Starting phenix.real_space_refine on Sat Jul 4 21:20:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nhp_12336/07_2026/7nhp_12336.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nhp_12336/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nhp_12336/07_2026/7nhp_12336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nhp_12336/07_2026/7nhp_12336.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nhp_12336/07_2026/7nhp_12336.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nhp_12336/07_2026/7nhp_12336.cif" model { file = "/net/cci-nas-00/data/ceres_data/7nhp_12336/07_2026/7nhp_12336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nhp_12336/07_2026/7nhp_12336.cif" } 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-6108/lib/python3.11/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: 4.61, 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: 2.31 Conformation dependent library (CDL) restraints added in 907.5 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: 0.52 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: 3.50 Time building geometry restraints manager: 2.91 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: 30031 4.74 - 9.48: 957 9.48 - 14.22: 261 14.22 - 18.96: 53 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: 10986 24.66 - 49.31: 668 49.31 - 73.97: 162 73.97 - 98.63: 65 98.63 - 123.29: 11 Dihedral angle restraints: 11892 sinusoidal: 5234 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 11889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.620: 2984 0.620 - 1.240: 18 1.240 - 1.860: 21 1.860 - 2.480: 12 2.480 - 3.099: 14 Chirality restraints: 3049 Sorted by residual: 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 3.10 2.00e-01 2.50e+01 2.40e+02 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 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: 3951 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" C10 BCR K 101 " 0.117 2.00e-02 2.50e+03 1.12e-01 1.56e+02 pdb=" C11 BCR K 101 " -0.115 2.00e-02 2.50e+03 pdb=" C34 BCR K 101 " -0.022 2.00e-02 2.50e+03 pdb=" C8 BCR K 101 " -0.122 2.00e-02 2.50e+03 pdb=" C9 BCR K 101 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA B 601 " -0.067 2.00e-02 2.50e+03 8.77e-02 1.15e+02 pdb=" C2A CLA B 601 " 0.130 2.00e-02 2.50e+03 pdb=" C4A CLA B 601 " -0.041 2.00e-02 2.50e+03 pdb=" CHA CLA B 601 " -0.010 2.00e-02 2.50e+03 pdb=" NA CLA B 601 " -0.113 2.00e-02 2.50e+03 pdb="MG CLA B 601 " 0.101 2.00e-02 2.50e+03 ... (remaining 3948 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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= 1.413 Angle : 2.192 23.701 31311 Z= 0.940 Chirality : 0.295 3.099 3049 Planarity : 0.015 0.113 3951 Dihedral : 18.458 123.286 7638 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/Z covalent geometry : bond 0.01229 / 0.60 (22702) covalent geometry : angle 2.19240 / 0.94 (31311) hydrogen bonds : bond 0.16862 / 10.91 ( 1010) hydrogen bonds : angle 6.38342 / 4.60 ( 2904) Misc. bond : bond 0.56796 / 37.90 ( 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 : 0.769 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: 0.5542 time to fit residues: 540.6396 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 : 0.735 ------------------------------------------------------------------------------- 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... 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 F 41 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN L 8 GLN 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 = 0.133478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097142 restraints weight = 35987.692| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.72 r_work: 0.3033 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 0.135 22714 Z= 0.210 Angle : 0.827 12.915 31311 Z= 0.385 Chirality : 0.049 0.324 3049 Planarity : 0.006 0.058 3951 Dihedral : 17.115 108.050 3619 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 5.19 % Allowed : 19.92 % Favored : 74.90 % 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: -0.55 (0.17), residues: 2314 helix: 0.45 (0.14), residues: 1310 sheet: 0.74 (0.65), residues: 63 loop : -1.60 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 358 TYR 0.021 0.002 TYR B 279 PHE 0.025 0.002 PHE B 246 TRP 0.026 0.002 TRP Z 33 HIS 0.014 0.002 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (22702) covalent geometry : angle 0.82741 / 0.39 (31311) hydrogen bonds : bond 0.06127 / 4.05 ( 1010) hydrogen bonds : angle 4.63525 / 3.34 ( 2904) Misc. bond : bond 0.03939 / 2.81 ( 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 709 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 610 time to evaluate : 0.822 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 19 ASN cc_start: 0.8762 (p0) cc_final: 0.8424 (p0) REVERT: A 104 GLU cc_start: 0.8689 (pt0) cc_final: 0.8358 (pt0) REVERT: A 126 TYR cc_start: 0.9253 (t80) cc_final: 0.9033 (t80) REVERT: A 140 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7629 (mmm-85) REVERT: A 229 GLU cc_start: 0.8195 (tp30) cc_final: 0.6970 (pm20) REVERT: A 241 GLN cc_start: 0.7961 (tm130) cc_final: 0.7534 (tm-30) REVERT: B 130 GLU cc_start: 0.8887 (pt0) cc_final: 0.8672 (pm20) REVERT: B 230 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7177 (mtt180) REVERT: B 326 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8893 (mtt180) REVERT: B 341 LYS cc_start: 0.9053 (mmtp) cc_final: 0.8689 (mmmm) REVERT: B 352 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8507 (mm-30) REVERT: C 55 MET cc_start: 0.8916 (tpt) cc_final: 0.8548 (mmt) REVERT: C 129 GLU cc_start: 0.6597 (mp0) cc_final: 0.6101 (mp0) REVERT: C 138 ASP cc_start: 0.8839 (p0) cc_final: 0.8549 (p0) REVERT: C 193 ASP cc_start: 0.8965 (t0) cc_final: 0.8537 (t0) REVERT: C 195 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8131 (mtp180) REVERT: C 227 TRP cc_start: 0.8362 (m100) cc_final: 0.8062 (m100) REVERT: C 277 PHE cc_start: 0.9486 (OUTLIER) cc_final: 0.8833 (t80) REVERT: C 336 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7105 (mm-30) REVERT: C 350 ARG cc_start: 0.5702 (pmt170) cc_final: 0.2682 (mpt90) REVERT: C 355 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8281 (mm-30) REVERT: C 371 ASP cc_start: 0.8250 (m-30) cc_final: 0.7612 (m-30) REVERT: D 27 PHE cc_start: 0.8266 (t80) cc_final: 0.8017 (t80) REVERT: D 100 ASP cc_start: 0.8547 (t0) cc_final: 0.7993 (t70) REVERT: D 101 PHE cc_start: 0.8984 (t80) cc_final: 0.8548 (t80) REVERT: D 224 GLN cc_start: 0.8239 (mt0) cc_final: 0.7274 (pt0) REVERT: D 323 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8756 (tm-30) REVERT: E 42 LEU cc_start: 0.9194 (tp) cc_final: 0.8837 (tp) REVERT: E 61 ARG cc_start: 0.8341 (mmm160) cc_final: 0.8039 (mmm160) REVERT: E 75 GLN cc_start: 0.8458 (tt0) cc_final: 0.8167 (mt0) REVERT: E 77 GLU cc_start: 0.9070 (tt0) cc_final: 0.8643 (mt-10) REVERT: E 82 GLN cc_start: 0.7384 (pt0) cc_final: 0.7142 (pp30) REVERT: H 17 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8396 (mm-30) REVERT: H 20 LYS cc_start: 0.8515 (ttpp) cc_final: 0.7965 (mmtt) REVERT: H 39 LEU cc_start: 0.9460 (tp) cc_final: 0.9234 (tm) REVERT: H 50 ASN cc_start: 0.9164 (t0) cc_final: 0.8860 (t160) REVERT: I 18 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8414 (pp) REVERT: M 5 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7492 (tp40) REVERT: M 28 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8352 (tm-30) REVERT: Z 57 LEU cc_start: 0.8612 (mt) cc_final: 0.8333 (mt) REVERT: Z 60 PHE cc_start: 0.8665 (m-80) cc_final: 0.8177 (m-80) REVERT: 1 67 LYS cc_start: 0.8697 (tppp) cc_final: 0.8305 (tppp) REVERT: 1 88 MET cc_start: 0.9320 (mmm) cc_final: 0.8947 (mmm) REVERT: 1 91 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8646 (tm-30) REVERT: 1 109 LEU cc_start: 0.8871 (pt) cc_final: 0.8337 (pp) REVERT: 1 114 LYS