Starting phenix.real_space_refine on Fri Aug 7 22:40:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gnw_51482/08_2026/9gnw_51482.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gnw_51482/08_2026/9gnw_51482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gnw_51482/08_2026/9gnw_51482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gnw_51482/08_2026/9gnw_51482.map" model { file = "/net/cci-nas-00/data/ceres_data/9gnw_51482/08_2026/9gnw_51482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gnw_51482/08_2026/9gnw_51482.cif" } resolution = 2.93 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: 11 Type Number sf(0) Gaussians Ca 1 9.91 5 Mn 4 7.51 5 Fe 2 7.16 5 P 6 5.49 5 Mg 35 5.21 5 S 67 5.16 5 Cl 2 4.86 5 Na 1 4.78 5 C 16500 2.51 5 N 3489 2.21 5 O 4097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24204 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2635 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain: "B" Number of atoms: 3785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3785 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 457} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 235 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "C" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3483 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 423} Chain: "D" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2766 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain: "E" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 621 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "F" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 252 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "H" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 503 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "I" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 265 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 2, 'TRANS': 30} Chain: "J" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 265 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "L" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 300 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "M" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 235 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "O" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1819 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1453 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "T" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 247 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "W" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 335 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "X" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 225 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "Z" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "U" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 235 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "A" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 463 Ad-hoc single atom residues: {'FE2': 1} Unusual residues: {' CL': 2, ' NA': 1, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 1, 'LMG': 2, 'OEX': 1, 'PHO': 1, 'SQD': 1} Classifications: {'undetermined': 14} Link IDs: {None: 12} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 64 Chain: "B" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1311 Unusual residues: {'3PH': 1, 'BCR': 2, 'C7Z': 1, 'CLA': 16, 'DGA': 1, 'DGD': 1, 'LMG': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1184 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 3, 'LMG': 3} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 1, 'LMG:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 523 Unusual residues: {'BCR': 1, 'CLA': 3, 'LHG': 3, 'LMG': 1, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 31 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: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'LMG': 1, 'RRX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'BCR': 1, 'LMU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.04, per 1000 atoms: 0.25 Number of scatterers: 24204 At special positions: 0 Unit cell: (130.29, 142.545, 127.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 11 Type Number sf(0) Fe 2 26.01 Mn 4 24.99 Ca 1 19.99 Cl 2 17.00 S 67 16.00 P 6 15.00 Mg 35 11.99 Na 1 11.00 O 4097 8.00 N 3489 7.00 C 16500 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=36, symmetry=0 Number of additional bonds: simple=36, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 995.6 milliseconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4700 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 13 sheets defined 59.