ASN cc_start: 0.8012 (t0) cc_final: 0.7743 (t0) REVERT: E 169 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: C 243 LYS cc_start: 0.8025 (tptt) cc_final: 0.7415 (tttt) REVERT: C 309 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6417 (mpt180) REVERT: D 219 ASN cc_start: 0.7931 (t0) cc_final: 0.7455 (t0) REVERT: D 223 GLN cc_start: 0.7773 (mt0) cc_final: 0.7244 (mt0) REVERT: D 232 THR cc_start: 0.8705 (m) cc_final: 0.8317 (p) REVERT: D 282 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: D 283 GLU cc_start: 0.7651 (tp30) cc_final: 0.7293 (tp30) REVERT: D 285 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.7499 (mmp-170) REVERT: D 362 ASP cc_start: 0.7985 (p0) cc_final: 0.7388 (m-30) REVERT: B 400 GLU cc_start: 0.8540 (tp30) cc_final: 0.7962 (tm-30) REVERT: B 401 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.8041 (mmm) outliers start: 51 outliers final: 27 residues processed: 239 average time/residue: 0.1269 time to fit residues: 45.2964 Evaluate side-chains 215 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 86 HIS Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain B residue 401 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 89 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 190 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 chunk 118 optimal weight: 6.9990 chunk 11 optimal weight: 0.0470 chunk 161 optimal weight: 9.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN ** B 424 ASN ** 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 = 0.4081 r_free = 0.4081 target = 0.134878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101926 restraints weight = 32972.851| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.38 r_work: 0.3464 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15160 Z= 0.112 Angle : 0.503 7.112 20556 Z= 0.263 Chirality : 0.038 0.232 2389 Planarity : 0.003 0.037 2657 Dihedral : 4.398 74.900 2127 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.45 % Allowed : 27.23 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.20), residues: 1959 helix: 1.98 (0.15), residues: 1251 sheet: -1.05 (0.45), residues: 144 loop : -2.19 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 206 TYR 0.020 0.001 TYR G 77 PHE 0.012 0.001 PHE E 218 TRP 0.008 0.001 TRP H 62 HIS 0.004 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00246 (15158) covalent geometry : angle 0.50349 (20556) hydrogen bonds : bond 0.04014 ( 885) hydrogen bonds : angle 3.92841 ( 2613) metal coordination : bond 0.00284 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 TYR cc_start: 0.8686 (m-80) cc_final: 0.8349 (m-80) REVERT: A 434 HIS cc_start: 0.7082 (OUTLIER) cc_final: 0.6801 (m-70) REVERT: H 1 MET cc_start: 0.7047 (mpp) cc_final: 0.6780 (mpp) REVERT: H 85 LYS cc_start: 0.7606 (mmtp) cc_final: 0.7387 (mttm) REVERT: H 91 TYR cc_start: 0.8364 (m-80) cc_final: 0.7980 (m-80) REVERT: H 110 MET cc_start: 0.7784 (ttt) cc_final: 0.7192 (ttp) REVERT: H 170 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7565 (pptt) REVERT: G 24 GLU cc_start: 0.8757 (pm20) cc_final: 0.8422 (mm-30) REVERT: G 206 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.7515 (ptm160) REVERT: F 170 GLN cc_start: 0.8229 (mt0) cc_final: 0.7873 (mt0) REVERT: F 236 MET cc_start: 0.6833 (tpp) cc_final: 0.6547 (ttt) REVERT: F 302 THR cc_start: 0.7820 (t) cc_final: 0.7561 (t) REVERT: E 57 LYS cc_start: 0.8412 (mmtp) cc_final: 0.7909 (tptt) REVERT: E 58 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8071 (mpp80) REVERT: E 82 MET cc_start: 0.8708 (tmm) cc_final: 0.8352 (ttm) REVERT: E 112 ASN cc_start: 0.8034 (t0) cc_final: 0.7767 (t0) REVERT: E 169 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: C 243 LYS cc_start: 0.8044 (tptt) cc_final: 0.7456 (tttt) REVERT: C 309 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6396 (mpt180) REVERT: D 219 ASN cc_start: 0.8000 (t0) cc_final: 0.7762 (t0) REVERT: D 232 THR cc_start: 0.8704 (m) cc_final: 0.8318 (p) REVERT: D 283 GLU cc_start: 0.7587 (tp30) cc_final: 0.7195 (tp30) REVERT: D 362 ASP cc_start: 0.7949 (p0) cc_final: 0.7401 (m-30) REVERT: B 400 GLU cc_start: 0.8522 (tp30) cc_final: 0.7933 (tm-30) REVERT: B 401 