cc_start: 0.8497 (mttt) cc_final: 0.8024 (mttm) REVERT: 1 116 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7470 (tpt-90) REVERT: 1 123 GLN cc_start: 0.9507 (mt0) cc_final: 0.9138 (tp-100) REVERT: 2 4 MET cc_start: 0.4076 (tpp) cc_final: 0.3780 (tmm) REVERT: 2 22 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7249 (tmm-80) REVERT: 2 52 THR cc_start: 0.8674 (m) cc_final: 0.8397 (t) REVERT: 2 62 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7228 (tp30) REVERT: 2 91 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8464 (pt0) REVERT: 2 96 ILE cc_start: 0.8255 (mt) cc_final: 0.7912 (mp) REVERT: 2 108 LEU cc_start: 0.7149 (mt) cc_final: 0.6543 (tt) REVERT: 2 112 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7848 (tppp) REVERT: 3 26 TRP cc_start: 0.7926 (m-10) cc_final: 0.6486 (m-90) outliers start: 99 outliers final: 31 residues processed: 646 average time/residue: 0.5703 time to fit residues: 427.1403 Evaluate side-chains 571 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 534 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 113 LEU 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 311 LYS 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 X residue 34 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 27 MET 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: 0.8980 chunk 198 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 187 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN B 282 GLN C 27 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN D 186 GLN F 41 GLN L 6 ASN M 4 ASN y 45 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 = 0.3688 r_free = 0.3688 target = 0.130763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094467 restraints weight = 36047.149| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.70 r_work: 0.2995 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 22714 Z= 0.163 Angle : 0.704 10.785 31311 Z= 0.336 Chirality : 0.044 0.216 3049 Planarity : 0.005 0.057 3951 Dihedral : 15.483 106.673 3590 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 5.29 % Allowed : 22.85 % 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: 0.22 (0.17), residues: 2314 helix: 1.06 (0.14), residues: 1309 sheet: 1.16 (0.66), residues: 63 loop : -1.25 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 1 130 TYR 0.018 0.001 TYR B 279 PHE 0.036 0.001 PHE 1 33 TRP 0.019 0.001 TRP C 51 HIS 0.010 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (22702) covalent geometry : angle 0.70426 / 0.34 (31311) hydrogen bonds : bond 0.05271 / 3.50 ( 1010) hydrogen bonds : angle 4.31274 / 3.12 ( 2904) Misc. bond : bond 0.03850 / 2.75 ( 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 671 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 570 time to evaluate : 0.768 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 19 ASN cc_start: 0.8802 (p0) cc_final: 0.8453 (p0) REVERT: A 104 GLU cc_start: 0.8586 (pt0) cc_final: 0.8203 (pt0) REVERT: A 140 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7648 (mmm-85) REVERT: A 229 GLU cc_start: 0.8187 (tp30) cc_final: 0.7091 (pm20) REVERT: A 238 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8125 (mmpt) REVERT: A 241 GLN cc_start: 0.7920 (tm130) cc_final: 0.7303 (tm-30) REVERT: B 230 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7227 (mtt180) REVERT: B 326 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8861 (mtt180) REVERT: B 352 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8444 (mm-30) REVERT: C 69 MET cc_start: 0.8974 (mtp) cc_final: 0.8757 (mtp) REVERT: C 138 ASP cc_start: 0.8887 (p0) cc_final: 0.8549 (p0) REVERT: C 141 ASP cc_start: 0.8564 (t0) cc_final: 0.8008 (t0) REVERT: C 189 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7722 (m-40) REVERT: C 193 ASP cc_start: 0.8782 (t0) cc_final: 0.8521 (t0) REVERT: C 195 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8149 (mtp180) REVERT: C 209 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: C 227 TRP cc_start: 0.8375 (m100) cc_final: 0.8128 (m100) REVERT: C 277 PHE cc_start: 0.9476 (OUTLIER) cc_final: 0.9045 (t80) REVERT: C 336 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7123 (mp0) REVERT: C 350 ARG cc_start: 0.5673 (pmt170) cc_final: 0.2537 (mmt180) REVERT: C 371 ASP cc_start: 0.8199 (m-30) cc_final: 0.7423 (m-30) REVERT: D 27 PHE cc_start: 0.8377 (t80) cc_final: 0.8094 (t80) REVERT: D 98 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8835 (mp10) REVERT: D 100 ASP cc_start: 0.8531 (t0) cc_final: 0.7991 (t70) REVERT: D 224 GLN cc_start: 0.8335 (mt0) cc_final: 0.7486 (pt0) REVERT: D 265 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8084 (ttp80) REVERT: D 323 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8803 (tm-30) REVERT: E 42 LEU cc_start: 0.9143 (tp) cc_final: 0.8862 (tp) REVERT: E 77 GLU cc_start: 0.8930 (tt0) cc_final: 0.8696 (mt-10) REVERT: E 82 GLN cc_start: 0.7646 (pt0) cc_final: 0.7374 (pp30) REVERT: H 17 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8283 (mm-30) REVERT: H 20 LYS cc_start: 0.8441 (ttpp) cc_final: 0.7984 (mmtt) REVERT: H 43 LEU cc_start: 0.9492 (mm) cc_final: 0.9278 (mt) REVERT: M 5 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7531 (tp40) REVERT: T 19 PHE cc_start: 0.8677 (m-80) cc_final: 0.8440 (m-80) REVERT: T 25 GLU cc_start: 0.7975 (tp30) cc_final: 0.7675 (tp30) REVERT: Z 39 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8073 (pp) REVERT: Z 60 PHE cc_start: 0.8677 (m-80) cc_final: 0.8397 (m-80) REVERT: 1 67 LYS cc_start: 0.8626 (tppp) cc_final: 0.8388 (tppp) REVERT: 1 88 MET cc_start: 0.9242 (mmm) cc_final: 0.8919 (mmm) REVERT: 1 91 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8635 (tm-30) REVERT: 1 109 LEU cc_start: 0.8974 (pt) cc_final: 0.8371 (pp) REVERT: 1 114 LYS cc_start: 0.8530 (mttt) cc_final: 0.7988 (mttm) REVERT: 1 116 ARG cc_start: 0.8032 (tpp80) cc_final: 0.7479 (tpt-90) REVERT: 1 123 GLN cc_start: 0.9530 (mt0) cc_final: 0.9116 (tp-100) REVERT: 1 128 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8990 (tt) REVERT: 1 130 ARG cc_start: 0.8586 (ttp-110) cc_final: 0.8353 (ptp-110) REVERT: 2 6 GLU cc_start: 0.5926 (pp20) cc_final: 0.5679 (pp20) REVERT: 2 22 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7598 (tmm-80) REVERT: 2 45 GLN cc_start: 0.7990 (mt0) cc_final: 0.7658 (mt0) REVERT: 2 46 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6572 (pm20) REVERT: 2 60 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7036 (tm-30) REVERT: 2 74 ASN cc_start: 0.8941 (m-40) cc_final: 0.8531 (m110) REVERT: 2 86 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7217 (pmt) REVERT: 2 91 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8595 (pt0) REVERT: 2 93 ASP cc_start: 0.9409 (m-30) cc_final: 0.9046 (p0) REVERT: 2 112 LYS cc_start: 0.8362 (ttpt) cc_final: 0.7927 (tppp) REVERT: 3 22 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8261 (tp-100) REVERT: 3 26 TRP cc_start: 0.7974 (m-10) cc_final: 0.6583 (m-90) outliers start: 101 outliers final: 47 residues processed: 614 average time/residue: 0.5621 time to fit residues: 400.0880 Evaluate side-chains 596 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 536 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 329 GLU 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 230 ARG 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 446 SER Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 237 ILE 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 316 VAL Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 14 LEU 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 17 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain M residue 5 GLN 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 56 ASN Chi-restraints excluded: chain 1 residue 101 TYR Chi-restraints excluded: chain 1 residue 128 LEU Chi-restraints excluded: chain 