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 33 through 54 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 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.813A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 4.216A 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 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.790A pdb=" N ILE A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 316 through 330 Processing helix chain 'B' and resid 7 through 13 removed outlier: 3.962A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 44 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 196 through 217 removed outlier: 3.609A pdb=" N ALA B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 206 " --> pdb=" O HIS B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 233 through 258 removed outlier: 3.611A pdb=" N VAL B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.791A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.691A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.807A pdb=" N GLY B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 Processing helix chain 'B' and resid 477 through 481 removed outlier: 4.019A pdb=" N ALA B 480 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 30 removed outlier: 4.307A pdb=" N GLY V 19 " --> pdb=" O VAL V 15 " (cutoff:3.500A) Proline residue: V 20 - end of helix Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 22 through 31 removed outlier: 6.377A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 62 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.855A pdb=" N GLY C 73 " --> pdb=" O TYR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.730A pdb=" N HIS C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 141 through 170 removed outlier: 3.570A pdb=" N PHE C 170 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 removed outlier: 3.952A pdb=" N TYR C 200 " --> pdb=" O ILE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.520A pdb=" N SER C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 312 Processing helix chain 'C' and resid 341 through 347 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 366 through 371 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 54 removed outlier: 4.046A pdb=" N LEU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.346A 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 66 through 70 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.042A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.234A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.580A pdb=" N PHE D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 194 through 221 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 263 through 291 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: 4.602A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'E' and resid 9 through 15 Processing helix chain 'E' and resid 16 through 24 removed outlier: 3.558A pdb=" N TRP E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 41 through 48 Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'F' and resid 16 through 25 removed outlier: 3.936A pdb=" N ILE F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 40 Processing helix chain 'H' and resid 24 through 36 Proline residue: H 32 - end of helix removed outlier: 4.328A pdb=" N GLU H 36 " --> pdb=" O PRO H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 69 Processing helix chain 'H' and resid 80 through 85 Processing helix chain 'I' and resid 2 through 25 removed outlier: 3.662A pdb=" N SER I 25 " --> pdb=" O PHE I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 30 Processing helix chain 'J' and resid 11 through 36 Processing helix chain 'K' and resid 12 through 17 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 18 through 25 Processing helix chain 'K' and resid 27 through 43 removed outlier: 3.876A pdb=" N ILE K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.483A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 33 Proline residue: M 18 - end of helix Processing helix chain 'O' and resid 63 through 70 removed outlier: 3.619A pdb=" N LEU O 70 " --> pdb=" O GLU O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 76 Processing helix chain 'O' and resid 93 through 97 Processing helix chain 'O' and resid 233 through 237 Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 133 through 141 Processing helix chain 'P' and resid 142 through 146 removed outlier: 3.754A pdb=" N LEU P 145 " --> pdb=" O GLY P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 199 Processing