Starting phenix.real_space_refine on Thu Mar 5 15:46:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nhp_12336/03_2026/7nhp_12336.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nhp_12336/03_2026/7nhp_12336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nhp_12336/03_2026/7nhp_12336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nhp_12336/03_2026/7nhp_12336.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nhp_12336/03_2026/7nhp_12336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nhp_12336/03_2026/7nhp_12336.map" } resolution = 2.72 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= 0.000 sd= 0.002 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: 9 Type Number sf(0) Gaussians Mn 1 7.51 5 Fe 2 7.16 5 P 1 5.49 5 Mg 35 5.21 5 S 74 5.16 5 Cl 1 4.86 5 C 15044 2.51 5 N 3200 2.21 5 O 3481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21839 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2627 Classifications: {'peptide': 335} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain: "B" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3909 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 32, 'TRANS': 463} Chain: "C" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3345 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain: "D" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2717 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 323} Chain: "E" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 635 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "F" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "H" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 511 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "I" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "K" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 293 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "M" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "T" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 241 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "X" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 254 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "y" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 208 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "Z" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 463 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "1" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "2" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 897 Classifications: {'peptide': 112} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "3" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 419 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 415 Unusual residues: {' CL': 1, ' MN': 1, 'BCR': 1, 'CLA': 4, 'LHG': 1, 'PHO': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 1160 Unusual residues: {'BCR': 3, 'CLA': 16} Classifications: {'undetermined': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 1075 Unusual residues: {'BCR': 3, 'CLA': 13, 'LMG': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 510 Unusual residues: {' FE': 1, 'BCR': 1, 'CLA': 2, 'LMG': 4, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.64, per 1000 atoms: 0.21 Number of scatterers: 21839 At special positions: 0 Unit cell: (132.98, 106.82, 143.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 2 26.01 Mn 1 24.99 Cl 1 17.00 S 74 16.00 P 1 15.00 Mg 35 11.99 O 3481 8.00 N 3200 7.00 C 15044 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 846.6 milliseconds 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 14 sheets defined 61.1% alpha, 4.3% 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 12 through 22 removed outlier: 4.263A pdb=" N ARG A 16 " --> pdb=" O ASN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 55 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.546A pdb=" N TRP A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 removed outlier: 4.586A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.611A pdb=" N ALA A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.554A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 255 through 263 removed outlier: 5.091A pdb=" N GLN A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 293 removed outlier: 4.298A pdb=" N HIS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.689A pdb=" N SER A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.511A pdb=" N ILE A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.037A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 42 removed outlier: 3.523A pdb=" N LEU B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 68 Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 194 through 219 removed outlier: 4.236A pdb=" N VAL B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 233 through 259 removed outlier: 4.112A pdb=" N VAL B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.944A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.619A pdb=" N SER B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.623A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 removed outlier: 6.538A pdb=" N GLY B 316 " --> pdb=" O ASP B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.512A pdb=" N ASP B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.533A pdb=" N TRP B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.744A pdb=" N ILE C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 61 Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.967A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 removed outlier: 3.529A pdb=" N PHE C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 169 removed outlier: 3.593A pdb=" N MET C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.121A pdb=" N ILE C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 217 through 242 removed outlier: 3.726A pdb=" N VAL C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 281 removed outlier: 3.634A pdb=" N TYR C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 4.184A pdb=" N SER C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.657A pdb=" N THR C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 52 removed outlier: 3.778A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 108 through 137 removed outlier: 3.996A pdb=" N THR D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.720A pdb=" N ILE D 150 " --> pdb=" O PHE D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 166 through 170 removed outlier: 4.119A pdb=" N PHE D 169 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.563A pdb=" N PHE D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 183 " --> pdb=" O PHE D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 220 removed outlier: 3.669A pdb=" N GLU D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 245 through 257 removed outlier: 3.632A pdb=" N ALA D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 290 removed outlier: 3.600A pdb=" N LEU D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 removed outlier: 3.784A pdb=" N ALA D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'E' and resid 9 through 15 removed outlier: 3.703A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 40 removed outlier: 3.964A pdb=" N ILE E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 47 removed outlier: 3.974A pdb=" N ASP E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 82 Processing helix chain 'F' and resid 17 through 25 Processing helix chain 'F' and resid 27 through 42 removed outlier: 3.551A pdb=" N ALA F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 Processing helix chain 'H' and resid 12 through 15 Processing helix chain 'H' and resid 27 through 50 removed outlier: 3.639A pdb=" N VAL H 33 " --> pdb=" O PRO H 29 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR H 49 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'I' and resid 2 through 23 Processing helix chain 'K' and resid 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 18 through 23 removed outlier: 3.762A pdb=" N ASP K 23 " --> pdb=" O ASP K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 26 No H-bonds generated for 'chain 'K' and resid 24 through 26' Processing helix chain 'K' and resid 27 through 43 removed outlier: 3.663A pdb=" N LEU K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 37 removed outlier: 4.241A pdb=" N SER L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 31 removed outlier: 3.928A pdb=" N LEU M 8 " --> pdb=" O ASN M 4 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE M 9 " --> pdb=" O GLN M 5 " (cutoff:3.500A) Proline residue: M 18 - end of helix Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'X' and resid 4 through 33 Processing helix chain 'y' and resid 22 through 42 removed outlier: 4.313A pdb=" N GLY y 32 " --> pdb=" O ILE y 28 " (cutoff:3.500A) Proline residue: y 33 - end of helix removed outlier: 4.145A pdb=" N ILE y 36 " --> pdb=" O GLY y 32 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU y 39 " --> pdb=" O ILE y 35 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL y 41 " --> pdb=" O PHE y 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 29 removed outlier: 4.192A pdb=" N ILE Z 21 " --> pdb=" O PHE Z 17 " (cutoff:3.500A) Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 32 through 58 removed outlier: 3.539A pdb=" N SER Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN Z 38 " --> pdb=" O ASP Z 34 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU Z 39 " --> pdb=" O ARG Z 35 " (cutoff:3.500A) Processing helix chain '1' and resid 32 through 49 removed outlier: 3.734A pdb=" N ASP 1 36 " --> pdb=" O ASN 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 56 through 76 removed outlier: 3.640A pdb=" N ALA 1 62 " --> pdb=" O LYS 1 58 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU 1 63 " --> pdb=" O ALA 1 59 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU 1 74 " --> pdb=" O ASP 1 70 " (cutoff:3.500A) Processing helix chain '1' and