2 residue 31 SER 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: 10.0000 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 199 GLN A 303 ASN B 374 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN L 6 ASN M 4 ASN Z 31 GLN Z 38 GLN Z 58 ASN 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093461 restraints weight = 35962.971| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.73 r_work: 0.2984 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 22714 Z= 0.147 Angle : 0.657 9.076 31311 Z= 0.316 Chirality : 0.043 0.219 3049 Planarity : 0.005 0.047 3951 Dihedral : 14.808 104.941 3587 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.45 % Allowed : 24.74 % Favored : 69.81 % 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: 0.51 (0.17), residues: 2314 helix: 1.32 (0.14), residues: 1316 sheet: 0.88 (0.64), residues: 65 loop : -1.13 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 308 TYR 0.018 0.001 TYR B 279 PHE 0.034 0.001 PHE 1 33 TRP 0.014 0.001 TRP C 51 HIS 0.008 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (22702) covalent geometry : angle 0.65671 / 0.32 (31311) hydrogen bonds : bond 0.04899 / 3.26 ( 1010) hydrogen bonds : angle 4.15097 / 2.98 ( 2904) Misc. bond : bond 0.03920 / 2.80 ( 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 668 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 564 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8714 (tt0) cc_final: 0.8425 (mm-30) REVERT: A 104 GLU cc_start: 0.8588 (pt0) cc_final: 0.8187 (pt0) REVERT: A 126 TYR cc_start: 0.9200 (t80) cc_final: 0.8994 (t80) REVERT: A 140 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7723 (mmm-85) REVERT: A 238 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7967 (mmpt) REVERT: A 241 GLN cc_start: 0.8033 (tm130) cc_final: 0.7323 (tm-30) REVERT: A 242 GLU cc_start: 0.7638 (mp0) cc_final: 0.7409 (mp0) REVERT: A 333 GLU cc_start: 0.8294 (tp30) cc_final: 0.7635 (tp30) REVERT: B 125 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6742 (p0) REVERT: B 130 GLU cc_start: 0.8929 (pt0) cc_final: 0.8550 (pm20) REVERT: B 210 ILE cc_start: 0.9134 (mm) cc_final: 0.8777 (mm) REVERT: B 214 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8891 (mm) REVERT: B 230 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7247 (mtt180) REVERT: B 326 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8996 (mtt180) REVERT: B 352 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8443 (mm-30) REVERT: C 69 MET cc_start: 0.8978 (mtp) cc_final: 0.8744 (mtp) REVERT: C 130 GLU cc_start: 0.8827 (pp20) cc_final: 0.8575 (tm-30) REVERT: C 138 ASP cc_start: 0.8834 (p0) cc_final: 0.8590 (p0) REVERT: C 141 ASP cc_start: 0.8362 (t0) cc_final: 0.7782 (t0) REVERT: C 185 ARG cc_start: 0.8576 (ttt-90) cc_final: 0.8345 (ttt-90) REVERT: C 193 ASP cc_start: 0.8737 (t0) cc_final: 0.8502 (t0) REVERT: C 195 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8155 (mtp180) REVERT: C 227 TRP cc_start: 0.8389 (m100) cc_final: 0.8127 (m100) REVERT: C 277 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.8853 (t80) REVERT: C 336 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7190 (mp0) REVERT: C 350 ARG cc_start: 0.5712 (pmt170) cc_final: 0.2521 (mmt180) REVERT: C 355 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8718 (mm-30) REVERT: C 371 ASP cc_start: 0.8202 (m-30) cc_final: 0.7434 (m-30) REVERT: C 435 ARG cc_start: 0.7694 (mmm-85) cc_final: 0.7371 (mmm160) REVERT: D 27 PHE cc_start: 0.8388 (t80) cc_final: 0.8025 (t80) REVERT: D 100 ASP cc_start: 0.8545 (t0) cc_final: 0.7991 (t70) REVERT: D 224 GLN cc_start: 0.8339 (mt0) cc_final: 0.7498 (pt0) REVERT: D 265 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7959 (ttp80) REVERT: D 323 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8826 (tm-30) REVERT: E 42 LEU cc_start: 0.9070 (tp) cc_final: 0.8726 (tp) REVERT: E 55 TYR cc_start: 0.9334 (m-80) cc_final: 0.8938 (m-80) REVERT: E 61 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7724 (mmm160) REVERT: E 77 GLU cc_start: 0.9057 (tt0) cc_final: 0.8658 (mt-10) REVERT: E 82 GLN cc_start: 0.7647 (pt0) cc_final: 0.7376 (pp30) REVERT: F 8 GLN cc_start: 0.2004 (OUTLIER) cc_final: 0.1639 (pm20) REVERT: H 17 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8221 (mm-30) REVERT: H 20 LYS cc_start: 0.8515 (ttpp) cc_final: 0.7985 (mmtt) REVERT: M 1 MET cc_start: 0.2929 (mpt) cc_final: 0.1604 (mpt) REVERT: M 5 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7489 (tp40) REVERT: T 19 PHE cc_start: 0.8680 (m-80) cc_final: 0.8461 (m-80) REVERT: T 25 GLU cc_start: 0.7975 (tp30) cc_final: 0.7639 (tp30) REVERT: Z 31 GLN cc_start: 0.6025 (OUTLIER) cc_final: 0.5755 (pp30) REVERT: Z 39 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8058 (pp) REVERT: Z 60 PHE cc_start: 0.8724 (m-80) cc_final: 0.8423 (m-80) REVERT: 1 67 LYS cc_start: 0.8707 (tppp) cc_final: 0.8475 (tppp) REVERT: 1 88 MET cc_start: 0.9229 (mmm) cc_final: 0.8922 (mmm) REVERT: 1 91 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8663 (tm-30) REVERT: 1 114 LYS cc_start: 0.8624 (mttt) cc_final: 0.8181 (mttm) REVERT: 1 116 ARG cc_start: 0.7994 (tpp80) cc_final: 0.7488 (tpt-90) REVERT: 1 123 GLN cc_start: 0.9501 (mt0) cc_final: 0.9160 (tp40) REVERT: 2 4 MET cc_start: 0.3375 (tmm) cc_final: 0.1348 (tpp) REVERT: 2 15 GLU cc_start: 0.8531 (tp30) cc_final: 0.8059 (tm-30) REVERT: 2 22 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7412 (tmm-80) REVERT: 2 45 GLN cc_start: 0.8077 (mt0) cc_final: 0.7705 (mt0) REVERT: 2 46 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: 2 59 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6612 (pm20) REVERT: 2 71 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8370 (ttmm) REVERT: 2 74 ASN cc_start: 0.8978 (m110) cc_final: 0.8530 (m-40) REVERT: 2 86 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7463 (pmt) REVERT: 2 91 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8623 (pt0) REVERT: 2 93 ASP cc_start: 0.9370 (m-30) cc_final: 0.9039 (p0) REVERT: 2 101 ARG cc_start: 0.7359 (mtt180) cc_final: 0.7004 (mtt180) REVERT: 2 112 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8001 (tppp) REVERT: 3 22 GLN cc_start: 0.8526 (tp40) cc_final: 0.8223 (tp-100) REVERT: 3 26 TRP cc_start: 0.7902 (m-10) cc_final: 0.6593 (m-90) outliers start: 104 outliers final: 44 residues processed: 612 average time/residue: 0.5500 time to fit residues: 388.5587 Evaluate side-chains 589 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 532 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 225 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 491 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 273 ILE 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 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 291 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 10 ILE 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 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 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 Z residue 39 LEU Chi-restraints excluded: chain 1 residue 101 TYR Chi-restraints excluded: chain 2 residue 46 GLU Chi-restraints excluded: chain 2 residue 59 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: 0.7980 chunk 19 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN A 296 ASN A 303 ASN B 374 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 239 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.092146 restraints weight = 36000.158| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.73 r_work: 0.2961 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 22714 Z= 0.156 Angle : 0.663 14.157 31311 Z= 0.319 Chirality : 0.043 0.214 3049 Planarity : 0.005 0.049 3951 Dihedral : 14.505 100.563 3584 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.85 % Rotamer: Outliers : 5.24 % Allowed : 24.95 % Favored : 69.81 % 