helix chain 'P' and resid 223 through 228 removed outlier: 3.808A pdb=" N LYS P 228 " --> pdb=" O LYS P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 241 removed outlier: 4.229A pdb=" N GLU P 233 " --> pdb=" O GLY P 229 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'W' and resid 72 through 76 Processing helix chain 'W' and resid 78 through 100 removed outlier: 3.876A pdb=" N GLY W 82 " --> pdb=" O ASP W 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 96 Processing helix chain 'Z' and resid 2 through 29 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 31 through 36 removed outlier: 3.646A pdb=" N GLU Z 35 " --> pdb=" O ASN Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 61 Processing helix chain 'U' and resid 102 through 114 Proline residue: U 112 - end of helix Processing helix chain 'U' and resid 117 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA2, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'B' and resid 322 through 323 removed outlier: 6.962A pdb=" N GLY B 322 " --> pdb=" O ARG D 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.856A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 409 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.856A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA B 337 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASP B 433 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 339 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE B 429 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA8, first strand: chain 'C' and resid 358 through 359 Processing sheet with id=AA9, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'O' and resid 125 through 129 removed outlier: 6.049A pdb=" N PHE O 107 " --> pdb=" O GLN O 297 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLN O 297 " --> pdb=" O PHE O 107 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N MET O 109 " --> pdb=" O TYR O 295 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR O 295 " --> pdb=" O MET O 109 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU O 293 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR O 291 " --> pdb=" O SER O 113 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP O 287 " --> pdb=" O LYS O 117 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU O 265 " --> pdb=" O VAL O 259 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL O 259 " --> pdb=" O GLU O 265 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA O 267 " --> pdb=" O ALA O 257 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LYS O 249 " --> pdb=" O PRO O 275 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP O 199 " --> pdb=" O ASP O 188 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP O 141 " --> pdb=" O CYS O 108 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS O 108 " --> pdb=" O ASP O 141 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET O 143 " --> pdb=" O LYS O 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 131 through 132 Processing sheet with id=AB3, first strand: chain 'P' and resid 75 through 79 Processing sheet with id=AB4, first strand: chain 'P' and resid 91 through 93 removed outlier: 6.479A pdb=" N VAL P 118 " --> pdb=" O VAL P 103 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG P 105 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU P 116 " --> pdb=" O ARG P 105 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR P 184 " --> pdb=" O THR P 175 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR P 175 " --> pdb=" O TYR P 184 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS P 186 " --> pdb=" O VAL P 173 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL P 173 " --> pdb=" O LYS P 186 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU P 188 " --> pdb=" O LEU P 171 " (cutoff:3.500A) 1187 hydrogen bonds defined for protein. 3318 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.71: 24813 1.71 - 2.23: 267 2.23 - 2.75: 5 2.75 - 3.28: 1 3.28 - 3.80: 4 Bond restraints: 25090 Sorted by residual: bond pdb=" C25 C7Z B 519 " pdb=" C26 C7Z B 519 " ideal model delta sigma weight residual 1.347 1.615 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C25 BCR A 409 " pdb=" C26 BCR A 409 " ideal model delta sigma weight residual 1.347 1.608 -0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C25 BCR D 405 " pdb=" C26 BCR D 405 " ideal model delta sigma weight residual 1.347 1.607 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C25 BCR J 101 " pdb=" C26 BCR J 101 " ideal model delta sigma weight residual 1.347 1.607 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C25 BCR B 518 " pdb=" C26 BCR B 518 " ideal model delta sigma weight residual 1.347 1.607 -0.260 2.00e-02 2.50e+03 1.69e+02 ... (remaining 25085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.56: 34147 6.56 - 13.12: 336 13.12 - 19.68: 34 19.68 - 26.24: 0 26.24 - 32.80: 1 Bond angle restraints: 34518 Sorted by residual: angle pdb=" CBB DGA B 523 " pdb=" CCB DGA B 523 " pdb=" CDB DGA B 523 " ideal model delta sigma weight residual 113.01 80.21 32.80 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C2 CLA A 405 " pdb=" C1 CLA A 405 " pdb=" O2A CLA A 405 " ideal model delta sigma weight residual 106.82 123.65 -16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C2 CLA C 509 " pdb=" C1 CLA C 509 " pdb=" O2A CLA C 509 " ideal model delta sigma weight residual 106.82 123.32 -16.50 3.00e+00 1.11e-01 3.03e+01 angle pdb=" C2 CLA B 514 " pdb=" C1 CLA B 514 " pdb=" O2A CLA B 514 " ideal model delta sigma weight residual 106.82 123.20 -16.38 3.00e+00 1.11e-01 2.98e+01 angle pdb=" C2 CLA C 503 " pdb=" C1 CLA C 503 " pdb=" O2A CLA C 503 " ideal model delta sigma weight residual 106.82 123.17 -16.35 3.00e+00 1.11e-01 2.97e+01 ... (remaining 34513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.21: 12626 25.21 - 50.42: 876 50.42 - 75.62: 216 75.62 - 100.83: 79 100.83 - 126.04: 57 Dihedral angle restraints: 13854 sinusoidal: 6470 harmonic: 7384 Sorted by residual: dihedral pdb=" C1 BCR B 517 " pdb=" C2 BCR B 517 " pdb=" C3 BCR B 517 " pdb=" C4 BCR B 517 " ideal model delta sinusoidal sigma weight residual -60.86 65.18 -126.04 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C4D PHO D 402 " pdb=" CBD PHO D 402 " pdb=" CHA PHO D 402 " pdb=" CGD PHO D 402 " ideal model delta sinusoidal sigma weight residual 243.52 117.56 125.96 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C27 BCR B 518 " pdb=" C28 BCR B 518 " pdb=" C29 BCR B 518 " pdb=" C30 BCR B 518 " ideal model delta sinusoidal sigma weight residual -60.81 63.31 -124.12 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 13851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 3387 0.154 - 0.308: 27 0.308 - 0.462: 2 0.462 - 0.616: 20 0.616 - 0.769: 13 Chirality restraints: 3449 Sorted by residual: chirality pdb=" C3A CLA C 512 " pdb=" C2A CLA C 512 " pdb=" C4A CLA C 512 " pdb=" CMA CLA C 512 " both_signs ideal model delta sigma weight residual False -2.76 -2.00 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C3A CLA B 504 " pdb=" C2A CLA B 504 " pdb=" C4A CLA B 504 " pdb=" CMA CLA B 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.00 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C3A CLA C 504 " pdb=" C2A CLA C 504 " pdb=" C4A CLA C 504 " pdb=" CMA CLA C 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.08 -0.68 2.00e-01 2.50e+01 1.17e+01 ... (remaining 3446 not shown) Planarity restraints: 4304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO A 407 " -0.068 2.00e-02 2.50e+03 1.14e-01 1.04e+03 pdb=" ND PHO A 407 " -0.106 2.00e-02 2.50e+03 pdb=" C1A PHO A 407 " -0.008 2.00e-02 2.50e+03 pdb=" C1B PHO A 407 " -0.037 2.00e-02 2.50e+03 pdb=" C1C PHO A 407 " -0.001 2.00e-02 2.50e+03 pdb=" C1D PHO A 407 " -0.015 2.00e-02 2.50e+03 pdb=" C2A PHO A 407 " 0.045 2.00e-02 2.50e+03 pdb=" C2B PHO A 407 " 0.108 2.00e-02 2.50e+03 pdb=" C2C PHO A 407 " -0.054 2.00e-02 2.50e+03 pdb=" C2D PHO A 407 " 0.036 2.00e-02 2.50e+03 pdb=" C3A PHO A 407 " -0.317 2.00e-02 2.50e+03 pdb=" C3B PHO A 407 " 0.146 2.00e-02 2.50e+03 pdb=" C3C PHO A 407 " -0.069 2.00e-02 2.50e+03 pdb=" C3D PHO A 407 " 0.061 2.00e-02 2.50e+03 pdb=" C4A PHO A 407 " -0.190 2.00e-02 2.50e+03 pdb=" C4B PHO A 407 " 0.030 2.00e-02 2.50e+03 pdb=" C4C PHO A 407 " -0.012 2.00e-02 2.50e+03 pdb=" C4D PHO A 407 " -0.001 2.00e-02 2.50e+03 pdb=" CAB PHO A 407 " 0.254 2.00e-02 2.50e+03 pdb=" CAC PHO A 407 " -0.124 2.00e-02 2.50e+03 pdb=" CAD PHO A 407 " 0.101 2.00e-02 2.50e+03 pdb=" CBD PHO A 407 " 0.171 2.00e-02 2.50e+03 pdb=" CHA PHO A 407 " 0.049 2.00e-02 2.50e+03 pdb=" CHB PHO A 407 " -0.133 2.00e-02 2.50e+03 pdb=" CHC PHO A 407 " 0.003 2.00e-02 2.50e+03 pdb=" CHD PHO A 407 " 0.019 2.00e-02 2.50e+03 pdb=" CMB PHO A 407 " 0.160 2.00e-02 2.50e+03 pdb=" CMC PHO A 407 " -0.101 2.00e-02 2.50e+03 pdb=" CMD PHO A 407 " 0.081 2.00e-02 2.50e+03 pdb=" NA PHO A 407 " -0.151 2.00e-02 2.50e+03 pdb=" NC PHO A 407 " 0.035 2.00e-02 2.50e+03 pdb=" OBD PHO A 407 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 402 " -0.014 2.00e-02 2.50e+03 7.05e-02 3.97e+02 pdb=" ND PHO D 402 " -0.149 2.00e-02 2.50e+03 pdb=" C1A PHO D 402 " 0.037 2.00e-02 2.50e+03 pdb=" C1B PHO D 402 " -0.006 2.00e-02 2.50e+03 pdb=" C1C PHO D 402 " -0.013 