resid 79 through 84 removed outlier: 3.542A pdb=" N LEU 1 84 " --> pdb=" O LEU 1 81 " (cutoff:3.500A) Processing helix chain '1' and resid 85 through 104 removed outlier: 3.841A pdb=" N THR 1 92 " --> pdb=" O MET 1 88 " (cutoff:3.500A) Processing helix chain '1' and resid 110 through 134 removed outlier: 3.555A pdb=" N LYS 1 114 " --> pdb=" O PRO 1 110 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS 1 133 " --> pdb=" O ASP 1 129 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER 1 134 " --> pdb=" O ARG 1 130 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 46 removed outlier: 3.614A pdb=" N GLN 2 45 " --> pdb=" O PRO 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 88 through 107 Processing helix chain '3' and resid 27 through 56 removed outlier: 3.953A pdb=" N LEU 3 37 " --> pdb=" O ARG 3 33 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 removed outlier: 3.578A pdb=" N VAL A 67 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 230 removed outlier: 5.123A pdb=" N LEU A 223 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU A 242 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG A 225 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLY A 240 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR A 227 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LYS A 238 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU A 229 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA 2 79 " --> pdb=" O LYS 2 71 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE 2 73 " --> pdb=" O PRO 2 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340 removed outlier: 5.615A pdb=" N ALA B 337 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASP B 433 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 339 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 347 Processing sheet with id=AA7, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.932A pdb=" N LEU B 370 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.541A pdb=" N GLY C 88 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB1, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AB2, first strand: chain 'C' and resid 358 through 359 Processing sheet with id=AB3, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain '2' and resid 5 through 8 1010 hydrogen bonds defined for protein. 2904 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: 4.09 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 6393 1.36 - 1.55: 15651 1.55 - 1.74: 382 1.74 - 1.93: 132 1.93 - 2.12: 144 Bond restraints: 22702 Sorted by residual: bond pdb=" C5 BCR K 101 " pdb=" C6 BCR K 101 " ideal model delta sigma weight residual 1.347 1.172 0.175 2.00e-02 2.50e+03 7.63e+01 bond pdb=" C5 BCR H 101 " pdb=" C6 BCR H 101 " ideal model delta sigma weight residual 1.347 1.182 0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" C33 BCR H 101 " pdb=" C5 BCR H 101 " ideal model delta sigma weight residual 1.503 1.360 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C1 BCR H 101 " pdb=" C6 BCR H 101 " ideal model delta sigma weight residual 1.532 1.393 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C33 BCR K 101 " pdb=" C5 BCR K 101 " ideal model delta sigma weight residual 1.503 1.364 0.139 2.00e-02 2.50e+03 4.80e+01 ... (remaining 22697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 30033 4.74 - 9.48: 955 9.48 - 14.22: 260 14.22 - 18.96: 54 18.96 - 23.70: 9 Bond angle restraints: 31311 Sorted by residual: angle pdb=" CB MET C 145 " pdb=" CG MET C 145 " pdb=" SD MET C 145 " ideal model delta sigma weight residual 112.70 136.40 -23.70 3.00e+00 1.11e-01 6.24e+01 angle pdb=" C4A CLA B 601 " pdb=" C3A CLA B 601 " pdb=" CMA CLA B 601 " ideal model delta sigma weight residual 112.13 88.70 23.43 3.00e+00 1.11e-01 6.10e+01 angle pdb=" C1A CLA B 601 " pdb=" C2A CLA B 601 " pdb=" CAA CLA B 601 " ideal model delta sigma weight residual 110.32 131.81 -21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" C2A CLA B 608 " pdb=" C3A CLA B 608 " pdb=" CMA CLA B 608 " ideal model delta sigma weight residual 112.13 133.26 -21.13 3.00e+00 1.11e-01 4.96e+01 angle pdb=" C3D CLA B 616 " pdb=" CAD CLA B 616 " pdb=" CBD CLA B 616 " ideal model delta sigma weight residual 107.10 86.74 20.36 3.00e+00 1.11e-01 4.61e+01 ... (remaining 31306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.66: 11239 24.66 - 49.31: 694 49.31 - 73.97: 169 73.97 - 98.63: 64 98.63 - 123.29: 19 Dihedral angle restraints: 12185 sinusoidal: 5527 harmonic: 6658 Sorted by residual: dihedral pdb=" CA ARG 2 27 " pdb=" C ARG 2 27 " pdb=" N ASP 2 28 " pdb=" CA ASP 2 28 " ideal model delta harmonic sigma weight residual 180.00 -132.91 -47.09 0 5.00e+00 4.00e-02 8.87e+01 dihedral pdb=" CA LEU A 343 " pdb=" C LEU A 343 " pdb=" N ALA A 344 " pdb=" CA ALA A 344 " ideal model delta harmonic sigma weight residual 0.00 35.78 -35.78 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA GLY K 44 " pdb=" C GLY K 44 " pdb=" N PHE K 45 " pdb=" CA PHE K 45 " ideal model delta harmonic sigma weight residual 180.00 146.58 33.42 0 5.00e+00 4.00e-02 4.47e+01 ... (remaining 12182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.619: 2984 0.619 - 1.238: 18 1.238 - 1.857: 21 1.857 - 2.476: 12 2.476 - 3.095: 14 Chirality restraints: 3049 Sorted by residual: chirality pdb=" C8 CLA B 608 " pdb=" C10 CLA B 608 " pdb=" C7 CLA B 608 " pdb=" C9 CLA B 608 " both_signs ideal model delta sigma weight residual False 2.59 -0.50 3.09 2.00e-01 2.50e+01 2.39e+02 chirality pdb=" C8 PHO D 407 " pdb=" C10 PHO D 407 " pdb=" C7 PHO D 407 " pdb=" C9 PHO D 407 " both_signs ideal model delta sigma weight residual False 2.59 -0.51 3.09 2.00e-01 2.50e+01 2.39e+02 chirality pdb=" C8 CLA C 505 " pdb=" C10 CLA C 505 " pdb=" C7 CLA C 505 " pdb=" C9 CLA C 505 " both_signs ideal model delta sigma weight residual False 2.59 -0.42 3.02 2.00e-01 2.50e+01 2.28e+02 ... (remaining 3046 not shown) Planarity restraints: 3945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 407 " -0.109 2.00e-02 2.50e+03 1.61e-01 2.08e+03 pdb=" ND PHO D 407 " -0.144 2.00e-02 2.50e+03 pdb=" C1A PHO D 407 " -0.091 2.00e-02 2.50e+03 pdb=" C1B PHO D 407 " 0.047 2.00e-02 2.50e+03 pdb=" C1C PHO D 407 " -0.197 2.00e-02 2.50e+03 pdb=" C1D PHO D 407 " -0.029 2.00e-02 2.50e+03 pdb=" C2A PHO D 407 " 0.168 2.00e-02 2.50e+03 pdb=" C2B PHO D 407 " 0.042 2.00e-02 2.50e+03 pdb=" C2C PHO D 407 " -0.015 2.00e-02 2.50e+03 pdb=" C2D PHO D 407 " 0.066 2.00e-02 2.50e+03 pdb=" C3A PHO D 407 " 0.298 2.00e-02 2.50e+03 pdb=" C3B PHO D 407 " -0.070 2.00e-02 2.50e+03 pdb=" C3C PHO D 407 " 0.102 2.00e-02 2.50e+03 pdb=" C3D PHO D 407 " -0.066 2.00e-02 2.50e+03 pdb=" C4A PHO D 407 " 0.071 2.00e-02 2.50e+03 pdb=" C4B PHO D 407 " -0.184 2.00e-02 2.50e+03 pdb=" C4C PHO D 407 " -0.078 2.00e-02 2.50e+03 pdb=" C4D PHO D 407 " -0.162 2.00e-02 2.50e+03 pdb=" CAB PHO D 407 " -0.092 2.00e-02 2.50e+03 pdb=" CAC PHO D 407 " 0.409 2.00e-02 2.50e+03 pdb=" CAD PHO D 407 " -0.023 2.00e-02 2.50e+03 pdb=" CBD PHO D 407 " -0.124 2.00e-02 2.50e+03 pdb=" CHA PHO D 407 " -0.150 2.00e-02 2.50e+03 pdb=" CHB PHO D 407 " 0.182 2.00e-02 2.50e+03 pdb=" CHC PHO D 407 " -0.184 2.00e-02 2.50e+03 pdb=" CHD PHO D 407 " -0.030 2.00e-02 2.50e+03 pdb=" CMB PHO D 407 " 0.257 2.00e-02 2.50e+03 pdb=" CMC PHO D 407 " 0.165 2.00e-02 2.50e+03 pdb=" CMD PHO D 407 " 0.296 2.00e-02 2.50e+03 pdb=" NA PHO D 407 " -0.117 2.00e-02 2.50e+03 pdb=" NC PHO D 407 " -0.244 2.00e-02 2.50e+03 pdb=" OBD PHO D 407 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO A 403 " -0.035 2.00e-02 2.50e+03 1.11e-01 9.79e+02 pdb=" ND PHO A 403 " -0.005 2.00e-02 2.50e+03 pdb=" C1A PHO A 403 " 0.032 2.00e-02 2.50e+03 pdb=" C1B PHO A 403 " -0.051 2.00e-02 2.50e+03 pdb=" C1C PHO A 403 " 0.056 2.00e-02 2.50e+03 pdb=" C1D PHO A 403 " -0.063 2.00e-02 2.50e+03 pdb=" C2A PHO A 403 " -0.033 2.00e-02 2.50e+03 pdb=" C2B PHO A 403 " 0.055 2.00e-02 2.50e+03 pdb=" C2C PHO A 403 " 0.016 2.00e-02 2.50e+03 pdb=" C2D PHO A 403 " -0.057 2.00e-02 2.50e+03 pdb=" C3A PHO A 403 " -0.299 2.00e-02 2.50e+03 pdb=" C3B PHO A 403 " 0.114 2.00e-02 2.50e+03 pdb=" C3C PHO A 403 " -0.081 2.00e-02 2.50e+03 pdb=" C3D PHO A 403 " 0.071 2.00e-02 2.50e+03 pdb=" C4A PHO A 403 " -0.169 2.00e-02 2.50e+03 pdb=" C4B PHO A 403 " 0.046 2.00e-02 2.50e+03 pdb=" C4C PHO A 403 " -0.066 2.00e-02 2.50e+03 pdb=" C4D PHO A 403 " 0.069 2.00e-02 2.50e+03 pdb=" CAB PHO A 403 " 0.195 2.00e-02 2.50e+03 pdb=" CAC PHO A 403 " -0.159 2.00e-02 2.50e+03 pdb=" CAD PHO A 403 " 0.131 2.00e-02 2.50e+03 pdb=" CBD PHO A 403 " 0.176 2.00e-02 2.50e+03 pdb=" CHA PHO A 403 " 0.096 2.00e-02 2.50e+03 pdb=" CHB PHO A 403 " -0.152 2.00e-02 2.50e+03 pdb=" CHC PHO A 403 " 0.043 2.00e-02 2.50e+03 pdb=" CHD PHO A 403 " -0.087 2.00e-02 2.50e+03 pdb=" CMB PHO A 403 " 0.053 2.00e-02 2.50e+03 pdb=" CMC PHO A 403 " 0.056 2.00e-02 2.50e+03 pdb=" CMD PHO A 403 " -0.118 2.00e-02 2.50e+03 pdb=" NA PHO A 403 " -0.078 2.00e-02 2.50e+03 pdb=" NC PHO A 403 " 0.051 2.00e-02 2.50e+03 pdb=" OBD PHO A 403 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR H 101 " 0.121 2.00e-02 2.50e+03 1.13e-01 1.60e+02 pdb=" C11 BCR H 101 " -0.117 2.00e-02 2.50e+03 pdb=" C34 BCR H 101 " -0.022 2.00e-02 2.50e+03 pdb=" C8 BCR H 101 " -0.123 2.00e-02 2.50e+03 pdb=" C9 BCR H 101 " 0.141 2.00e-02 2.50e+03 ... (remaining 3942 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 39 2.52 - 3.11: 14928 3.11 - 3.71: 31954 3.71 - 4.30: 48712 4.30 - 4.90: 78765 Nonbonded interactions: 174398 Sorted by model distance: nonbonded pdb=" NE2 HIS A 215 " pdb="FE FE D 401 " model vdw 1.924 2.340 nonbonded pdb=" NE2 HIS D 214 " pdb="FE FE D 401 " model vdw 1.947 2.340 nonbonded pdb=" OD2 ASP C 309 " pdb=" OH TYR C 328 " model vdw 2.079 3.040 nonbonded pdb=" O PHE 1 33 " pdb=" OG1 THR 1 37 " model vdw 2.187 3.040 nonbonded pdb=" NH1 ARG C 29 " pdb=" NH1 ARG K 46 " model vdw 2.194 3.200 ... (remaining 174393 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 19.