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7990 (mmm) outliers start: 51 outliers final: 33 residues processed: 228 average time/residue: 0.1253 time to fit residues: 42.8447 Evaluate side-chains 219 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 86 HIS Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain B residue 401 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 51 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN G 183 ASN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN B 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.133003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099840 restraints weight = 32817.269| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.34 r_work: 0.3383 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15160 Z= 0.152 Angle : 0.539 8.656 20556 Z= 0.282 Chirality : 0.039 0.163 2389 Planarity : 0.004 0.042 2657 Dihedral : 4.449 71.966 2127 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.72 % Allowed : 27.36 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.20), residues: 1959 helix: 1.93 (0.15), residues: 1249 sheet: -1.12 (0.44), residues: 145 loop : -2.19 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 206 TYR 0.014 0.001 TYR F 113 PHE 0.016 0.001 PHE E 218 TRP 0.009 0.001 TRP D 370 HIS 0.007 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00356 (15158) covalent geometry : angle 0.53896 (20556) hydrogen bonds : bond 0.04365 ( 885) hydrogen bonds : angle 4.02154 ( 2613) metal coordination : bond 0.00500 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.7020 (OUTLIER) cc_final: 0.6723 (m-70) REVERT: H 1 MET cc_start: 0.7053 (mpp) cc_final: 0.6820 (mpp) REVERT: H 85 LYS cc_start: 0.7649 (mmtp) cc_final: 0.7415 (mttm) REVERT: H 91 TYR cc_start: 0.8491 (m-80) cc_final: 0.8159 (m-80) REVERT: H 110 MET cc_start: 0.7912 (ttt) cc_final: 0.7346 (ttp) REVERT: H 170 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7504 (pptt) REVERT: G 24 GLU cc_start: 0.8822 (pm20) cc_final: 0.8481 (mm-30) REVERT: G 206 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.7560 (ptm160) REVERT: F 170 GLN cc_start: 0.8204 (mt0) cc_final: 0.7831 (mt0) REVERT: F 236 MET cc_start: 0.6863 (tpp) cc_final: 0.6640 (ttt) REVERT: E 57 LYS cc_start: 0.8421 (mmtp) cc_final: 0.7921 (tptt) REVERT: E 58 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8138 (mpp80) REVERT: E 82 MET cc_start: 0.8748 (tmm) cc_final: 0.8383 (ttm) REVERT: E 169 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7580 (m-80) REVERT: C 142 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.7252 (mmm160) REVERT: C 246 SER cc_start: 0.6146 (m) cc_final: 0.5825 (t) REVERT: C 309 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6336 (mpt180) REVERT: D 283 GLU cc_start: 0.7507 (tp30) cc_final: 0.7219 (tp30) REVERT: D 362 ASP cc_start: 0.8059 (p0) cc_final: 0.7456 (m-30) outliers start: 55 outliers final: 40 residues processed: 229 average time/residue: 0.1211 time to fit residues: 41.6027 Evaluate side-chains 218 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 86 HIS Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 424 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 148 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.133512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.100317 restraints weight = 33187.636| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.37 r_work: 0.3431 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15160 Z= 0.130 Angle : 0.526 8.872 20556 Z= 0.274 Chirality : 0.039 0.165 2389 Planarity : 0.003 0.041 2657 Dihedral : 4.435 72.266 2127 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.45 % Allowed : 27.64 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.20), residues: 1959 helix: 1.96 (0.15), residues: 1248 sheet: -0.97 (0.45), residues: 144 loop : -2.18 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 206 TYR 0.012 0.001 TYR F 113 PHE 0.019 0.001 PHE C 237 TRP 0.008 0.001 TRP H 62 HIS 0.006 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00296 (15158) covalent geometry : angle 0.52624 (20556) hydrogen bonds : bond 0.04159 ( 885) hydrogen bonds : angle 3.95634 ( 2613) metal