2.00e-02 2.50e+03 pdb=" C1D PHO D 402 " -0.080 2.00e-02 2.50e+03 pdb=" C2A PHO D 402 " 0.092 2.00e-02 2.50e+03 pdb=" C2B PHO D 402 " -0.054 2.00e-02 2.50e+03 pdb=" C2C PHO D 402 " 0.062 2.00e-02 2.50e+03 pdb=" C2D PHO D 402 " -0.065 2.00e-02 2.50e+03 pdb=" C3A PHO D 402 " 0.128 2.00e-02 2.50e+03 pdb=" C3B PHO D 402 " -0.070 2.00e-02 2.50e+03 pdb=" C3C PHO D 402 " 0.072 2.00e-02 2.50e+03 pdb=" C3D PHO D 402 " -0.045 2.00e-02 2.50e+03 pdb=" C4A PHO D 402 " 0.059 2.00e-02 2.50e+03 pdb=" C4B PHO D 402 " -0.042 2.00e-02 2.50e+03 pdb=" C4C PHO D 402 " -0.012 2.00e-02 2.50e+03 pdb=" C4D PHO D 402 " -0.058 2.00e-02 2.50e+03 pdb=" CAB PHO D 402 " -0.087 2.00e-02 2.50e+03 pdb=" CAC PHO D 402 " 0.148 2.00e-02 2.50e+03 pdb=" CAD PHO D 402 " -0.008 2.00e-02 2.50e+03 pdb=" CBD PHO D 402 " 0.094 2.00e-02 2.50e+03 pdb=" CHA PHO D 402 " 0.022 2.00e-02 2.50e+03 pdb=" CHB PHO D 402 " 0.042 2.00e-02 2.50e+03 pdb=" CHC PHO D 402 " -0.011 2.00e-02 2.50e+03 pdb=" CHD PHO D 402 " -0.018 2.00e-02 2.50e+03 pdb=" CMB PHO D 402 " -0.048 2.00e-02 2.50e+03 pdb=" CMC PHO D 402 " 0.143 2.00e-02 2.50e+03 pdb=" CMD PHO D 402 " -0.052 2.00e-02 2.50e+03 pdb=" NA PHO D 402 " 0.027 2.00e-02 2.50e+03 pdb=" NC PHO D 402 " -0.057 2.00e-02 2.50e+03 pdb=" OBD PHO D 402 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C CLA B 515 " -0.005 2.00e-02 2.50e+03 7.57e-02 8.59e+01 pdb=" C3C CLA B 515 " 0.100 2.00e-02 2.50e+03 pdb=" C4C CLA B 515 " -0.054 2.00e-02 2.50e+03 pdb=" CHD CLA B 515 " -0.001 2.00e-02 2.50e+03 pdb=" NC CLA B 515 " -0.121 2.00e-02 2.50e+03 pdb="MG CLA B 515 " 0.082 2.00e-02 2.50e+03 ... (remaining 4301 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 29 2.30 - 2.95: 11079 2.95 - 3.60: 36252 3.60 - 4.25: 62303 4.25 - 4.90: 105151 Nonbonded interactions: 214814 Sorted by model distance: nonbonded pdb=" OE2 GLU A 189 " pdb=" O1 OEX A 401 " model vdw 1.654 3.040 nonbonded pdb=" OE2 GLU A 189 " pdb="MN1 OEX A 401 " model vdw 2.115 3.060 nonbonded pdb=" O ARG B 7 " pdb=" OG1 THR B 10 " model vdw 2.199 3.040 nonbonded pdb=" OG SER C 391 " pdb=" OD1 ASN C 393 " model vdw 2.203 3.040 nonbonded pdb=" O ALA B 155 " pdb=" OG1 THR B 159 " model vdw 2.204 3.040 ... (remaining 214809 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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 : 0.024 0.448 25126 Z= 1.623 Angle : 1.492 32.798 34518 Z= 0.545 Chirality : 0.077 0.769 3449 Planarity : 0.008 0.114 4304 Dihedral : 20.595 126.041 9154 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 3.72 % Allowed : 6.21 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.17), residues: 2576 helix: 1.71 (0.14), residues: 1334 sheet: 0.66 (0.39), residues: 190 loop : -0.19 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 60 TYR 0.012 0.001 TYR B 390 PHE 0.023 0.002 PHE B 246 TRP 0.019 0.001 TRP A 131 HIS 0.006 0.002 HIS C 106 Details of bonding type rmsd/Z covalent geometry : bond 0.02046 / 1.02 (25090) covalent geometry : angle 1.49240 / 0.55 (34518) hydrogen bonds : bond 0.13100 / 8.65 ( 1182) hydrogen bonds : angle 5.80670 / 4.36 ( 3318) Misc. bond : bond 0.34526 / 22.11 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 484 time to evaluate : 0.877 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: D 308 ASP cc_start: 0.8213 (t0) cc_final: 0.7438 (t0) REVERT: E 75 GLN cc_start: 0.8692 (tt0) cc_final: 0.8459 (tt0) REVERT: I 26 ASN cc_start: 0.8459 (t0) cc_final: 0.8153 (t0) REVERT: O 98 LYS cc_start: 0.8105 (ttpp) cc_final: 0.7829 (tttm) REVERT: P 124 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7355 (p0) REVERT: P 125 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7624 (mptp) REVERT: P 183 THR cc_start: 0.8377 (p) cc_final: 0.7827 (p) REVERT: W 65 MET cc_start: 0.7394 (mmm) cc_final: 0.7104 (tpp) REVERT: W 103 LEU cc_start: 0.4669 (OUTLIER) cc_final: 0.4050 (pp) outliers start: 79 outliers final: 18 residues processed: 539 average time/residue: 0.5765 time to fit residues: 364.8387 Evaluate side-chains 355 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 334 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 87 ASN C 299 GLN D 142 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.081764 restraints weight = 38950.698| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.93 r_work: 0.2703 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.328 25126 Z= 0.192 Angle : 0.693 16.286 34518 Z= 0.310 Chirality : 0.044 0.282 3449 Planarity : 0.005 0.062 4304 Dihedral : 20.590 122.163 4786 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.72 % Favored : 97.24 % Rotamer: Outliers : 4.33 % Allowed : 13.28 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.17), residues: 2576 helix: 1.89 (0.14), residues: 1326 sheet: 0.56 (0.38), residues: 190 loop : -0.08 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 122 TYR 0.030 0.001 TYR A 262 PHE 0.020 0.001 PHE B 246 TRP 0.021 0.001 TRP A 131 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (25090) covalent geometry : angle 0.69284 / 0.31 (34518) hydrogen bonds : bond 0.05014 / 3.37 ( 1182) hydrogen bonds : angle 4.86776 / 3.62 ( 3318) Misc. bond : bond 0.05955 / 3.