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.018 0.696 22714 Z= 1.411 Angle : 2.193 23.701 31311 Z= 0.941 Chirality : 0.295 3.095 3049 Planarity : 0.016 0.161 3945 Dihedral : 18.695 123.286 7931 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.83 % Favored : 93.82 % Rotamer: Outliers : 1.36 % Allowed : 9.33 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.15), residues: 2314 helix: -1.27 (0.12), residues: 1296 sheet: -0.22 (0.65), residues: 63 loop : -2.44 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.002 ARG A 269 TYR 0.053 0.005 TYR E 19 PHE 0.135 0.006 PHE C 424 TRP 0.040 0.004 TRP C 24 HIS 0.077 0.005 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.01216 (22702) covalent geometry : angle 2.19329 (31311) hydrogen bonds : bond 0.16862 ( 1010) hydrogen bonds : angle 6.38342 ( 2904) Misc. bond : bond 0.56796 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 828 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.9407 (mt) cc_final: 0.9170 (mm) REVERT: A 60 ILE cc_start: 0.9312 (tt) cc_final: 0.9030 (tp) REVERT: A 140 ARG cc_start: 0.7419 (mtp85) cc_final: 0.7183 (mmm-85) REVERT: A 163 ILE cc_start: 0.9151 (mt) cc_final: 0.8884 (mt) REVERT: A 170 ASP cc_start: 0.8541 (m-30) cc_final: 0.8324 (m-30) REVERT: A 225 ARG cc_start: 0.7639 (ptp-170) cc_final: 0.7415 (ptp-110) REVERT: A 229 GLU cc_start: 0.8265 (tp30) cc_final: 0.7063 (pm20) REVERT: A 241 GLN cc_start: 0.8080 (tm130) cc_final: 0.7331 (tm-30) REVERT: A 242 GLU cc_start: 0.7359 (mp0) cc_final: 0.7037 (mt-10) REVERT: B 341 LYS cc_start: 0.9165 (mmtp) cc_final: 0.8804 (mmmm) REVERT: B 352 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7808 (mm-30) REVERT: B 433 ASP cc_start: 0.7814 (t0) cc_final: 0.7500 (t0) REVERT: C 48 ILE cc_start: 0.8841 (mt) cc_final: 0.8552 (mp) REVERT: C 128 LEU cc_start: 0.8328 (mp) cc_final: 0.7945 (tt) REVERT: C 185 ARG cc_start: 0.8176 (ttt-90) cc_final: 0.7889 (ttt-90) REVERT: C 216 ASN cc_start: 0.7910 (p0) cc_final: 0.7643 (p0) REVERT: C 227 TRP cc_start: 0.8385 (m100) cc_final: 0.8062 (m100) REVERT: C 262 TYR cc_start: 0.8876 (m-10) cc_final: 0.8501 (m-80) REVERT: C 282 ASN cc_start: 0.9026 (t0) cc_final: 0.8763 (t0) REVERT: C 287 SER cc_start: 0.8753 (p) cc_final: 0.8522 (p) REVERT: C 350 ARG cc_start: 0.4639 (pmt170) cc_final: 0.2512 (mtp85) REVERT: C 355 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7816 (mm-30) REVERT: C 369 LYS cc_start: 0.8568 (mttt) cc_final: 0.8353 (tppt) REVERT: C 371 ASP cc_start: 0.8474 (m-30) cc_final: 0.8133 (m-30) REVERT: C 376 GLN cc_start: 0.9053 (mt0) cc_final: 0.8673 (mt0) REVERT: C 423 PHE cc_start: 0.8943 (t80) cc_final: 0.8705 (t80) REVERT: D 27 PHE cc_start: 0.7890 (t80) cc_final: 0.7608 (t80) REVERT: D 100 ASP cc_start: 0.8637 (t0) cc_final: 0.8174 (t70) REVERT: D 105 CYS cc_start: 0.9033 (m) cc_final: 0.8566 (m) REVERT: E 62 SER cc_start: 0.8910 (p) cc_final: 0.8685 (p) REVERT: F 40 MET cc_start: 0.9468 (mtt) cc_final: 0.9265 (mtp) REVERT: F 41 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8460 (mp-120) REVERT: H 6 TRP cc_start: 0.8561 (t60) cc_final: 0.7836 (t60) REVERT: H 20 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8036 (mmtt) REVERT: H 50 ASN cc_start: 0.9240 (t0) cc_final: 0.9030 (t160) REVERT: L 13 ASN cc_start: 0.8761 (p0) cc_final: 0.8490 (p0) REVERT: M 4 ASN cc_start: 0.6536 (m-40) cc_final: 0.6013 (m110) REVERT: M 28 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8211 (tm-30) REVERT: T 25 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: 1 41 ILE cc_start: 0.8877 (mt) cc_final: 0.8613 (mp) REVERT: 1 82 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8504 (mtp180) REVERT: 1 88 MET cc_start: 0.9308 (mmm) cc_final: 0.9052 (mmm) REVERT: 1 90 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8994 (tmm) REVERT: 1 109 LEU cc_start: 0.8795 (pt) cc_final: 0.8578 (pp) REVERT: 1 118 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8899 (tm-30) REVERT: 1 121 PHE cc_start: 0.8747 (m-10) cc_final: 0.8336 (m-80) REVERT: 2 15 GLU cc_start: 0.8101 (tp30) cc_final: 0.7847 (tm-30) REVERT: 2 25 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.6865 (ttp-110) REVERT: 2 35 MET cc_start: 0.7715 (mpp) cc_final: 0.7377 (mpp) REVERT: 2 52 THR cc_start: 0.8581 (m) cc_final: 0.8273 (t) REVERT: 2 74 ASN cc_start: 0.8603 (m-40) cc_final: 0.8159 (m-40) REVERT: 2 84 TYR cc_start: 0.8537 (t80) cc_final: 0.7412 (t80) REVERT: 2 88 SER cc_start: 0.7745 (p) cc_final: 0.7210 (t) REVERT: 2 93 ASP cc_start: 0.9162 (m-30) cc_final: 0.8956 (p0) REVERT: 2 96 ILE cc_start: 0.8204 (mt) cc_final: 0.7945 (mp) REVERT: 2 97 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.7954 (mtm-85) REVERT: 2 100 ASP cc_start: 0.8505 (m-30) cc_final: 0.8303 (m-30) REVERT: 3 27 THR cc_start: 0.8237 (p) cc_final: 0.8020 (p) outliers start: 26 outliers final: 15 residues processed: 840 average time/residue: 0.5147 time to fit residues: 499.5439 Evaluate side-chains 611 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 593 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain Z residue 16 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 81 LEU Chi-restraints excluded: chain 1 residue 82 ARG Chi-restraints excluded: chain 1 residue 90 MET Chi-restraints excluded: chain 3 residue 37 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 191 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN A 303 ASN A 304 HIS B 179 GLN B 281 GLN B 318 ASN B 490 GLN C 120 HIS C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 HIS D 186 GLN D 322 ASN E 58 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN L 8 GLN y 45 ASN Z 31 GLN Z 58 ASN 1 95 ASN 1 106 ASN 1 119 GLN ** 3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097131 restraints weight = 35977.767| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.71 r_work: 0.3034 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 22714 Z= 0.220 Angle : 0.837 12.678 31311 Z= 0.388 Chirality : 0.049 0.303 3049 Planarity : 0.006 0.056 3945 Dihedral : 17.678 118.073 3912 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 5.35 % Allowed : 20.07 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2314 helix: 0.46 (0.14), residues: 1309 sheet: 1.01 (0.70), residues: 53 loop : -1.61 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 2 22 TYR 0.021 0.002 TYR B 279 PHE 0.025 0.002 PHE B 246 TRP 0.027 0.002 TRP Z 33 HIS 0.013 0.002 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00469 (22702) covalent geometry : angle 0.83725 (31311) hydrogen bonds : bond 0.06105 ( 1010) hydrogen bonds : angle 4.62947 ( 2904) Misc. bond : bond 0.03850 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 610 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.8745 (p0) cc_final: 0.8431 (p0) REVERT: A 104 GLU cc_start: 0.8690 (pt0) cc_final: 0.8352 (pt0) REVERT: A 140 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7614 (mmm-85) REVERT: A 229 GLU cc_start: 0.8188 (tp30) cc_final: 0.6962 (pm20) REVERT: A 241 GLN cc_start: 0.7952 (tm130) cc_final: 0.7513 (tm-30) REVERT: B 130 GLU cc_start: 0.8847 (pt0) cc_final: 0.8635 (pm20) REVERT: B 230 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7175 (mtt180) REVERT: B 326 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8894 (mtt180) REVERT: B 341 LYS cc_start: 0.9051 (mmtp) cc_final: 0.8693 (mmmm) REVERT: B 352 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8500 (mm-30) REVERT: C 55 MET cc_start: 0.8917 (tpt) cc_final: 0.8550 (mmt) REVERT: C 69 MET cc_start: 0.8851 (mtm) cc_final: 0.8651 (mtp) REVERT: C 138 ASP cc_start: 0.8876 (p0) cc_final: 0.8031 (p0) REVERT: C 193 ASP cc_start: 0.8961 (t0) cc_final: 0.8658 (t0) REVERT: C 195 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8149 (mtp180) REVERT: C 227 TRP cc_start: 0.8352 (m100) cc_final: 0.8074 (m100) REVERT: C 277 PHE cc_start: 0.9483 (OUTLIER) cc_final: 0.8820 (t80) REVERT: C 336 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7169 (mm-30) REVERT: C 350 ARG cc_start: 0.5704 (pmt170) cc_final: 0.2620 (mmp-170) REVERT: C 355 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8262 (mm-30) REVERT: C 371 ASP cc_start: 0.8269 (m-30) cc_final: 0.7615 (m-30) REVERT: D 27 PHE cc_start: 0.8257 (t80) cc_final: 0.8009 (t80) REVERT: D 100 ASP cc_start: 0.8552 (t0) cc_final: 0.8005 (t70) REVERT: D 101 PHE cc_start: 0.8953 (t80) cc_final: 0.8526 (t80) REVERT: D 224 GLN cc_start: 0.8229 (mt0) cc_final: 0.7263 (pt0) REVERT: D 323 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8757 (tm-30) REVERT: E 61 ARG cc_start: 0.8336 (mmm160) cc_final: 0.8038 (mmm160) REVERT: E 75 GLN cc_start: 0.8453 (tt0) cc_final: 0.8165 (mt0) REVERT: E 77 GLU cc_start: 0.9073 (tt0) cc_final: 0.8638 (mt-10) REVERT: E 82 GLN cc_start: 0.7363 (pt0) cc_final: 0.7097 (pp30) REVERT: H 17 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8398 (mm-30) REVERT: H 20 LYS cc_start: 0.8508 (ttpp) cc_final: 0.7977 (mmtt) REVERT: H 39 LEU cc_start: 0.9459 (tp) cc_final: 0.9211 (tm) REVERT: H 50 ASN cc_start: 0.9166 (t0) cc_final: 0.8859 (t160) REVERT: I 18 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8403 (pp) REVERT: M 5 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7487 (tp40) REVERT: M 28 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8346 (tm-30) REVERT: T 25 GLU cc_start: 0.7689 (tp30) cc_final: 0.7472 (tp30) REVERT: Z 60 PHE cc_start: 0.8663 (m-80) cc_final: 0.8349 (m-80) REVERT: 1 67 LYS cc_start: 0.8659 (tppp) cc_final: 0.8295 (tppp) REVERT: 1 88 MET cc_start: 0.9307 (mmm) cc_final: 0.8935 (mmm) REVERT: 1 91 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8648 (tm-30) REVERT: 1 109 LEU cc_start: 0.8871 (pt) cc_final: 0.8332 (pp) REVERT: 1 114 LYS cc_start: 0.8560 (mttt) cc_final: 0.8072 (mttm) REVERT: 1 116 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7527 (tpt-90) REVERT: 1 123 GLN cc_start: 0.9519 (mt0) cc_final: 0.9150 (tp-100) REVERT: 2 4 MET cc_start: 0.4009 (tpp) cc_final: 0.3649 (tmm) REVERT: 2 22 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7234 (tmm-80) REVERT: 2 45 GLN cc_start: 0.8063 (mt0) cc_final: 0.7742 (mt0) REVERT: 2 52 THR cc_start: 0.8663 (m) cc_final: 0.8389 (t) REVERT: 2 62 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7112 (tp30) REVERT: 2 91 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8390 (pt0) REVERT: 2 96 ILE cc_start: 0.8248 (mt) cc_final: 0.7915 (mp) REVERT: 2 108 LEU cc_start: 0.7191 (mt) cc_final: 0.6581 (tt) REVERT: 2 112 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7824 (tppp) REVERT: 3 26 TRP cc_start: 0.7915 (m-10) cc_final: 0.6481 (m-90) outliers start: 102 outliers final: 32 residues processed: 650 average time/residue: 0.5293 time to fit residues: 397.0655 Evaluate side-chains 573 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 535 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain M residue 5 GLN Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain 1 residue 81 LEU Chi-restraints excluded: chain 2 residue 73 ILE Chi-restraints excluded: chain 3 residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 116 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 154 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 199 GLN B 282 GLN C 27 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 432 HIS D 186 GLN L 6 ASN M 4 ASN Z 31 GLN Z 38 GLN 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097268 restraints weight = 35843.691| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.71 r_work: 0.3043 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 22714 Z= 0.135 Angle : 0.683 11.018 31311 Z= 0.326 Chirality : 0.043 0.222 3049 Planarity : 0.005 0.060 3945 Dihedral : 16.118 119.223 3885 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 4.77 % Allowed : 23.38 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2314 helix: 1.06 (0.14), residues: 1310 sheet: 1.13 (0.65), residues: 63 loop : -1.25 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 1 130 TYR 0.018 0.001 TYR E 19 PHE 0.033 0.001 PHE 1 33 TRP 0.018 0.001 TRP C 51 HIS 0.010 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00295 (22702) covalent geometry : angle 0.68345 (31311) hydrogen bonds : bond 0.04934 ( 1010) hydrogen bonds : angle 4.25734 ( 2904) Misc. bond : bond 0.02482 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 587 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.8745 (p0) cc_final: 0.8427 (p0) REVERT: A 64 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8054 (mpp80) REVERT: A 104 GLU cc_start: 0.8589 (pt0) cc_final: 0.8383 (pt0) REVERT: A 140 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7669 (mmm-85) REVERT: A 229 GLU cc_start: 0.8207 (tp30) cc_final: 0.7155 (pm20) REVERT: A 238 LYS cc_start: 0.8293 (mtpp) cc_final: 0.8071 (mmpt) REVERT: A 241 GLN cc_start: 0.7905 (tm130) cc_final: 0.7323 (tm-30) REVERT: B 130 GLU cc_start: 0.8861 (pt0) cc_final: 0.8521 (pm20) REVERT: B 230 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7236 (mtt180) REVERT: B 352 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 374 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8392 (p0) REVERT: C 193 ASP cc_start: 0.8907 (t0) cc_final: 0.8636 (t0) REVERT: C 195 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8124 (mtp180) REVERT: C 227 TRP cc_start: 0.8407 (m100) cc_final: 0.8141 (m100) REVERT: C 277 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.9087 (t80) REVERT: C 336 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7146 (mm-30) REVERT: C 350 ARG cc_start: 0.5685 (pmt170) cc_final: 0.2569 (mmt180) REVERT: C 371 ASP cc_start: 0.8223 (m-30) cc_final: 0.7494 (m-30) REVERT: D 27 PHE cc_start: 0.8334 (t80) cc_final: 0.8054 (t80) REVERT: D 100 ASP cc_start: 0.8513 (t0) cc_final: 0.7977 (t70) REVERT: D 101 PHE cc_start: 0.9027 (t80) cc_final: 0.8778 (t80) REVERT: D 224 GLN cc_start: 0.8270 (mt0) cc_final: 0.7429 (pt0) REVERT: D 265 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.8144 (ttp80) REVERT: D 323 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8808 (tm-30) REVERT: E 42 LEU cc_start: 0.9124 (tp) cc_final: 0.8768 (tp) REVERT: E 71 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8379 (mm-30) REVERT: E 77 GLU cc_start: 0.8935 (tt0) cc_final: 0.8709 (mt-10) REVERT: E 82 GLN cc_start: 0.7616 (pt0) cc_final: 0.7340 (pp30) REVERT: H 17 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8261 (mm-30) REVERT: H 20 LYS cc_start: 0.8477 (ttpp) cc_final: 0.7964 (mmtt) REVERT: H 63 LYS cc_start: 0.9008 (mttm) cc_final: 0.8788 (mtpp) REVERT: M 5 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7517 (tp40) REVERT: T 25 GLU cc_start: 0.7764 (tp30) cc_final: 0.7480 (tp30) REVERT: Z 39 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8048 (pp) REVERT: Z 60 PHE cc_start: 0.8659 (m-80) cc_final: 0.8229 (m-80) REVERT: 1 67 LYS cc_start: 0.8612 (tppp) cc_final: 0.8383 (tppp) REVERT: 1 88 MET cc_start: 0.9249 (mmm) cc_final: 0.8932 (mmm) REVERT: 1 91 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8649 (tm-30) REVERT: 1 109 LEU cc_start: 0.8913 (pt) cc_final: 0.8330 (pp) REVERT: 1 114 LYS cc_start: 0.8506 (mttt) cc_final: 0.8014 (mttm) REVERT: 1 116 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7563 (tpt-90) REVERT: 1 123 GLN cc_start: 0.9520 (mt0) cc_final: 0.9128 (tp-100) REVERT: 1 130 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8327 (ptp-110) REVERT: 2 6 GLU cc_start: 0.5922 (pp20) cc_final: 0.5658 (pp20) REVERT: 2 22 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7576 (tmm-80) REVERT: 2 45 GLN cc_start: 0.8093 (mt0) cc_final: 0.7694 (mt0) REVERT: 2 46 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: 2 60 GLU cc_start: 0.7275 (tm-30) cc_final: 0.7012 (tm-30) REVERT: 2 62 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7108 (tp30) REVERT: 2 74 ASN cc_start: 0.8957 (m-40) cc_final: 0.8531 (m110) REVERT: 2 86 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7207 (pmt) REVERT: 2 91 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8604 (pt0) REVERT: 2 93 ASP cc_start: 0.9394 (m-30) cc_final: 0.9037 (p0) REVERT: 2 112 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7837 (tppt) REVERT: 3 22 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8252 (tp-100) REVERT: 3 26 TRP cc_start: 0.7941 (m-10) cc_final: 0.6504 (m-90) outliers start: 91 outliers final: 34 residues processed: 623 average time/residue: 0.5113 time to fit residues: 368.6300 Evaluate side-chains 583 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 540 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain M residue 5 GLN Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 1 residue 101 TYR Chi-restraints excluded: chain 2 residue 46 GLU Chi-restraints excluded: chain 2 residue 73 ILE Chi-restraints excluded: chain 2 residue 85 THR Chi-restraints excluded: chain 2 residue 86 MET Chi-restraints excluded: chain 3 residue 22 GLN Chi-restraints excluded: chain 3 residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN E 58 GLN L 6 ASN Z 31 GLN Z 38 GLN Z 58 ASN 1 56 ASN 1 106 ASN ** 3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.128263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091020 restraints weight = 36296.172| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.74 r_work: 0.2947 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 22714 Z= 0.191 Angle : 0.694 9.210 31311 Z= 0.333 Chirality : 0.045 0.285 3049 Planarity : 0.005 0.047 3945 Dihedral : 15.479 118.610 3880 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.03 % Allowed : 24.00 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2314 helix: 1.29 (0.14), residues: 1316 sheet: 0.90 (0.66), residues: 65 loop : -1.13 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 3 33 TYR 0.019 0.002 TYR B 279 PHE 0.020 0.002 PHE B 246 TRP 0.016 0.001 TRP C 353 HIS 0.009 0.002 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00440 (22702) covalent geometry : angle 0.69450 (31311) hydrogen bonds : bond 0.05367 ( 1010) hydrogen bonds : angle 4.21218 ( 2904) Misc. bond : bond 0.05272 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 567 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7914 (mtp180) cc_final: 0.7586 (mtm110) REVERT: A 65 GLU cc_start: 0.8620 (tt0) cc_final: 0.8365 (mm-30) REVERT: A 104 GLU cc_start: 0.8636 (pt0) cc_final: 0.8397 (pt0) REVERT: A 140 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7734 (mmm-85) REVERT: A 238 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7951 (mmpt) REVERT: A 241 GLN cc_start: 0.8144 (tm130) cc_final: 0.7419 (tm-30) REVERT: A 333 GLU cc_start: 0.8362 (tp30) cc_final: 0.7704 (tp30) REVERT: B 125 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6805 (p0) REVERT: B 214 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8930 (mm) REVERT: B 230 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7231 (mtt180) REVERT: B 326 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8933 (mtt180) REVERT: B 341 LYS cc_start: 0.9058 (mmtp) cc_final: 0.8618 (mmmm) REVERT: B 352 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8439 (mm-30) REVERT: C 130 GLU cc_start: 0.8935 (pp20) cc_final: 0.8685 (tm-30) REVERT: C 141 ASP cc_start: 0.8374 (t0) cc_final: 0.7899 (t0) REVERT: C 175 ASP cc_start: 0.9079 (t0) cc_final: 0.8780 (t0) REVERT: C 193 ASP cc_start: 0.8743 (t0) cc_final: 0.8320 (t70) REVERT: C 195 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8259 (mtp180) REVERT: C 227 TRP cc_start: 0.8389 (m100) cc_final: 0.8147 (m100) REVERT: C 277 PHE cc_start: 0.9480 (OUTLIER) cc_final: 0.8844 (t80) REVERT: C 336 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7242 (mp0) REVERT: C 350 ARG cc_start: 0.5830 (pmt170) cc_final: 0.2528 (mmt180) REVERT: C 355 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8749 (mm-30) REVERT: C 371 ASP cc_start: 0.8131 (m-30) cc_final: 0.7496 (m-30) REVERT: D 27 PHE cc_start: 0.8403 (t80) cc_final: 0.8083 (t80) REVERT: D 100 ASP cc_start: 0.8567 (t0) cc_final: 0.7987 (t70) REVERT: D 224 GLN cc_start: 0.8294 (mt0) cc_final: 