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: 0.65 (0.17), residues: 2314 helix: 1.41 (0.14), residues: 1323 sheet: 1.08 (0.62), residues: 65 loop : -1.07 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 25 TYR 0.018 0.001 TYR B 279 PHE 0.035 0.001 PHE 1 33 TRP 0.012 0.001 TRP C 51 HIS 0.007 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (22702) covalent geometry : angle 0.66326 / 0.32 (31311) hydrogen bonds : bond 0.04889 / 3.25 ( 1010) hydrogen bonds : angle 4.15192 / 2.98 ( 2904) Misc. bond : bond 0.04447 / 3.18 ( 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 639 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 539 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8717 (tt0) cc_final: 0.8468 (mm-30) REVERT: A 104 GLU cc_start: 0.8636 (pt0) cc_final: 0.8391 (pt0) REVERT: A 126 TYR cc_start: 0.9203 (t80) cc_final: 0.8931 (t80) REVERT: A 140 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7682 (mmm-85) REVERT: A 238 LYS cc_start: 0.8350 (mtpp) cc_final: 0.7969 (mmpt) REVERT: A 241 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: A 333 GLU cc_start: 0.8341 (tp30) cc_final: 0.7710 (tp30) REVERT: B 125 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6809 (p0) REVERT: B 130 GLU cc_start: 0.8949 (pt0) cc_final: 0.8498 (pm20) REVERT: B 210 ILE cc_start: 0.9089 (mm) cc_final: 0.8740 (mm) REVERT: B 214 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8873 (mm) REVERT: B 230 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7250 (mtt180) REVERT: B 352 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8440 (mm-30) REVERT: C 69 MET cc_start: 0.9100 (mtp) cc_final: 0.8832 (mtp) REVERT: C 138 ASP cc_start: 0.8858 (p0) cc_final: 0.8607 (p0) REVERT: C 141 ASP cc_start: 0.8421 (t0) cc_final: 0.7771 (t0) REVERT: C 175 ASP cc_start: 0.8883 (t0) cc_final: 0.8569 (t0) REVERT: C 193 ASP cc_start: 0.8687 (t0) cc_final: 0.8379 (t0) REVERT: C 195 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8232 (mtp180) REVERT: C 209 GLU cc_start: 0.8370 (pm20) cc_final: 0.7973 (pm20) REVERT: C 227 TRP cc_start: 0.8376 (m100) cc_final: 0.8136 (m100) REVERT: C 277 PHE cc_start: 0.9463 (OUTLIER) cc_final: 0.8871 (t80) REVERT: C 336 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7104 (mp0) REVERT: C 350 ARG cc_start: 0.5614 (pmt170) cc_final: 0.2425 (mmt180) REVERT: C 355 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8755 (mm-30) REVERT: C 371 ASP cc_start: 0.8215 (m-30) cc_final: 0.7589 (m-30) REVERT: C 430 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8229 (mm) REVERT: D 27 PHE cc_start: 0.8417 (t80) cc_final: 0.8056 (t80) REVERT: D 100 ASP cc_start: 0.8555 (t0) cc_final: 0.7991 (t70) REVERT: D 224 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: D 265 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7978 (ttp80) REVERT: D 323 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8835 (tm-30) REVERT: E 42 LEU cc_start: 0.8986 (tp) cc_final: 0.8641 (tp) REVERT: E 55 TYR cc_start: 0.9388 (m-80) cc_final: 0.8953 (m-80) REVERT: E 61 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7588 (mmp-170) REVERT: E 77 GLU cc_start: 0.8943 (tt0) cc_final: 0.8712 (mt-10) REVERT: E 82 GLN cc_start: 0.7664 (pt0) cc_final: 0.7414 (pp30) REVERT: F 8 GLN cc_start: 0.1936 (OUTLIER) cc_final: 0.1549 (pm20) REVERT: H 4 ARG cc_start: 0.8916 (mmm160) cc_final: 0.8592 (tpp80) REVERT: H 9 ASP cc_start: 0.8638 (m-30) cc_final: 0.8196 (m-30) REVERT: H 17 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8265 (mm-30) REVERT: H 20 LYS cc_start: 0.8496 (ttpp) cc_final: 0.7984 (mmtt) REVERT: K 13 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: M 5 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7492 (tp40) REVERT: T 25 GLU cc_start: 0.7985 (tp30) cc_final: 0.7651 (tp30) REVERT: y 27 MET cc_start: 0.8632 (tmm) cc_final: 0.8338 (tmm) REVERT: Z 17 PHE cc_start: 0.8815 (t80) cc_final: 0.8600 (t80) REVERT: Z 60 PHE cc_start: 0.8801 (m-80) cc_final: 0.8451 (m-80) REVERT: 1 88 MET cc_start: 0.9189 (mmm) cc_final: 0.8911 (mmm) REVERT: 1 114 LYS cc_start: 0.8668 (mttt) cc_final: 0.8186 (mttm) REVERT: 1 119 GLN cc_start: 0.9225 (mt0) cc_final: 0.8974 (mm110) REVERT: 1 122 LYS cc_start: 0.9001 (ptpt) cc_final: 0.8781 (ptpt) REVERT: 1 123 GLN cc_start: 0.9574 (mt0) cc_final: 0.9233 (tp40) REVERT: 2 6 GLU cc_start: 0.6264 (pp20) cc_final: 0.5899 (tm-30) REVERT: 2 22 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7439 (tmm-80) REVERT: 2 46 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6679 (pm20) REVERT: 2 60 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7639 (tm-30) REVERT: 2 74 ASN cc_start: 0.9047 (m110) cc_final: 0.8598 (m-40) REVERT: 2 86 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7558 (pmt) REVERT: 2 91 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8664 (pt0) REVERT: 2 93 ASP cc_start: 0.9425 (m-30) cc_final: 0.9081 (p0) REVERT: 2 112 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8054 (tppp) REVERT: 3 22 GLN cc_start: 0.8427 (tp40) cc_final: 0.8057 (tp-100) REVERT: 3 26 TRP cc_start: 0.7893 (m-10) cc_final: 0.6587 (m-90) outliers start: 100 outliers final: 50 residues processed: 585 average time/residue: 0.5451 time to fit residues: 368.5402 Evaluate side-chains 597 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 534 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 42 LEU 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 223 LEU 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 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 214 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 ILE 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 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 296 GLU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 224 GLN 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 28 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 59 ASN 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 5 GLN Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain T residue 3 THR 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 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: 5.9990 chunk 161 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 0.0770 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN A 303 ASN B 282 GLN B 374 ASN C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091789 restraints weight = 36075.045| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.74 r_work: 0.2952 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 22714 Z= 0.147 Angle : 0.652 10.101 31311 Z= 0.314 Chirality : 0.042 0.216 3049 Planarity : 0.005 0.050 3951 Dihedral : 14.201 88.649 3584 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.24 % Allowed : 25.58 % Favored : 69.18 % 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: 1.52 (0.14), residues: 1325 sheet: 1.19 (0.60), residues: 72 loop : -1.00 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 25 TYR 0.017 0.001 TYR B 279 PHE 0.037 0.001 PHE 1 33 TRP 0.012 0.001 TRP C 51 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (22702) covalent geometry : angle 0.65181 / 0.31 (31311) hydrogen bonds : bond 0.04705 / 3.13 ( 1010) hydrogen bonds : angle 4.07653 / 2.92 ( 2904) Misc. bond : bond 0.04412 / 3.15 ( 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 652 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 552 time to evaluate : 0.847 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 65 GLU cc_start: 0.8825 (tt0) cc_final: 0.8592 (mm-30) REVERT: A 104 GLU cc_start: 0.8625 (pt0) cc_final: 0.8389 (pt0) REVERT: A 126 TYR cc_start: 0.9235 (t80) cc_final: 0.8996 (t80) REVERT: A 140 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7738 (mmm-85) REVERT: A 229 GLU cc_start: 0.8023 (tp30) cc_final: 0.7013 (pm20) REVERT: A 238 LYS cc_start: 0.8308 (mtpp) cc_final: 0.8052 (mmpt) REVERT: A 241 