coordination : bond 0.00355 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 85 LYS cc_start: 0.7619 (mmtp) cc_final: 0.7378 (mttm) REVERT: H 91 TYR cc_start: 0.8487 (m-80) cc_final: 0.8171 (m-80) REVERT: H 110 MET cc_start: 0.8094 (ttt) cc_final: 0.7532 (ttp) REVERT: H 170 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7490 (pptt) REVERT: G 24 GLU cc_start: 0.8813 (pm20) cc_final: 0.8464 (mm-30) REVERT: G 206 ARG cc_start: 0.8341 (ttp-110) cc_final: 0.7839 (ptm160) REVERT: F 170 GLN cc_start: 0.8210 (mt0) cc_final: 0.7826 (mt0) REVERT: E 57 LYS cc_start: 0.8403 (mmtp) cc_final: 0.7892 (tptt) REVERT: E 58 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8124 (mpp80) REVERT: E 82 MET cc_start: 0.8708 (tmm) cc_final: 0.8393 (ttm) REVERT: E 169 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: E 272 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8469 (t0) REVERT: C 243 LYS cc_start: 0.7953 (tptt) cc_final: 0.7181 (tttm) REVERT: C 246 SER cc_start: 0.6138 (m) cc_final: 0.5816 (t) REVERT: C 309 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6349 (mpt180) REVERT: D 283 GLU cc_start: 0.7457 (tp30) cc_final: 0.7139 (tp30) REVERT: D 362 ASP cc_start: 0.8003 (p0) cc_final: 0.7461 (m-30) REVERT: B 401 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8049 (mmm) outliers start: 51 outliers final: 38 residues processed: 220 average time/residue: 0.1238 time to fit residues: 40.9730 Evaluate side-chains 217 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 86 HIS Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 272 ASP Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain B residue 401 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.133030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.099775 restraints weight = 32789.937| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.35 r_work: 0.3423 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15160 Z= 0.144 Angle : 0.543 8.943 20556 Z= 0.282 Chirality : 0.039 0.168 2389 Planarity : 0.003 0.042 2657 Dihedral : 4.453 71.556 2127 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.31 % Allowed : 27.77 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.20), residues: 1959 helix: 1.93 (0.15), residues: 1247 sheet: -1.26 (0.43), residues: 155 loop : -2.16 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 206 TYR 0.018 0.001 TYR E 147 PHE 0.019 0.001 PHE C 237 TRP 0.009 0.001 TRP D 370 HIS 0.007 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00335 (15158) covalent geometry : angle 0.54296 (20556) hydrogen bonds : bond 0.04207 ( 885) hydrogen bonds : angle 3.97753 ( 2613) metal coordination : bond 0.00411 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 85 LYS cc_start: 0.7631 (mmtp) cc_final: 0.7382 (mttm) REVERT: H 91 TYR cc_start: 0.8563 (m-80) cc_final: 0.8274 (m-80) REVERT: H 110 MET cc_start: 0.8064 (ttt) cc_final: 0.7513 (ttp) REVERT: H 170 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7558 (pptt) REVERT: G 24 GLU cc_start: 0.8790 (pm20) cc_final: 0.8441 (mm-30) REVERT: G 206 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.7728 (ptm160) REVERT: F 170 GLN cc_start: 0.8181 (mt0) cc_final: 0.7791 (mt0) REVERT: F 236 MET cc_start: 0.6790 (tpp) cc_final: 0.6564 (ttt) REVERT: E 57 LYS cc_start: 0.8416 (mmtp) cc_final: 0.7889 (tptt) REVERT: E 58 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8130 (mpp80) REVERT: E 82 MET cc_start: 0.8729 (tmm) cc_final: 0.8412 (ttm) REVERT: E 102 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7953 (mp) REVERT: E 169 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: E 272 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8498 (t0) REVERT: C 243 LYS cc_start: 0.7980 (tptt) cc_final: 0.7212 (tttm) REVERT: C 246 SER cc_start: 0.6186 (m) cc_final: 0.5855 (t) REVERT: C 309 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6347 (mpt180) REVERT: D 219 ASN cc_start: 0.7742 (t0) cc_final: 0.7524 (t0) REVERT: D 232 THR cc_start: 0.8715 (m) cc_final: 0.8406 (t) REVERT: D 283 GLU cc_start: 0.7403 (tp30) cc_final: 0.7183 (tp30) outliers start: 49 outliers final: 38 residues processed: 218 average time/residue: 0.1286 time to