0.7453 (pt0) REVERT: D 265 ARG cc_start: 0.8431 (ttp-110) cc_final: 0.8156 (ttp80) REVERT: D 323 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8820 (tm-30) REVERT: E 42 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8573 (tp) REVERT: E 55 TYR cc_start: 0.9445 (m-80) cc_final: 0.9007 (m-80) REVERT: E 61 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7789 (mmm160) REVERT: E 77 GLU cc_start: 0.9063 (tt0) cc_final: 0.8648 (mt-10) REVERT: E 82 GLN cc_start: 0.7635 (pt0) cc_final: 0.7373 (pp30) REVERT: F 8 GLN cc_start: 0.2032 (OUTLIER) cc_final: 0.1688 (pm20) REVERT: H 4 ARG cc_start: 0.8926 (mmm160) cc_final: 0.8670 (tpp80) REVERT: H 9 ASP cc_start: 0.8622 (m-30) cc_final: 0.8109 (m-30) REVERT: H 17 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8281 (mm-30) REVERT: H 20 LYS cc_start: 0.8523 (ttpp) cc_final: 0.7994 (mmtt) REVERT: M 1 MET cc_start: 0.2647 (mpt) cc_final: 0.1703 (mpt) REVERT: M 5 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7478 (tp40) REVERT: T 25 GLU cc_start: 0.7862 (tp30) cc_final: 0.7610 (tp30) REVERT: Z 31 GLN cc_start: 0.6033 (OUTLIER) cc_final: 0.5713 (pp30) REVERT: Z 60 PHE cc_start: 0.8727 (m-80) cc_final: 0.8431 (m-80) REVERT: 1 33 PHE cc_start: 0.8771 (t80) cc_final: 0.8541 (t80) REVERT: 1 37 THR cc_start: 0.9575 (t) cc_final: 0.9341 (p) REVERT: 1 67 LYS cc_start: 0.8747 (tppp) cc_final: 0.8518 (tppp) REVERT: 1 88 MET cc_start: 0.9207 (mmm) cc_final: 0.8893 (mmm) REVERT: 1 91 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8607 (tm-30) REVERT: 1 114 LYS cc_start: 0.8611 (mttt) cc_final: 0.8155 (mttm) REVERT: 1 123 GLN cc_start: 0.9522 (mt0) cc_final: 0.9153 (tp40) REVERT: 2 4 MET cc_start: 0.3935 (tmm) cc_final: 0.1774 (tpp) REVERT: 2 15 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7044 (tm-30) REVERT: 2 22 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7401 (tmm-80) REVERT: 2 45 GLN cc_start: 0.8207 (mt0) cc_final: 0.7866 (mt0) REVERT: 2 46 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6644 (pm20) REVERT: 2 74 ASN cc_start: 0.9053 (m110) cc_final: 0.8553 (m-40) REVERT: 2 86 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7461 (pmt) REVERT: 2 91 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8610 (pt0) REVERT: 2 93 ASP cc_start: 0.9386 (m-30) cc_final: 0.9050 (p0) REVERT: 2 101 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6749 (mtt90) REVERT: 2 112 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8008 (tppp) REVERT: 3 22 GLN cc_start: 0.8551 (tp40) cc_final: 0.8198 (tp-100) REVERT: 3 26 TRP cc_start: 0.7900 (m-10) cc_final: 0.6584 (m-90) outliers start: 115 outliers final: 52 residues processed: 614 average time/residue: 0.5520 time to fit residues: 388.7256 Evaluate side-chains 597 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 533 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 GLN Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain 2 residue 46 GLU Chi-restraints excluded: chain 2 residue 73 ILE Chi-restraints excluded: chain 2 residue 86 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 141 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 199 GLN A 296 ASN A 303 ASN B 374 ASN C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 239 GLN D 322 ASN L 6 ASN Z 31 GLN Z 38 GLN Z 58 ASN 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093409 restraints weight = 35691.796| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.73 r_work: 0.2986 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 22714 Z= 0.128 Angle : 0.647 13.900 31311 Z= 0.310 Chirality : 0.042 0.211 3049 Planarity : 0.005 0.048 3945 Dihedral : 15.088 119.288 3876 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.85 % Rotamer: Outliers : 4.93 % Allowed : 26.00 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2314 helix: 1.49 (0.14), residues: 1322 sheet: 1.09 (0.60), residues: 70 loop : -1.06 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 25 TYR 0.016 0.001 TYR B 279 PHE 0.022 0.001 PHE I 19 TRP 0.013 0.001 TRP C 51 HIS 0.007 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00287 (22702) covalent geometry : angle 0.64702 (31311) hydrogen bonds : bond 0.04601 ( 1010) hydrogen bonds : angle 4.07476 ( 2904) Misc. bond : bond 0.03821 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 556 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7201 (mtm180) REVERT: A 65 GLU cc_start: 0.8621 (tt0) cc_final: 0.8401 (mm-30) REVERT: A 104 GLU cc_start: 0.8627 (pt0) cc_final: 0.8393 (pt0) REVERT: A 140 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7778 (mmm-85) REVERT: A 238 LYS cc_start: 0.8342 (mtpp) cc_final: 0.7949 (mmpt) REVERT: A 241 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: A 333 GLU cc_start: 0.8359 (tp30) cc_final: 0.7726 (tp30) REVERT: B 125 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6856 (p0) REVERT: B 130 GLU cc_start: 0.8895 (pt0) cc_final: 0.8363 (pm20) REVERT: B 214 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8857 (mm) REVERT: B 230 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7257 (mtt180) REVERT: B 352 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8435 (mm-30) REVERT: C 130 GLU cc_start: 0.8929 (pp20) cc_final: 0.8646 (tm-30) REVERT: C 141 ASP cc_start: 0.8306 (t0) cc_final: 0.7729 (t0) REVERT: C 175 ASP cc_start: 0.8921 (t0) cc_final: 0.8648 (t0) REVERT: C 193 ASP cc_start: 0.8767 (t0) cc_final: 0.8352 (t70) REVERT: C 195 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8271 (mtp180) REVERT: C 227 TRP cc_start: 0.8387 (m100) cc_final: 0.8109 (m100) REVERT: C 277 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.8870 (t80) REVERT: C 336 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7166 (mp0) REVERT: C 350 ARG cc_start: 0.5622 (pmt170) cc_final: 0.2424 (mmt180) REVERT: C 355 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8781 (mm-30) REVERT: C 371 ASP cc_start: 0.8199 (m-30) cc_final: 0.7566 (m-30) REVERT: C 430 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8203 (mm) REVERT: D 27 PHE cc_start: 0.8411 (t80) cc_final: 0.8131 (t80) REVERT: D 100 ASP cc_start: 0.8558 (t0) cc_final: 0.7977 (t70) REVERT: D 224 GLN cc_start: 0.8283 (mt0) cc_final: 0.7538 (pt0) REVERT: D 265 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8088 (ttp80) REVERT: D 323 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8824 (tm-30) REVERT: E 42 LEU cc_start: 0.9015 (tp) cc_final: 0.8555 (tp) REVERT: E 55 TYR cc_start: 0.9414 (m-80) cc_final: 0.8957 (m-80) REVERT: E 61 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7921 (mmm160) REVERT: E 77 GLU cc_start: 0.8947 (tt0) cc_final: 0.8711 (mt-10) REVERT: E 82 GLN cc_start: 0.7712 (pt0) cc_final: 0.7465 (pp30) REVERT: H 9 ASP cc_start: 0.8630 (m-30) cc_final: 0.8404 (m-30) REVERT: H 17 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8221 (mm-30) REVERT: H 20 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8018 (mmtt) REVERT: I 18 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8131 (pp) REVERT: K 13 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: M 1 MET cc_start: 0.2371 (mpt) cc_final: 0.1555 (mpt) REVERT: T 19 PHE cc_start: 0.8677 (m-10) cc_final: 0.8475 (m-80) REVERT: T 25 GLU cc_start: 0.7936 (tp30) cc_final: 0.7623 (tp30) REVERT: y 27 MET cc_start: 0.8632 (tmm) cc_final: 0.8330 (tmm) REVERT: Z 17 PHE cc_start: 0.8794 (t80) cc_final: 0.8567 (t80) REVERT: Z 60 PHE cc_start: 0.8773 (m-80) cc_final: 0.8436 (m-80) REVERT: 1 33 PHE cc_start: 0.8733 (t80) cc_final: 0.8487 (t80) REVERT: 1 37 THR cc_start: 0.9545 (t) cc_final: 0.9302 (p) REVERT: 1 67 LYS cc_start: 0.8733 (tppp) cc_final: 0.8498 (tppp) REVERT: 1 88 MET cc_start: 0.9172 (mmm) cc_final: 0.8893 (mmm) REVERT: 1 91 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8678 (tm-30) REVERT: 1 114 LYS cc_start: 0.8710 (mttt) cc_final: 0.8229 (mttm) REVERT: 1 119 GLN cc_start: 0.9188 (mt0) cc_final: 0.8941 (mm-40) REVERT: 1 123 GLN cc_start: 0.9492 (mt0) cc_final: 0.9156 (tp40) REVERT: 2 15 GLU cc_start: 0.7933 (tm-30) cc_final: 0.6789 (tm-30) REVERT: 2 22 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7505 (tmm-80) REVERT: 2 45 GLN cc_start: 0.8234 (mt0) cc_final: 0.7911 (mt0) REVERT: 2 46 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6626 (pm20) REVERT: 2 74 ASN cc_start: 0.9080 (m110) cc_final: 0.8613 (m-40) REVERT: 2 86 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7613 (pmt) REVERT: 2 91 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8626 (pt0) REVERT: 2 93 ASP cc_start: 0.9398 (m-30) cc_final: 0.9047 (p0) REVERT: 2 105 SER cc_start: 0.7272 (t) cc_final: 0.6617 (p) REVERT: 2 112 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8124 (tppp) REVERT: 3 22 GLN cc_start: 0.8491 (tp40) cc_final: 0.8166 (tp-100) REVERT: 3 26 TRP cc_start: 0.7892 (m-10) cc_final: 0.6586 (m-90) outliers start: 94 outliers final: 39 residues processed: 599 average time/residue: 0.5448 time to fit residues: 373.4203 Evaluate side-chains 594 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 544 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain 1 residue 101 TYR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 46 GLU Chi-restraints excluded: chain 2 residue 73 ILE Chi-restraints excluded: chain 2 residue 86 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 122 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN B 282 GLN C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN L 6 ASN Z 31 GLN Z 58 ASN 1 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.090769 restraints weight = 36106.985| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.74 r_work: 0.2949 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 22714 Z= 0.172 Angle : 0.675 11.421 31311 Z= 0.322 Chirality : 0.044 0.247 3049 Planarity : 0.005 0.048 3945 Dihedral : 14.898 119.101 3873 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.77 % Allowed : 26.57 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2314 helix: 1.54 (0.14), residues: 1322 