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: A 333 GLU cc_start: 0.8450 (tp30) cc_final: 0.7811 (tp30) REVERT: B 125 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6774 (p0) REVERT: B 130 GLU cc_start: 0.8927 (pt0) cc_final: 0.8430 (pm20) REVERT: B 210 ILE cc_start: 0.9080 (mm) cc_final: 0.8838 (mp) REVERT: B 214 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8882 (mm) REVERT: B 230 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7242 (mtt180) REVERT: B 352 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8439 (mm-30) REVERT: C 130 GLU cc_start: 0.8877 (pp20) cc_final: 0.8527 (tm-30) REVERT: C 138 ASP cc_start: 0.8828 (p0) cc_final: 0.8578 (p0) REVERT: C 141 ASP cc_start: 0.8491 (t0) cc_final: 0.7797 (t0) REVERT: C 175 ASP cc_start: 0.8884 (t0) cc_final: 0.8663 (t0) REVERT: C 193 ASP cc_start: 0.8698 (t0) cc_final: 0.8370 (t0) REVERT: C 195 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8273 (mtp180) REVERT: C 209 GLU cc_start: 0.8433 (pm20) cc_final: 0.7999 (pm20) REVERT: C 227 TRP cc_start: 0.8402 (m100) cc_final: 0.8136 (m100) REVERT: C 277 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.8844 (t80) REVERT: C 336 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7214 (mm-30) REVERT: C 350 ARG cc_start: 0.5724 (pmt170) cc_final: 0.2431 (mmt180) REVERT: C 371 ASP cc_start: 0.8204 (m-30) cc_final: 0.7579 (m-30) REVERT: C 435 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7498 (mmm160) REVERT: D 27 PHE cc_start: 0.8436 (t80) cc_final: 0.8073 (t80) REVERT: D 100 ASP cc_start: 0.8612 (t0) cc_final: 0.8078 (t70) REVERT: D 224 GLN cc_start: 0.8329 (mt0) cc_final: 0.7583 (pt0) REVERT: D 265 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7996 (ttp80) REVERT: D 323 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8842 (tm-30) REVERT: E 42 LEU cc_start: 0.8992 (tp) cc_final: 0.8634 (tp) REVERT: E 55 TYR cc_start: 0.9411 (m-80) cc_final: 0.8918 (m-80) REVERT: E 61 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7588 (mmp-170) REVERT: E 77 GLU cc_start: 0.9058 (tt0) cc_final: 0.8663 (mt-10) REVERT: E 82 GLN cc_start: 0.7702 (pt0) cc_final: 0.7485 (pp30) REVERT: F 8 GLN cc_start: 0.1883 (OUTLIER) cc_final: 0.1497 (pm20) REVERT: H 17 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8279 (mm-30) REVERT: K 13 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: T 25 GLU cc_start: 0.8008 (tp30) cc_final: 0.7655 (tp30) REVERT: y 27 MET cc_start: 0.8674 (tmm) cc_final: 0.8211 (tmm) REVERT: Z 31 GLN cc_start: 0.5873 (OUTLIER) cc_final: 0.5509 (pp30) REVERT: Z 60 PHE cc_start: 0.8808 (m-80) cc_final: 0.8415 (m-80) REVERT: 1 88 MET cc_start: 0.9219 (mmm) cc_final: 0.8838 (mmm) REVERT: 1 91 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8593 (tm-30) REVERT: 1 114 LYS cc_start: 0.8699 (mttt) cc_final: 0.8004 (mptp) REVERT: 1 123 GLN cc_start: 0.9528 (mt0) cc_final: 0.9184 (tp40) REVERT: 2 4 MET cc_start: 0.2500 (pp-130) cc_final: 0.0330 (tpp) REVERT: 2 6 GLU cc_start: 0.6458 (pp20) cc_final: 0.6107 (tm-30) REVERT: 2 22 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7584 (tmm-80) REVERT: 2 25 ARG cc_start: 0.8391 (tpt-90) cc_final: 0.8093 (tpt-90) REVERT: 2 46 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: 2 74 ASN cc_start: 0.9120 (m110) cc_final: 0.8645 (m-40) REVERT: 2 86 MET cc_start: 0.7943 (ptp) cc_final: 0.7565 (pmt) REVERT: 2 91 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8657 (pt0) REVERT: 2 93 ASP cc_start: 0.9398 (m-30) cc_final: 0.9007 (p0) REVERT: 2 105 SER cc_start: 0.7363 (t) cc_final: 0.7010 (p) REVERT: 2 111 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7180 (tm-30) REVERT: 2 112 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8283 (tppp) REVERT: 3 22 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8159 (tp-100) REVERT: 3 26 TRP cc_start: 0.7890 (m-10) cc_final: 0.6593 (m-90) outliers start: 100 outliers final: 53 residues processed: 598 average time/residue: 0.5360 time to fit residues: 371.1372 Evaluate side-chains 602 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 538 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 42 LEU 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 223 LEU Chi-restraints excluded: chain A residue 241 GLN 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 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 C residue 113 LEU 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 261 SER Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 296 GLU 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 291 LEU Chi-restraints excluded: chain D residue 332 GLN 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 28 THR Chi-restraints excluded: chain H residue 37 LEU 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 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 T residue 3 THR 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 1 residue 33 PHE Chi-restraints excluded: chain 1 residue 125 GLU 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 22 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 206 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 204 optimal weight: 0.4980 chunk 92 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 82 optimal weight: 0.0770 chunk 117 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 322 ASN E 58 GLN L 4 ASN 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 = 0.3635 r_free = 0.3635 target = 0.127096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089722 restraints weight = 36427.276| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.75 r_work: 0.2915 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 22714 Z= 0.192 Angle : 0.688 11.309 31311 Z= 0.334 Chirality : 0.044 0.219 3049 Planarity : 0.005 0.049 3951 Dihedral : 14.046 86.067 3580 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.51 % Allowed : 26.73 % Favored : 68.76 % 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: 1.50 (0.14), residues: 1318 sheet: 0.86 (0.63), residues: 75 loop : -0.91 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 25 TYR 0.018 0.001 TYR B 279 PHE 0.037 0.002 PHE 1 33 TRP 0.019 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (22702) covalent geometry : angle 0.68820 / 0.33 (31311) hydrogen bonds : bond 0.05112 / 3.42 ( 1010) hydrogen bonds : angle 4.18116 / 2.99 ( 2904) Misc. bond : bond 0.05517 / 3.94 ( 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 640 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 554 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8830 (tt0) cc_final: 0.8609 (mm-30) REVERT: A 104 GLU cc_start: 0.8630 (pt0) cc_final: 0.8371 (pt0) REVERT: A 140 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7694 (mmm-85) REVERT: A 183 MET cc_start: 0.9479 (mtm) cc_final: 0.9229 (mtp) REVERT: A 229 GLU cc_start: 0.7963 (tp30) cc_final: 0.6999 (pm20) REVERT: A 238 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8001 (mmpt) REVERT: A 333 GLU cc_start: 0.8522 (tp30) cc_final: 0.7914 (tp30) REVERT: B 210 ILE cc_start: 0.9062 (mm) cc_final: 0.8850 (mp) REVERT: B 214 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8938 (mm) REVERT: B 230 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7262 (mtt180) REVERT: B 352 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8444 (mm-30) REVERT: C 130 GLU cc_start: 0.8853 (pp20) cc_final: 0.8585 (tm-30) REVERT: C 141 ASP cc_start: 0.8564 (t0) cc_final: 0.7824 (t0) REVERT: C 175 ASP cc_start: 0.8916 (t0) cc_final: 0.8658 (t0) REVERT: C 193 ASP cc_start: 0.8676 (t0) cc_final: 0.8319 (t70) REVERT: C 195 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8331 (mtp180) REVERT: C 209 GLU cc_start: 0.8370 (pm20) cc_final: 0.8004 (pm20) REVERT: C 227 TRP cc_start: 0.8414 (m100) cc_final: 0.8147 (m100) REVERT: C 277 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.8857 (t80) REVERT: C 336 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 