fit residues: 41.6006 Evaluate side-chains 218 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 86 HIS Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 272 ASP Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain B residue 401 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 31 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 7 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.132962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099664 restraints weight = 32925.294| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.36 r_work: 0.3422 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15160 Z= 0.152 Angle : 0.558 9.231 20556 Z= 0.291 Chirality : 0.039 0.176 2389 Planarity : 0.003 0.043 2657 Dihedral : 4.467 71.268 2127 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.31 % Allowed : 27.91 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.20), residues: 1959 helix: 1.94 (0.15), residues: 1243 sheet: -1.29 (0.43), residues: 155 loop : -2.16 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 206 TYR 0.018 0.001 TYR E 147 PHE 0.016 0.001 PHE C 237 TRP 0.009 0.001 TRP D 370 HIS 0.007 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00355 (15158) covalent geometry : angle 0.55807 (20556) hydrogen bonds : bond 0.04237 ( 885) hydrogen bonds : angle 3.98926 ( 2613) metal coordination : bond 0.00487 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 TYR cc_start: 0.8747 (m-80) cc_final: 0.8410 (m-80) REVERT: H 85 LYS cc_start: 0.7653 (mmtp) cc_final: 0.7401 (mttm) REVERT: H 91 TYR cc_start: 0.8589 (m-80) cc_final: 0.8296 (m-80) REVERT: H 110 MET cc_start: 0.8051 (ttt) cc_final: 0.7527 (ttp) REVERT: H 170 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7500 (pptt) REVERT: G 24 GLU cc_start: 0.8772 (pm20) cc_final: 0.8426 (mm-30) REVERT: G 206 ARG cc_start: 0.8344 (ttp-110) cc_final: 0.7821 (ptm160) REVERT: F 170 GLN cc_start: 0.8193 (mt0) cc_final: 0.7802 (mt0) REVERT: F 236 MET cc_start: 0.6769 (tpp) cc_final: 0.6546 (ttt) REVERT: E 57 LYS cc_start: 0.8389 (mmtp) cc_final: 0.7893 (tptt) REVERT: E 58 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8131 (mpp80) REVERT: E 82 MET cc_start: 0.8743 (tmm) cc_final: 0.8418 (ttm) REVERT: E 102 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7977 (mp) REVERT: E 272 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8513 (t0) REVERT: C 243 LYS cc_start: 0.7980 (tptt) cc_final: 0.7211 (tttm) REVERT: C 246 SER cc_start: 0.6209 (m) cc_final: 0.5874 (t) REVERT: C 309 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6356 (mpt180) REVERT: D 232 THR cc_start: 0.8717 (m) cc_final: 0.8411 (t) outliers start: 49 outliers final: 40 residues processed: 211 average time/residue: 0.1309 time to fit residues: 40.8878 Evaluate side-chains 211 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 86 HIS Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 272 ASP Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 192 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 7 GLN G 169 ASN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.134628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101666 restraints weight = 32745.406| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.35 r_work: 0.3439 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15160 Z= 0.118 Angle : 0.547 11.069 20556 Z= 0.282 Chirality : 0.038 0.170 2389 Planarity : 0.003 0.044 2657 Dihedral : 4.421 73.248 2127 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.04 % Allowed : 28.45 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.20), residues: 1959 helix: 2.05 (0.15), residues: 1244 sheet: -0.87 (0.45), residues: 144 loop : -2.12 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 285 TYR 0.017 0.001 TYR E 147 PHE 0.017 0.001 PHE C 237 TRP 0.008 0.001 TRP G 194 HIS 0.006 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00262 (15158) covalent geometry : angle 0.54727 (20556) hydrogen bonds : bond 0.03841 ( 885) hydrogen bonds : angle 3.87948 ( 2613) metal coordination : bond 0.00268 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4193.85 seconds wall clock time: 72 minutes 36.14 seconds (4356.14 seconds total)