sheet: 0.64 (0.63), residues: 75 loop : -0.97 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 1 130 TYR 0.018 0.001 TYR B 279 PHE 0.024 0.001 PHE I 19 TRP 0.011 0.001 TRP C 51 HIS 0.007 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00400 (22702) covalent geometry : angle 0.67489 (31311) hydrogen bonds : bond 0.04892 ( 1010) hydrogen bonds : angle 4.10401 ( 2904) Misc. bond : bond 0.04979 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 541 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7258 (mtm180) REVERT: A 65 GLU cc_start: 0.8733 (tt0) cc_final: 0.8517 (mm-30) REVERT: A 104 GLU cc_start: 0.8620 (pt0) cc_final: 0.8376 (pt0) REVERT: A 140 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7757 (mmm-85) REVERT: A 187 GLN cc_start: 0.9374 (tp40) cc_final: 0.9128 (tm130) REVERT: A 238 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7817 (mmpt) REVERT: A 241 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: A 333 GLU cc_start: 0.8442 (tp30) cc_final: 0.7819 (tp30) REVERT: B 125 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6868 (p0) REVERT: B 130 GLU cc_start: 0.8916 (pt0) cc_final: 0.8439 (pm20) REVERT: B 214 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8864 (mm) REVERT: B 230 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7246 (mtt180) REVERT: B 352 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8436 (mm-30) REVERT: C 130 GLU cc_start: 0.8947 (pp20) cc_final: 0.8649 (tm-30) REVERT: C 141 ASP cc_start: 0.8365 (t0) cc_final: 0.7745 (t0) REVERT: C 175 ASP cc_start: 0.8967 (t0) cc_final: 0.8613 (t70) REVERT: C 193 ASP cc_start: 0.8729 (t0) cc_final: 0.8277 (t70) REVERT: C 195 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8294 (mtp180) REVERT: C 209 GLU cc_start: 0.8763 (pm20) cc_final: 0.8353 (pm20) REVERT: C 227 TRP cc_start: 0.8406 (m100) cc_final: 0.8144 (m100) REVERT: C 277 PHE cc_start: 0.9476 (OUTLIER) cc_final: 0.8884 (t80) REVERT: C 330 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7473 (pmm) REVERT: C 336 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7239 (mm-30) REVERT: C 350 ARG cc_start: 0.5720 (pmt170) cc_final: 0.2424 (mmt180) REVERT: C 371 ASP cc_start: 0.8193 (m-30) cc_final: 0.7558 (m-30) REVERT: C 430 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8210 (mm) REVERT: D 27 PHE cc_start: 0.8429 (t80) cc_final: 0.8078 (t80) REVERT: D 100 ASP cc_start: 0.8601 (t0) cc_final: 0.8062 (t70) REVERT: D 129 GLN cc_start: 0.8689 (mt0) cc_final: 0.8483 (mt0) REVERT: D 265 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8133 (ttp80) REVERT: D 323 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8846 (tm-30) REVERT: E 55 TYR cc_start: 0.9458 (m-80) cc_final: 0.9040 (m-80) REVERT: E 61 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7611 (mmp-170) REVERT: E 77 GLU cc_start: 0.9059 (tt0) cc_final: 0.8671 (mt-10) REVERT: E 82 GLN cc_start: 0.7721 (pt0) cc_final: 0.7484 (pp30) REVERT: F 8 GLN cc_start: 0.1896 (OUTLIER) cc_final: 0.1478 (pm20) REVERT: H 4 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8833 (mmm-85) REVERT: H 9 ASP cc_start: 0.8724 (m-30) cc_final: 0.8407 (m-30) REVERT: H 20 LYS cc_start: 0.8496 (ttpp) cc_final: 0.7993 (mmtt) REVERT: I 18 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8236 (pp) REVERT: K 13 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: M 1 MET cc_start: 0.2326 (mpt) cc_final: 0.1661 (mpt) REVERT: T 25 GLU cc_start: 0.7974 (tp30) cc_final: 0.7667 (tp30) REVERT: y 27 MET cc_start: 0.8645 (tmm) cc_final: 0.8269 (tmm) REVERT: Z 60 PHE cc_start: 0.8786 (m-80) cc_final: 0.8395 (m-80) REVERT: 1 33 PHE cc_start: 0.8696 (t80) cc_final: 0.8434 (t80) REVERT: 1 37 THR cc_start: 0.9520 (t) cc_final: 0.9274 (p) REVERT: 1 67 LYS cc_start: 0.8719 (tppp) cc_final: 0.8476 (tppp) REVERT: 1 88 MET cc_start: 0.9152 (mmm) cc_final: 0.8882 (mmm) REVERT: 1 114 LYS cc_start: 0.8748 (mttt) cc_final: 0.8282 (mttm) REVERT: 1 123 GLN cc_start: 0.9511 (mt0) cc_final: 0.9169 (tp40) REVERT: 2 4 MET cc_start: 0.2313 (pp-130) cc_final: 0.0101 (tpp) REVERT: 2 15 GLU cc_start: 0.8010 (tm-30) cc_final: 0.6759 (tm-30) REVERT: 2 22 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7613 (tmm-80) REVERT: 2 25 ARG cc_start: 0.8438 (tpt-90) cc_final: 0.8127 (tpt-90) REVERT: 2 45 GLN cc_start: 0.8279 (mt0) cc_final: 0.7886 (mt0) REVERT: 2 46 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6880 (pm20) REVERT: 2 71 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8241 (ttmm) REVERT: 2 86 MET cc_start: 0.7977 (ptp) cc_final: 0.7524 (pmt) REVERT: 2 91 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8633 (pt0) REVERT: 2 93 ASP cc_start: 0.9396 (m-30) cc_final: 0.8995 (p0) REVERT: 2 101 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.6468 (mtm-85) REVERT: 2 105 SER cc_start: 0.7182 (t) cc_final: 0.6839 (p) REVERT: 2 111 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7250 (tm-30) REVERT: 2 112 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8280 (tppp) REVERT: 3 22 GLN cc_start: 0.8446 (tp40) cc_final: 0.8106 (tp-100) REVERT: 3 26 TRP cc_start: 0.7896 (m-10) cc_final: 0.6575 (m-90) outliers start: 91 outliers final: 45 residues processed: 582 average time/residue: 0.5406 time to fit residues: 361.4133 Evaluate side-chains 587 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 530 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 46 GLU Chi-restraints excluded: chain 2 residue 73 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 206 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 174 optimal weight: 0.0020 chunk 204 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.5690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN A 296 ASN A 303 ASN C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN E 58 GLN L 6 ASN Z 31 GLN Z 58 ASN 1 106 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090190 restraints weight = 36287.938| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.75 r_work: 0.2931 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 22714 Z= 0.161 Angle : 0.667 10.766 31311 Z= 0.321 Chirality : 0.044 0.225 3049 Planarity : 0.004 0.049 3945 Dihedral : 14.660 119.467 3873 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.77 % Allowed : 27.25 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.18), residues: 2314 helix: 1.59 (0.15), residues: 1314 sheet: 1.06 (0.63), residues: 72 loop : -0.90 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 25 TYR 0.017 0.001 TYR A 135 PHE 0.028 0.001 PHE 1 121 TRP 0.012 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00375 (22702) covalent geometry : angle 0.66674 (31311) hydrogen bonds : bond 0.04866 ( 1010) hydrogen bonds : angle 4.09820 ( 2904) Misc. bond : bond 0.04901 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 547 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7893 (mtp180) cc_final: 0.7279 (mtm180) REVERT: A 104 GLU cc_start: 0.8619 (pt0) cc_final: 0.8404 (pt0) REVERT: A 140 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7716 (mmm-85) REVERT: A 187 GLN cc_start: 0.9382 (tp40) cc_final: 0.9135 (tm130) REVERT: A 229 GLU cc_start: 0.7961 (tp30) cc_final: 0.7033 (pm20) REVERT: A 238 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7944 (mmpt) REVERT: A 241 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: A 333 GLU cc_start: 0.8512 (tp30) cc_final: 0.7887 (tp30) REVERT: B 125 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6846 (p0) REVERT: B 130 GLU cc_start: 0.8879 (pt0) cc_final: 0.8339 (pm20) REVERT: B 214 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8858 (mm) REVERT: B 230 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7219 (mtt180) REVERT: B 352 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8390 (mm-30) REVERT: C 130 GLU cc_start: 0.8946 (pp20) cc_final: 0.8556 (tm-30) REVERT: C 141 ASP cc_start: 0.8474 (t0) cc_final: 0.7849 (t0) REVERT: C 175 ASP cc_start: 0.8966 (t0) cc_final: 0.8686 (t70) REVERT: C 193 ASP cc_start: 0.8701 (t0) cc_final: 0.8246 (t70) REVERT: C 195 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8296 (mtp180) REVERT: C 209 GLU cc_start: 0.8775 (pm20) cc_final: 0.8374 (pm20) REVERT: C 227 TRP cc_start: 0.8397 (m100) cc_final: 0.8134 (m100) REVERT: C 277 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.8853 (t80) REVERT: C 336 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7368 (mm-30) REVERT: C 350 ARG cc_start: 0.5725 (pmt170) cc_final: 0.2270 (mmt180) REVERT: C 371 ASP cc_start: 0.8223 (m-30) cc_final: 0.7558 (m-30) REVERT: C 430 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8235 (mm) REVERT: D 27 PHE cc_start: 0.8429 (t80) cc_final: 0.8099 (t80) REVERT: D 100 ASP cc_start: 0.8608 (t0) cc_final: 0.8063 (t70) REVERT: D 224 GLN cc_start: 0.8398 (mt0) cc_final: 0.7675 (pt0) REVERT: D 265 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8146 (ttp80) REVERT: D 323 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8858 (tm-30) REVERT: E 55 TYR cc_start: 0.9461 (m-80) cc_final: 0.9028 (m-80) REVERT: E 77 GLU cc_start: 0.8909 (tt0) cc_final: 0.8692 (mt-10) REVERT: E 82 GLN cc_start: 0.7610 (pt0) cc_final: 0.7391 (pp30) REVERT: F 8 GLN cc_start: 0.1970 (OUTLIER) cc_final: 0.1519 (pm20) REVERT: H 4 ARG cc_start: 0.9125 (mmm-85) cc_final: 0.8859 (mmm-85) REVERT: H 9 ASP cc_start: 0.8734 (m-30) cc_final: 0.8380 (m-30) REVERT: I 18 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8222 (pp) REVERT: K 13 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: K 18 PHE cc_start: 0.8258 (m-80) cc_final: 0.8048 (m-80) REVERT: M 1 MET cc_start: 0.2145 (mpt) cc_final: 0.1776 (mpt) REVERT: T 25 GLU cc_start: 0.8005 (tp30) cc_final: 0.7673 (tp30) REVERT: Z 31 GLN cc_start: 0.5984 (OUTLIER) cc_final: 0.5545 (pp30) REVERT: Z 57 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8227 (tp) REVERT: 1 33 PHE cc_start: 0.8622 (t80) cc_final: 0.8349 (t80) REVERT: 1 37 THR cc_start: 0.9498 (t) cc_final: 0.9264 (p) REVERT: 1 67 LYS cc_start: 0.8724 (tppp) cc_final: 0.8482 (tppp) REVERT: 1 88 MET cc_start: 0.9187 (mmm) cc_final: 0.8871 (mmm) REVERT: 1 91 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8693 (tm-30) REVERT: 1 114 LYS cc_start: 0.8843 (mttt) cc_final: 0.8378 (mttm) REVERT: 1 116 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8173 (tpp-160) REVERT: 1 123 GLN cc_start: 0.9419 (mt0) cc_final: 0.9150 (tp40) REVERT: 2 4 MET cc_start: 0.2566 (pp-130) cc_final: 0.0675 (tpp) REVERT: 2 15 GLU cc_start: 0.7856 (tm-30) cc_final: 0.6835 (tm-30) REVERT: 2 22 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7566 (tmm-80) REVERT: 2 25 ARG cc_start: 0.8493 (tpt-90) cc_final: 0.8287 (tpt-90) REVERT: 2 45 GLN cc_start: 0.8303 (mt0) cc_final: 0.8010 (mt0) REVERT: 2 46 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: 2 62 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7284 (tp30) REVERT: 2 71 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8395 (ttmm) REVERT: 2 74 ASN cc_start: 0.9109 (m110) cc_final: 0.8639 (m-40) REVERT: 2 86 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7383 (pmt) REVERT: 2 91 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8665 (pt0) REVERT: 2 93 ASP cc_start: 0.9371 (m-30) cc_final: 0.8973 (p0) REVERT: 2 105 SER cc_start: 0.7144 (t) cc_final: 0.6819 (p) REVERT: 2 112 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8356 (tppp) REVERT: 3 22 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7968 (tp-100) REVERT: 3 26 TRP cc_start: 0.7902 (m-10) cc_final: 0.6590 (m-90) outliers start: 91 outliers final: 50 residues processed: 586 average time/residue: 0.5625 time to fit residues: 382.9097 Evaluate side-chains 603 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 538 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 24 MET Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 46 GLU Chi-restraints excluded: chain 2 residue 73 ILE Chi-restraints excluded: chain 2 residue 86 MET Chi-restraints excluded: chain 3 residue 22 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 166 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN B 282 GLN C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN L 6 ASN Z 31 GLN Z 58 ASN 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.089197 restraints weight = 36074.948| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.73 r_work: 0.2910 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 22714 Z= 0.183 Angle : 0.697 10.879 31311 Z= 0.337 Chirality : 0.045 0.236 3049 Planarity : 0.005 0.049 3945 Dihedral : 14.589 119.474 3873 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 4.25 % Allowed : 28.51 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2314 helix: 1.57 (0.14), residues: 1318 sheet: 1.13 (0.68), residues: 65 loop : -0.81 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 2 25 TYR 0.018 0.001 TYR B 279 PHE 0.033 0.002 PHE 1 121 TRP 0.023 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00426 (22702) covalent geometry : angle 0.69696 (31311) hydrogen bonds : bond 0.05016 ( 1010) hydrogen bonds : angle 4.11777 ( 2904) Misc. bond : bond 0.05439 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 551 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7666 (mtm180) REVERT: A 20 TRP cc_start: 0.8814 (OUTLIER) cc_final: 0.8251 (t-100) REVERT: A 104 GLU cc_start: 0.8637 (pt0) cc_final: 0.8414 (pt0) REVERT: A 140 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7497 (mmm-85) REVERT: A 183 MET cc_start: 0.9474 (mtm) cc_final: 0.9152 (mtp) REVERT: A 238 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7825 (mmpt) REVERT: A 333 GLU cc_start: 0.8550 (tp30) cc_final: 0.7928 (tp30) REVERT: B 125 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6763 (p0) REVERT: B 130 GLU cc_start: 0.8896 (pt0) cc_final: 0.8325 (pm20) REVERT: B 214 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8859 (mm) REVERT: B 230 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7268 (mtt180) REVERT: B 352 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8376 (mm-30) REVERT: C 130 GLU cc_start: 0.8909 (pp20) cc_final: 0.8532 (tm-30) REVERT: C 141 ASP cc_start: 0.8445 (t0) cc_final: 0.7790 (t0) REVERT: C 175 ASP cc_start: 0.8806 (t0) cc_final: 0.8533 (t0) REVERT: C 193 ASP cc_start: 0.8691 (t0) cc_final: 0.8234 (t70) REVERT: C 195 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8324 (mtp180) REVERT: C 209 GLU cc_start: 0.8838 (pm20) cc_final: 0.8461 (pm20) REVERT: C 227 TRP cc_start: 0.8423 (m100) cc_final: 0.8171 (m100) REVERT: C 277 PHE cc_start: 0.9487 (OUTLIER) cc_final: 0.8826 (t80) REVERT: C 336 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7330 (mm-30) REVERT: C 350 ARG cc_start: 0.5777 (pmt170) cc_final: 0.2333 (mpt90) REVERT: C 371 ASP cc_start: 0.8236 (m-30) cc_final: 0.7553 (m-30) REVERT: C 430 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8234 (mm) REVERT: D 27 PHE cc_start: 0.8451 (t80) cc_final: 0.8100 (t80) REVERT: D 100 ASP cc_start: 0.8601 (t0) cc_final: 0.8032 (t70) REVERT: D 224 GLN cc_start: 0.8439 (mt0) cc_final: 0.7741 (pt0) REVERT: D 323 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8837 (tm-30) REVERT: E 55 TYR cc_start: 0.9477 (m-80) cc_final: 0.9043 (m-80) REVERT: E 77 GLU cc_start: 0.9028 (tt0) cc_final: 0.8629 (mt-10) REVERT: E 82 GLN cc_start: 0.7651 (pt0) cc_final: 0.7410 (pp30) REVERT: F 8 GLN cc_start: 0.2019 (OUTLIER) cc_final: 0.1520 (pm20) REVERT: H 4 ARG cc_start: 0.9154 (mmm-85) cc_final: 0.8871 (mmm-85) REVERT: H 9 ASP cc_start: 0.8720 (m-30) cc_final: 0.8359 (m-30) REVERT: T 25 GLU cc_start: 0.8024 (tp30) cc_final: 0.7684 (tp30) REVERT: Z 57 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8243 (tp) REVERT: 1 33 PHE cc_start: 0.8577 (t80) cc_final: 0.8304 (t80) REVERT: 1 37 THR cc_start: 0.9472 (t) cc_final: 0.9210 (p) REVERT: 1 67 LYS cc_start: 0.8735 (tppp) cc_final: 0.8525 (tppp) REVERT: 1 88 MET cc_start: 0.9180 (mmm) cc_final: 0.8847 (mmm) REVERT: 1 91 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8734 (tm-30) REVERT: 1 114 LYS cc_start: 0.8854 (mttt) cc_final: 0.8161 (mttm) REVERT: 1 123 GLN cc_start: 0.9352 (mt0) cc_final: 0.9146 (tp40) REVERT: 2 4 MET cc_start: 0.2600 (pp-130) cc_final: 0.0715 (tpp) REVERT: 2 15 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7646 (tm-30) REVERT: 2 22 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7577 (tmm-80) REVERT: 2 25 ARG cc_start: 0.8477 (tpt-90) cc_final: 0.7852 (tpt-90) REVERT: 2 45 GLN cc_start: 0.8318 (mt0) cc_final: 0.8006 (mt0) REVERT: 2 46 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: 2 74 ASN cc_start: 0.9146 (m110) cc_final: 0.8673 (m-40) REVERT: 2 86 MET cc_start: 0.7840 (ptp) cc_final: 0.7526 (pmm) REVERT: 2 91 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8699 (pt0) REVERT: 2 93 ASP cc_start: 0.9366 (m-30) cc_final: 0.8957 (p0) REVERT: 2 101 ARG cc_start: 0.7081 (mtm-85) cc_final: 0.6631 (mtm-85) REVERT: 2 105 SER cc_start: 0.7001 (t) cc_final: 0.6672 (p) REVERT: 2 112 LYS cc_start: 0.8830 (ttpt) cc_final: 0.8188 (tppp) REVERT: 3 26 TRP cc_start: 0.7907 (m-10) cc_final: 0.6600 (m-90) outliers start: 81 outliers final: 45 residues processed: 592 average time/residue: 0.5365 time to fit residues: 366.2176 Evaluate side-chains 594 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 539 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 46 GLU Chi-restraints excluded: chain 2 residue 73 ILE Chi-restraints excluded: chain 3 residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 50 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 153 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 HIS ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN L 4 ASN L 6 ASN M 33 GLN Z 31 GLN Z 58 ASN 1 106 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.092191 restraints weight = 36110.273| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.73 r_work: 0.2961 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 22714 Z= 0.131 Angle : 0.675 15.985 31311 Z= 0.326 Chirality : 0.043 0.211 3049 Planarity : 0.005 0.055 3945 Dihedral : 14.358 119.610 3873 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.94 % Allowed : 30.40 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2314 helix: 1.69 (0.15), residues: 1309 sheet: 1.09 (0.67), residues: 67 loop : -0.72 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 1 116 TYR 0.018 0.001 TYR A 135 PHE 0.042 0.001 PHE 1 121 TRP 0.014 0.001 TRP Z 33 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00297 (22702) covalent geometry : angle 0.67522 (31311) hydrogen bonds : bond 0.04405 ( 1010) hydrogen bonds : angle 4.03750 ( 2904) Misc. bond : bond 0.04194 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 547 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7421 (mtm180) REVERT: A 140 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7593 (mmm-85) REVERT: A 238 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7841 (mmpt) REVERT: A 239 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: A 241 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8727 (tm-30) REVERT: A 303 ASN cc_start: 0.8416 (p0) cc_final: 0.7935 (p0) REVERT: A 333 GLU cc_start: 0.8555 (tp30) cc_final: 0.7950 (tp30) REVERT: B 214 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8833 (mm) REVERT: B 230 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7188 (mtt180) REVERT: B 352 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8409 (mm-30) REVERT: C 130 GLU cc_start: 0.8863 (pp20) cc_final: 0.8519 (tm-30) REVERT: C 141 ASP cc_start: 0.8419 (t0) cc_final: 0.7764 (t0) REVERT: C 175 ASP cc_start: 0.8746 (t0) cc_final: 0.8517 (t0) REVERT: C 193 ASP cc_start: 0.8705 (t0) cc_final: 0.8286 (t70) REVERT: C 209 GLU cc_start: 0.8810 (pm20) cc_final: 0.8479 (pm20) REVERT: C 227 TRP cc_start: 0.8418 (m100) cc_final: 0.8165 (m100) REVERT: C 277 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.8847 (t80) REVERT: C 336 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7323 (mm-30) REVERT: C 