350 ARG cc_start: 0.5732 (pmt170) cc_final: 0.2437 (mmt180) REVERT: C 371 ASP cc_start: 0.8262 (m-30) cc_final: 0.7589 (m-30) REVERT: D 27 PHE cc_start: 0.8445 (t80) cc_final: 0.8082 (t80) REVERT: D 100 ASP cc_start: 0.8613 (t0) cc_final: 0.8051 (t70) REVERT: D 224 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: D 265 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8041 (ttp80) REVERT: D 323 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8854 (tm-30) REVERT: E 42 LEU cc_start: 0.8988 (tp) cc_final: 0.8608 (tp) REVERT: E 55 TYR cc_start: 0.9447 (m-80) cc_final: 0.8899 (m-80) REVERT: E 77 GLU cc_start: 0.8913 (tt0) cc_final: 0.8565 (mt-10) REVERT: E 82 GLN cc_start: 0.7617 (pt0) cc_final: 0.7403 (pp30) REVERT: F 8 GLN cc_start: 0.2119 (OUTLIER) cc_final: 0.1652 (pm20) REVERT: K 13 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: T 25 GLU cc_start: 0.8034 (tp30) cc_final: 0.7679 (tp30) REVERT: 1 88 MET cc_start: 0.9190 (mmm) cc_final: 0.8858 (mmm) REVERT: 1 91 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8670 (tm-30) REVERT: 1 114 LYS cc_start: 0.8821 (mttt) cc_final: 0.8397 (mttm) REVERT: 1 123 GLN cc_start: 0.9497 (mt0) cc_final: 0.9184 (tp40) REVERT: 2 4 MET cc_start: 0.2581 (pp-130) cc_final: 0.0655 (tpp) REVERT: 2 6 GLU cc_start: 0.6604 (pp20) cc_final: 0.6160 (tm-30) REVERT: 2 22 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7591 (tmm-80) REVERT: 2 25 ARG cc_start: 0.8539 (tpt-90) cc_final: 0.8011 (tpt-90) REVERT: 2 45 GLN cc_start: 0.8168 (mt0) cc_final: 0.7885 (mt0) REVERT: 2 46 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: 2 71 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8123 (ttmm) REVERT: 2 74 ASN cc_start: 0.9131 (m110) cc_final: 0.8693 (m-40) REVERT: 2 86 MET cc_start: 0.7924 (ptp) cc_final: 0.7526 (pmm) REVERT: 2 91 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8660 (pt0) REVERT: 2 93 ASP cc_start: 0.9392 (m-30) cc_final: 0.8954 (p0) REVERT: 2 105 SER cc_start: 0.7181 (t) cc_final: 0.6855 (p) REVERT: 2 112 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8295 (tppp) REVERT: 3 22 GLN cc_start: 0.8290 (tp40) cc_final: 0.8035 (tp-100) REVERT: 3 26 TRP cc_start: 0.7886 (m-10) cc_final: 0.6565 (m-90) outliers start: 86 outliers final: 52 residues processed: 594 average time/residue: 0.5447 time to fit residues: 373.3213 Evaluate side-chains 599 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 539 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 42 LEU 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 228 THR Chi-restraints excluded: chain A residue 239 PHE 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 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 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 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 311 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 224 GLN 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 28 THR Chi-restraints excluded: chain H residue 37 LEU 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 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 T residue 3 THR 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 33 PHE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 25 optimal weight: 0.0670 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 30.0000 chunk 29 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 322 ASN L 6 ASN M 33 GLN Z 31 GLN Z 58 ASN 1 56 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 = 0.3621 r_free = 0.3621 target = 0.126072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088927 restraints weight = 36163.651| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.73 r_work: 0.2902 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 22714 Z= 0.191 Angle : 0.707 9.756 31311 Z= 0.343 Chirality : 0.045 0.220 3049 Planarity : 0.005 0.050 3951 Dihedral : 13.916 85.303 3580 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 5.03 % Allowed : 27.41 % Favored : 67.56 % 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: 0.83 (0.18), residues: 2314 helix: 1.50 (0.14), residues: 1313 sheet: 1.21 (0.74), residues: 60 loop : -0.84 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 476 TYR 0.019 0.001 TYR B 279 PHE 0.039 0.002 PHE 1 33 TRP 0.013 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (22702) covalent geometry : angle 0.70669 / 0.34 (31311) hydrogen bonds : bond 0.05134 / 3.43 ( 1010) hydrogen bonds : angle 4.18695 / 3.00 ( 2904) Misc. bond : bond 0.05624 / 4.02 ( 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 646 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 550 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8845 (tt0) cc_final: 0.8628 (mm-30) REVERT: A 104 GLU cc_start: 0.8667 (pt0) cc_final: 0.8440 (pt0) REVERT: A 140 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7484 (mmm-85) REVERT: A 237 TYR cc_start: 0.4740 (OUTLIER) cc_final: 0.4331 (m-10) REVERT: A 238 LYS cc_start: 0.8349 (mtpp) cc_final: 0.7905 (mmpt) REVERT: A 241 GLN cc_start: 0.9051 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 242 GLU cc_start: 0.7825 (mp0) cc_final: 0.7567 (mp0) REVERT: A 333 GLU cc_start: 0.8562 (tp30) cc_final: 0.7961 (tp30) REVERT: B 125 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6807 (p0) REVERT: B 130 GLU cc_start: 0.8946 (pt0) cc_final: 0.8408 (pm20) REVERT: B 210 ILE cc_start: 0.9035 (mm) cc_final: 0.8816 (mp) REVERT: B 214 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8920 (mm) REVERT: B 230 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7265 (mtt180) REVERT: B 352 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8424 (mm-30) REVERT: C 130 GLU cc_start: 0.8828 (pp20) cc_final: 0.8623 (tm-30) REVERT: C 141 ASP cc_start: 0.8610 (t0) cc_final: 0.8279 (t0) REVERT: C 175 ASP cc_start: 0.8938 (t0) cc_final: 0.8662 (t0) REVERT: C 193 ASP cc_start: 0.8652 (t0) cc_final: 0.8282 (t70) REVERT: C 195 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8367 (mtp180) REVERT: C 209 GLU cc_start: 0.8323 (pm20) cc_final: 0.7929 (pm20) REVERT: C 227 TRP cc_start: 0.8436 (m100) cc_final: 0.8186 (m100) REVERT: C 277 PHE cc_start: 0.9503 (OUTLIER) cc_final: 0.8874 (t80) REVERT: C 336 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7314 (mm-30) REVERT: C 350 ARG cc_start: 0.5821 (pmt170) cc_final: 0.2448 (mmt-90) REVERT: C 371 ASP cc_start: 0.8235 (m-30) cc_final: 0.7579 (m-30) REVERT: D 27 PHE cc_start: 0.8464 (t80) cc_final: 0.8105 (t80) REVERT: D 100 ASP cc_start: 0.8605 (t0) cc_final: 0.8014 (t70) REVERT: D 224 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7756 (pt0) REVERT: D 265 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8026 (ttp80) REVERT: D 323 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8827 (tm-30) REVERT: E 42 LEU cc_start: 0.8962 (tp) cc_final: 0.8574 (tp) REVERT: E 55 TYR cc_start: 0.9471 (m-80) cc_final: 0.9013 (m-80) REVERT: E 61 ARG cc_start: 0.8281 (mmm160) cc_final: 0.7590 (mmp-170) REVERT: E 77 GLU cc_start: 0.8904 (tt0) cc_final: 0.8549 (mt-10) REVERT: E 82 GLN cc_start: 0.7621 (pt0) cc_final: 0.7393 (pp30) REVERT: F 8 GLN cc_start: 0.2038 (OUTLIER) cc_final: 0.1530 (pm20) REVERT: T 25 GLU cc_start: 0.8057 (tp30) cc_final: 0.7678 (tp30) REVERT: Z 31 GLN cc_start: 0.5729 (OUTLIER) cc_final: 0.5414 (pp30) REVERT: 1 88 MET cc_start: 0.9181 (mmm) cc_final: 0.8886 (mmm) REVERT: 1 114 LYS cc_start: 0.8799 (mttt) cc_final: 0.8529 (mmtt) REVERT: 1 123 GLN cc_start: 0.9380 (mt0) cc_final: 0.9147 (tp40) REVERT: 2 4 MET cc_start: 0.2583 (pp-130) cc_final: 0.0691 (tpp) REVERT: 2 6 GLU cc_start: 0.6572 (pp20) cc_final: 0.6080 (tm-30) REVERT: 2 22 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7621 (tmm-80) REVERT: 2 46 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: 2 71 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8508 (ttmm) REVERT: 2 74 ASN cc_start: 0.9165 (m110) cc_final: 