350 ARG cc_start: 0.5707 (pmt170) cc_final: 0.2265 (mmt180) REVERT: C 371 ASP cc_start: 0.8190 (m-30) cc_final: 0.7523 (m-30) REVERT: C 430 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8265 (mm) REVERT: D 27 PHE cc_start: 0.8420 (t80) cc_final: 0.8128 (t80) REVERT: D 100 ASP cc_start: 0.8581 (t0) cc_final: 0.8026 (t70) REVERT: D 186 GLN cc_start: 0.9430 (tp40) cc_final: 0.9138 (tp40) REVERT: D 224 GLN cc_start: 0.8417 (mt0) cc_final: 0.7765 (pt0) REVERT: D 323 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8848 (tm-30) REVERT: E 55 TYR cc_start: 0.9440 (m-80) cc_final: 0.8921 (m-80) REVERT: E 77 GLU cc_start: 0.8888 (tt0) cc_final: 0.8553 (mt-10) REVERT: E 82 GLN cc_start: 0.7613 (pt0) cc_final: 0.7315 (pp30) REVERT: H 4 ARG cc_start: 0.9090 (mmm-85) cc_final: 0.8710 (tpp80) REVERT: H 9 ASP cc_start: 0.8725 (m-30) cc_final: 0.8201 (m-30) REVERT: I 18 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8044 (pp) REVERT: M 1 MET cc_start: 0.0707 (mpt) cc_final: -0.0518 (OUTLIER) REVERT: T 25 GLU cc_start: 0.8031 (tp30) cc_final: 0.7678 (tp30) REVERT: Z 31 GLN cc_start: 0.5699 (OUTLIER) cc_final: 0.5347 (pp30) REVERT: 1 33 PHE cc_start: 0.8551 (t80) cc_final: 0.8263 (t80) REVERT: 1 37 THR cc_start: 0.9444 (t) cc_final: 0.9198 (p) REVERT: 1 48 ILE cc_start: 0.8675 (pt) cc_final: 0.8352 (pp) REVERT: 1 67 LYS cc_start: 0.8729 (tppp) cc_final: 0.8517 (tppp) REVERT: 1 88 MET cc_start: 0.9148 (mmm) cc_final: 0.8821 (mmm) REVERT: 1 91 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8780 (tm-30) REVERT: 1 114 LYS cc_start: 0.8731 (mttt) cc_final: 0.8386 (mttm) REVERT: 2 4 MET cc_start: 0.2486 (pp-130) cc_final: 0.0452 (tpp) REVERT: 2 15 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7523 (tm-30) REVERT: 2 22 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7540 (tmm-80) REVERT: 2 25 ARG cc_start: 0.8453 (tpt-90) cc_final: 0.8148 (tpt-90) REVERT: 2 42 LYS cc_start: 0.8967 (mmtp) cc_final: 0.8603 (mmtp) REVERT: 2 45 GLN cc_start: 0.8344 (mt0) cc_final: 0.8065 (mt0) REVERT: 2 46 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: 2 74 ASN cc_start: 0.9166 (m110) cc_final: 0.8701 (m-40) REVERT: 2 86 MET cc_start: 0.7728 (ptp) cc_final: 0.7475 (pmm) REVERT: 2 91 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8748 (pt0) REVERT: 2 93 ASP cc_start: 0.9365 (m-30) cc_final: 0.8920 (p0) REVERT: 2 101 ARG cc_start: 0.6965 (mtm-85) cc_final: 0.6532 (mtm-85) REVERT: 2 112 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8571 (tppp) REVERT: 3 26 TRP cc_start: 0.7888 (m-10) cc_final: 0.6600 (m-90) outliers start: 56 outliers final: 37 residues processed: 571 average time/residue: 0.5560 time to fit residues: 364.5655 Evaluate side-chains 583 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 539 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 46 GLU Chi-restraints excluded: chain 2 residue 73 ILE Chi-restraints excluded: chain 3 residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 215 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 282 GLN C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN C 386 HIS ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN L 6 ASN M 33 GLN Z 31 GLN 1 56 ASN 1 106 ASN 3 22 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.088959 restraints weight = 36291.743| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.73 r_work: 0.2909 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 22714 Z= 0.190 Angle : 0.720 10.675 31311 Z= 0.350 Chirality : 0.045 0.243 3049 Planarity : 0.005 0.052 3945 Dihedral : 14.416 119.388 3873 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.94 % Allowed : 30.45 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.18), residues: 2314 helix: 1.59 (0.14), residues: 1313 sheet: 1.01 (0.74), residues: 60 loop : -0.68 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 1 116 TYR 0.019 0.001 TYR A 135 PHE 0.044 0.002 PHE 1 121 TRP 0.035 0.001 TRP Z 33 HIS 0.006 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00444 (22702) covalent geometry : angle 0.72036 (31311) hydrogen bonds : bond 0.04969 ( 1010) hydrogen bonds : angle 4.13618 ( 2904) Misc. bond : bond 0.05509 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 545 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7592 (mtm180) REVERT: A 140 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7659 (mmm-85) REVERT: A 238 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7853 (mmpt) REVERT: A 241 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8686 (tm-30) REVERT: A 291 SER cc_start: 0.9302 (m) cc_final: 0.9091 (p) REVERT: A 303 ASN cc_start: 0.8494 (p0) cc_final: 0.8047 (p0) REVERT: A 333 GLU cc_start: 0.8650 (tp30) cc_final: 0.8029 (tp30) REVERT: B 130 GLU cc_start: 0.8924 (pt0) cc_final: 0.8512 (pm20) REVERT: B 214 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8867 (mm) REVERT: B 230 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7167 (mtt180) REVERT: B 352 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8415 (mm-30) REVERT: C 126 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7128 (tm-30) REVERT: C 130 GLU cc_start: 0.8848 (pp20) cc_final: 0.8543 (tm-30) REVERT: C 141 ASP cc_start: 0.8427 (t0) cc_final: 0.7854 (t0) REVERT: C 193 ASP cc_start: 0.8740 (t0) cc_final: 0.8281 (t70) REVERT: C 209 GLU cc_start: 0.8844 (pm20) cc_final: 0.8539 (pm20) REVERT: C 227 TRP cc_start: 0.8455 (m100) cc_final: 0.8204 (m100) REVERT: C 268 SER cc_start: 0.9151 (t) cc_final: 0.8752 (m) REVERT: C 277 PHE cc_start: 0.9497 (OUTLIER) cc_final: 0.8845 (t80) REVERT: C 336 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7324 (mm-30) REVERT: C 350 ARG cc_start: 0.5871 (pmt170) cc_final: 0.2405 (mmt-90) REVERT: C 354 LEU cc_start: 0.8932 (tp) cc_final: 0.8674 (mp) REVERT: C 371 ASP cc_start: 0.8251 (m-30) cc_final: 0.7608 (m-30) REVERT: C 430 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8257 (mm) REVERT: D 27 PHE cc_start: 0.8455 (t80) cc_final: 0.8164 (t80) REVERT: D 100 ASP cc_start: 0.8623 (t0) cc_final: 0.8098 (t70) REVERT: D 224 GLN cc_start: 0.8507 (mt0) cc_final: 0.7993 (pt0) REVERT: D 323 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8854 (tm-30) REVERT: E 55 TYR cc_start: 0.9467 (m-80) cc_final: 0.9041 (m-80) REVERT: E 61 ARG cc_start: 0.8248 (mmm160) cc_final: 0.7607 (mmm160) REVERT: E 77 GLU cc_start: 0.8895 (tt0) cc_final: 0.8552 (mt-10) REVERT: E 82 GLN cc_start: 0.7695 (pt0) cc_final: 0.7414 (pp30) REVERT: H 4 ARG cc_start: 0.9161 (mmm-85) cc_final: 0.8873 (mmm-85) REVERT: H 9 ASP cc_start: 0.8759 (m-30) cc_final: 0.8402 (m-30) REVERT: T 25 GLU cc_start: 0.8049 (tp30) cc_final: 0.7710 (tp30) REVERT: Z 30 PRO cc_start: 0.7873 (Cg_endo) cc_final: 0.7669 (Cg_exo) REVERT: Z 31 GLN cc_start: 0.5858 (OUTLIER) cc_final: 0.5606 (pp30) REVERT: 1 33 PHE cc_start: 0.8673 (t80) cc_final: 0.8378 (t80) REVERT: 1 37 THR cc_start: 0.9414 (t) cc_final: 0.9085 (p) REVERT: 1 48 ILE cc_start: 0.8671 (pt) cc_final: 0.8343 (pp) REVERT: 1 67 LYS cc_start: 0.8743 (tppp) cc_final: 0.8444 (tppp) REVERT: 1 88 MET cc_start: 0.9173 (mmm) cc_final: 0.8861 (mmm) REVERT: 1 91 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8777 (tm-30) REVERT: 1 114 LYS cc_start: 0.8725 (mttt) cc_final: 0.8295 (mttm) REVERT: 2 4 MET cc_start: 0.2134 (pp-130) cc_final: 0.0287 (tpp) REVERT: 2 15 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7533 (tm-30) REVERT: 2 22 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7577 (tmm-80) REVERT: 2 42 LYS cc_start: 0.8992 (mmtp) cc_final: 0.8565 (mmtp) REVERT: 2 45 GLN cc_start: 0.8385 (mt0) cc_final: 0.8062 (mt0) REVERT: 2 46 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: 2 74 ASN cc_start: 0.9197 (m110) cc_final: 0.8695 (m-40) REVERT: 2 86 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7530 (pmm) REVERT: 2 91 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8798 (pt0) REVERT: 2 93 ASP cc_start: 0.9355 (m-30) cc_final: 0.8883 (p0) REVERT: 2 101 ARG cc_start: 0.6987 (mtm-85) cc_final: 0.6694 (mtt180) REVERT: 2 105 SER cc_start: 0.7122 (t) cc_final: 0.6790 (p) REVERT: 2 112 LYS cc_start: 0.8959 (ttpt) cc_final: 0.8676 (tppp) REVERT: 3 26 TRP cc_start: 0.7915 (m-10) cc_final: 0.6616 (m-90) outliers start: 56 outliers final: 42 residues processed: 569 average time/residue: 0.5573 time to fit residues: 362.9366 Evaluate side-chains 584 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 535 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain 1 residue 63 GLU Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 46 GLU Chi-restraints excluded: chain 2 residue 73 ILE Chi-restraints excluded: chain 2 residue 86 MET Chi-restraints excluded: chain 3 residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 35 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 HIS ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN L 6 ASN Z 31 GLN 1 56 ASN 1 106 ASN 3 22 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088918 restraints weight = 36187.886| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.74 r_work: 0.2920 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 22714 Z= 0.210 Angle : 0.877 59.181 31311 Z= 0.453 Chirality : 0.045 0.433 3049 Planarity : 0.005 0.135 3945 Dihedral : 14.425 119.448 3873 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 3.20 % Allowed : 30.40 % Favored : 66.40 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.18), residues: 2314 helix: 1.58 (0.14), residues: 1313 sheet: 1.00 (0.74), residues: 60 loop : -0.68 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG 1 130 TYR 0.071 0.002 TYR A 246 PHE 0.043 0.002 PHE 1 121 TRP 0.031 0.001 TRP Z 33 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00477 (22702) covalent geometry : angle 0.87740 (31311) hydrogen bonds : bond 0.04923 ( 1010) hydrogen bonds : angle 4.14129 ( 2904) Misc. bond : bond 0.05453 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9186.51 seconds wall clock time: 156 minutes 18.12 seconds (9378.12 seconds total)