0.8593 (m-40) REVERT: 2 86 MET cc_start: 0.7854 (ptp) cc_final: 0.7543 (pmm) REVERT: 2 91 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8687 (pt0) REVERT: 2 93 ASP cc_start: 0.9366 (m-30) cc_final: 0.8963 (p0) REVERT: 2 101 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7058 (mtt180) REVERT: 2 105 SER cc_start: 0.7053 (t) cc_final: 0.6710 (p) REVERT: 2 112 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8393 (tppp) REVERT: 3 26 TRP cc_start: 0.7921 (m-10) cc_final: 0.6618 (m-90) outliers start: 96 outliers final: 55 residues processed: 594 average time/residue: 0.5312 time to fit residues: 365.7048 Evaluate side-chains 601 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 536 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 42 LEU 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 237 TYR Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 303 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 234 ILE Chi-restraints excluded: chain B residue 245 VAL 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 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 409 SER Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 224 GLN 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 37 LEU 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 I residue 18 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain T residue 3 THR 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 2 residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 50 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 109 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 303 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN M 32 GLN 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 = 0.3639 r_free = 0.3639 target = 0.127115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.090765 restraints weight = 36039.443| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.68 r_work: 0.2931 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 22714 Z= 0.149 Angle : 0.695 9.819 31311 Z= 0.338 Chirality : 0.044 0.219 3049 Planarity : 0.005 0.051 3951 Dihedral : 13.714 84.352 3580 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.83 % Allowed : 28.93 % 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: 0.95 (0.18), residues: 2314 helix: 1.58 (0.14), residues: 1311 sheet: 1.07 (0.73), residues: 60 loop : -0.76 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 1 116 TYR 0.018 0.001 TYR A 135 PHE 0.034 0.001 PHE Z 17 TRP 0.012 0.001 TRP C 51 HIS 0.016 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (22702) covalent geometry : angle 0.69461 / 0.34 (31311) hydrogen bonds : bond 0.04761 / 3.17 ( 1010) hydrogen bonds : angle 4.12321 / 2.96 ( 2904) Misc. bond : bond 0.05087 / 3.63 ( 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 625 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 552 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TRP cc_start: 0.8824 (OUTLIER) cc_final: 0.8225 (t-100) REVERT: A 104 GLU cc_start: 0.8641 (pt0) cc_final: 0.8416 (pt0) REVERT: A 140 ARG cc_start: 0.7945 (mtp85) cc_final: 0.7643 (mmm-85) REVERT: A 237 TYR cc_start: 0.4799 (OUTLIER) cc_final: 0.4413 (m-10) REVERT: A 238 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7865 (mmpt) REVERT: A 239 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: A 241 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 242 GLU cc_start: 0.7822 (mp0) cc_final: 0.7592 (mp0) REVERT: A 275 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8881 (mp) REVERT: A 333 GLU cc_start: 0.8561 (tp30) cc_final: 0.7962 (tp30) REVERT: B 125 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6846 (p0) REVERT: B 130 GLU cc_start: 0.8896 (pt0) cc_final: 0.8349 (pm20) REVERT: B 210 ILE cc_start: 0.9021 (mm) cc_final: 0.8750 (mp) REVERT: B 214 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8858 (mm) REVERT: B 230 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7183 (mtt180) REVERT: B 352 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 489 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: C 130 GLU cc_start: 0.8872 (pp20) cc_final: 0.8635 (tm-30) REVERT: C 141 ASP cc_start: 0.8623 (t0) cc_final: 0.8049 (t0) REVERT: C 145 MET cc_start: 0.8472 (mtt) cc_final: 0.8268 (mtt) REVERT: C 155 VAL cc_start: 0.8924 (t) cc_final: 0.8640 (m) REVERT: C 175 ASP cc_start: 0.8943 (t0) cc_final: 0.8647 (t0) REVERT: C 193 ASP cc_start: 0.8682 (t0) cc_final: 0.8331 (t70) REVERT: C 195 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8366 (mtp180) REVERT: C 209 GLU cc_start: 0.8325 (pm20) cc_final: 0.7983 (pm20) REVERT: C 227 TRP cc_start: 0.8445 (m100) cc_final: 0.8183 (m100) REVERT: C 277 PHE cc_start: 0.9486 (OUTLIER) cc_final: 0.8831 (t80) REVERT: C 336 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7328 (mm-30) REVERT: C 350 ARG cc_start: 0.5891 (pmt170) cc_final: 0.2491 (mmt180) REVERT: C 371 ASP cc_start: 0.8248 (m-30) cc_final: 0.7614 (m-30) REVERT: D 27 PHE cc_start: 0.8464 (t80) cc_final: 0.8107 (t80) REVERT: D 100 ASP cc_start: 0.8600 (t0) cc_final: 0.8064 (t70) REVERT: D 224 GLN cc_start: 0.8433 (mt0) cc_final: 0.7844 (pt0) REVERT: D 265 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7991 (ttp80) REVERT: D 323 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8843 (tm-30) REVERT: E 42 LEU cc_start: 0.8962 (tp) cc_final: 0.8568 (tp) REVERT: E 55 TYR cc_start: 0.9451 (m-80) cc_final: 0.8988 (m-80) REVERT: E 61 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7288 (mmp-170) REVERT: E 77 GLU cc_start: 0.8906 (tt0) cc_final: 0.8548 (mt-10) REVERT: E 82 GLN cc_start: 0.7751 (pt0) cc_final: 0.7498 (pp30) REVERT: F 8 GLN cc_start: 0.1955 (OUTLIER) cc_final: 0.1484 (pm20) REVERT: H 4 ARG cc_start: 0.9049 (mmm-85) cc_final: 0.8662 (tpp80) REVERT: T 25 GLU cc_start: 0.8051 (tp30) cc_final: 0.7678 (tp30) REVERT: Z 31 GLN cc_start: 0.6082 (OUTLIER) cc_final: 0.5625 (pp30) REVERT: Z 57 LEU cc_start: 0.8480 (mp) cc_final: 0.8267 (tp) REVERT: 1 48 ILE cc_start: 0.8725 (pt) cc_final: 0.8385 (pp) REVERT: 1 88 MET cc_start: 0.9180 (mmm) cc_final: 0.8791 (mmm) REVERT: 1 91 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8624 (tm-30) REVERT: 1 114 LYS cc_start: 0.8796 (mttt) cc_final: 0.8145 (mptp) REVERT: 1 123 GLN cc_start: 0.9406 (mt0) cc_final: 0.9180 (tp40) REVERT: 1 131 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7658 (pt0) REVERT: 2 4 MET cc_start: 0.2303 (pp-130) cc_final: 0.0382 (tpp) REVERT: 2 6 GLU cc_start: 0.6592 (pp20) cc_final: 0.6112 (tm-30) REVERT: 2 22 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7517 (tmm-80) REVERT: 2 25 ARG cc_start: 0.8433 (tpt-90) cc_final: 0.8082 (tpt-90) REVERT: 2 45 GLN cc_start: 0.8221 (mt0) cc_final: 0.7982 (mp10) REVERT: 2 46 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: 2 71 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8444 (ttmm) REVERT: 2 86 MET cc_start: 0.7838 (ptp) cc_final: 0.7485 (pmm) REVERT: 2 91 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8757 (pt0) REVERT: 2 93 ASP cc_start: 0.9362 (m-30) cc_final: 0.8927 (p0) REVERT: 2 101 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7066 (mtt180) REVERT: 2 112 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8303 (tppp) REVERT: 3 26 TRP cc_start: 0.7925 (m-10) cc_final: 0.6629 (m-90) outliers start: 73 outliers final: 43 residues processed: 584 average time/residue: 0.5680 time to fit residues: 383.5696 Evaluate side-chains 594 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 538 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 TRP 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 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 275 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 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 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 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 409 SER Chi-restraints excluded: chain D residue 69 GLU 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 37 LEU 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 M residue 3 VAL Chi-restraints excluded: chain T residue 3 THR 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 125 GLU Chi-restraints excluded: chain 1 residue 128 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 215 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 209 optimal weight: 0.0980 chunk 165 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 GLN ** 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 M 33 GLN Z 31 GLN Z 58 ASN 1 106 ASN 1 119 GLN 3 22 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091756 restraints weight = 35981.030| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.71 r_work: 0.2950 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 22714 Z= 0.137 Angle : 0.706 10.586 31311 Z= 0.345 Chirality : 0.044 0.397 3049 Planarity : 0.005 0.057 3951 Dihedral : 13.495 83.528 3580 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.04 % Allowed : 30.03 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.18), residues: 2314 helix: 1.64 (0.14), residues: 1314 sheet: 1.05 (0.72), residues: 60 loop : -0.71 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 1 130 TYR 0.017 0.001 TYR A 135 PHE 0.054 0.001 PHE 1 121 TRP 0.029 0.001 TRP Z 33 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (22702) covalent geometry : angle 0.70634 / 0.35 (31311) hydrogen bonds : bond 0.04469 / 2.97 ( 1010) hydrogen bonds : angle 4.09630 / 2.94 ( 2904) Misc. bond : bond 0.04349 / 3.11 ( 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 603 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 545 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7668 (mmm-85) REVERT: A 237 TYR cc_start: 0.4731 (OUTLIER) cc_final: 0.4391 (m-10) REVERT: A 238 LYS cc_start: 0.8270 (mtpp) cc_final: 0.7857 (mmpt) REVERT: A 239 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: A 242 GLU cc_start: 0.7773 (mp0) cc_final: 0.7489 (mp0) REVERT: A 333 GLU cc_start: 0.8584 (tp30) cc_final: 0.7973 (tp30) REVERT: B 125 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.6980 (OUTLIER) REVERT: B 130 GLU cc_start: 0.8888 (pt0) cc_final: 0.8459 (pm20) REVERT: B 210 ILE cc_start: 0.9027 (mm) cc_final: 0.8750 (mp) REVERT: B 214 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8856 (mm) REVERT: B 230 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7197 (mtt180) REVERT: B 352 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8432 (mm-30) REVERT: B 489 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7192 (mm-30) REVERT: C 130 GLU cc_start: 0.8882 (pp20) cc_final: 0.8612 (tm-30) REVERT: C 141 ASP cc_start: 0.8526 (t0) cc_final: 0.7884 (t0) REVERT: C 175 ASP cc_start: 0.8948 (t0) cc_final: 0.8658 (t0) REVERT: C 193 ASP cc_start: 0.8687 (t0) cc_final: 0.8345 (t70) REVERT: C 195 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8383 (mtp180) REVERT: C 209 GLU cc_start: 0.8305 (pm20) cc_final: 0.7999 (pm20) REVERT: C 227 TRP cc_start: 0.8471 (m100) cc_final: 0.8202 (m100) REVERT: C 277 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.8864 (t80) REVERT: C 336 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7296 (mm-30) REVERT: C 371 ASP cc_start: 0.8324 (m-30) cc_final: 0.7645 (m-30) REVERT: D 27 PHE cc_start: 0.8461 (t80) cc_final: 0.8094 (t80) REVERT: D 100 ASP cc_start: 0.8595 (t0) cc_final: 0.8040 (t70) REVERT: D 186 GLN cc_start: 0.9431 (tp40) cc_final: 0.9113 (tp40) REVERT: D 224 GLN cc_start: 0.8443 (mt0) cc_final: 0.7827 (pt0) REVERT: D 265 ARG cc_start: 0.8317 (ttp80) cc_final: 0.8004 (ttp80) REVERT: D 323 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8834 (tm-30) REVERT: E 42 LEU cc_start: 0.8948 (tp) cc_final: 0.8546 (tp) REVERT: E 55 TYR cc_start: 0.9441 (m-80) cc_final: 0.8913 (m-80) REVERT: E 61 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7340 (mmp-170) REVERT: E 77 GLU cc_start: 0.8886 (tt0) cc_final: 0.8528 (mt-10) REVERT: E 82 GLN cc_start: 0.7747 (pt0) cc_final: 0.7476 (pp30) REVERT: F 8 GLN cc_start: 0.1886 (OUTLIER) cc_final: 0.1415 (pm20) REVERT: H 4 ARG cc_start: 0.9055 (mmm-85) cc_final: 0.8630 (tpp80) REVERT: I 18 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8173 (pp) REVERT: M 1 MET cc_start: 0.1934 (mpt) cc_final: 0.1151 (mpt) REVERT: T 25 GLU cc_start: 0.8060 (tp30) cc_final: 0.7665 (tp30) REVERT: X 7 LEU cc_start: 0.9041 (tp) cc_final: 0.8761 (tt) REVERT: X 11 PHE cc_start: 0.8943 (m-10) cc_final: 0.8739 (m-10) REVERT: Z 31 GLN cc_start: 0.5721 (OUTLIER) cc_final: 0.5478 (pp30) REVERT: 1 32 ASN cc_start: 0.7855 (t0) cc_final: 0.7290 (t0) REVERT: 1 48 ILE cc_start: 0.8680 (pt) cc_final: 0.8351 (pp) REVERT: 1 88 MET cc_start: 0.9166 (mmm) cc_final: 0.8857 (mmm) REVERT: 1 114 LYS cc_start: 0.8804 (mttt) cc_final: 0.8158 (mptp) REVERT: 1 116 ARG cc_start: 0.8348 (tpp-160) cc_final: 0.7976 (tpm170) REVERT: 2 4 MET cc_start: 0.2399 (pp-130) cc_final: 0.0451 (tpp) REVERT: 2 6 GLU cc_start: 0.6551 (pp20) cc_final: 0.6041 (tm-30) REVERT: 2 22 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7503 (tmm-80) REVERT: 2 46 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: 2 71 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8427 (ttmm) REVERT: 2 86 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7511 (pmm) REVERT: 2 93 ASP cc_start: 0.9350 (m-30) cc_final: 0.8903 (p0) REVERT: 2 101 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7203 (mtt180) REVERT: 2 112 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8662 (tppp) REVERT: 3 26 TRP cc_start: 0.7944 (m-10) cc_final: 0.6671 (m-90) outliers start: 58 outliers final: 33 residues processed: 575 average time/residue: 0.5904 time to fit residues: 392.1083 Evaluate side-chains 582 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 537 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 46 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 PHE 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 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 B residue 489 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 195 ARG 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 348 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 409 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 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 T residue 3 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 35 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 126 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 172 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 Z 58 ASN 1 32 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 = 0.3656 r_free = 0.3656 target = 0.128858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.092629 restraints weight = 35877.615| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.73 r_work: 0.2974 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 22714 Z= 0.135 Angle : 0.700 10.829 31311 Z= 0.344 Chirality : 0.043 0.221 3049 Planarity : 0.005 0.052 3951 Dihedral : 13.289 84.850 3580 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.67 % Allowed : 30.61 % Favored : 66.72 % 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: 1.05 (0.18), residues: 2314 helix: 1.66 (0.14), residues: 1314 sheet: 0.66 (0.67), residues: 70 loop : -0.68 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 435 TYR 0.017 0.001 TYR 2 55 PHE 0.061 0.001 PHE 1 121 TRP 0.029 0.001 TRP Z 33 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (22702) covalent geometry : angle 0.70047 / 0.34 (31311) hydrogen bonds : bond 0.04321 / 2.85 ( 1010) hydrogen bonds : angle 4.09074 / 2.93 ( 2904) Misc. bond : bond 0.03952 / 2.82 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9262.84 seconds wall clock time: 157 minutes 58.98 seconds (9478.98 seconds total)