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 346 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 246 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8996 (p90) REVERT: C 162 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8683 (tt) REVERT: C 165 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9130 (mp) REVERT: D 11 LYS cc_start: 0.9055 (mtmm) cc_final: 0.8550 (ttmm) REVERT: D 14 TRP cc_start: 0.8431 (OUTLIER) cc_final: 0.8216 (p-90) REVERT: D 16 ASP cc_start: 0.8929 (m-30) cc_final: 0.8298 (m-30) REVERT: D 20 ASP cc_start: 0.8503 (m-30) cc_final: 0.8271 (m-30) REVERT: D 100 ASP cc_start: 0.8679 (t70) cc_final: 0.8148 (t0) REVERT: D 302 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8557 (mm-30) REVERT: D 308 ASP cc_start: 0.8625 (t0) cc_final: 0.8080 (t0) REVERT: E 75 GLN cc_start: 0.8929 (tt0) cc_final: 0.8659 (tt0) REVERT: H 84 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8151 (mt) REVERT: I 26 ASN cc_start: 0.8972 (t0) cc_final: 0.8330 (t0) REVERT: J 9 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.4613 (pmm150) REVERT: M 5 ILE cc_start: 0.8912 (tp) cc_final: 0.8624 (mm) REVERT: P 64 ASN cc_start: 0.8182 (t0) cc_final: 0.7924 (t0) REVERT: P 107 GLU cc_start: 0.8106 (tt0) cc_final: 0.7864 (tm-30) REVERT: P 122 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8601 (ttmt) REVERT: P 176 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8138 (mm-30) REVERT: U 109 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7734 (mtt180) REVERT: U 122 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8175 (ttm-80) outliers start: 92 outliers final: 31 residues processed: 398 average time/residue: 0.4923 time to fit residues: 234.2271 Evaluate side-chains 362 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 324 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 14 TRP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 122 LYS Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 103 THR Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 233 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 151 optimal weight: 0.0170 chunk 126 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 87 ASN F 40 GLN H 69 ASN H 79 ASN ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 238 GLN O 297 GLN P 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.083198 restraints weight = 38818.503| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.00 r_work: 0.2716 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.277 25126 Z= 0.131 Angle : 0.609 15.856 34518 Z= 0.276 Chirality : 0.041 0.242 3449 Planarity : 0.004 0.041 4304 Dihedral : 17.878 120.340 4772 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 3.63 % Allowed : 14.97 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.17), residues: 2576 helix: 2.00 (0.14), residues: 1325 sheet: 0.65 (0.37), residues: 189 loop : -0.08 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 265 TYR 0.026 0.001 TYR A 262 PHE 0.018 0.001 PHE B 246 TRP 0.022 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (25090) covalent geometry : angle 0.60918 / 0.28 (34518) hydrogen bonds : bond 0.04289 / 2.88 ( 1182) hydrogen bonds : angle 4.59194 / 3.42 ( 3318) Misc. bond : bond 0.05035 / 2.74 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 349 time to evaluate : 0.678 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 59 ASP cc_start: 0.8932 (t70) cc_final: 0.8694 (t0) REVERT: B 83 GLU cc_start: 0.7891 (mp0) cc_final: 0.7590 (mp0) REVERT: V 29 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8089 (mmm-85) REVERT: C 165 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9067 (mp) REVERT: C 460 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7645 (tm) REVERT: D 11 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8567 (ttmm) REVERT: D 16 ASP cc_start: 0.8946 (m-30) cc_final: 0.8333 (m-30) REVERT: D 20 ASP cc_start: 0.8567 (m-30) cc_final: 0.8265 (m-30) REVERT: D 100 ASP cc_start: 0.8662 (t70) cc_final: 0.8061 (t0) REVERT: D 302 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8448 (mm-30) REVERT: D 308 ASP cc_start: 0.8507 (t0) cc_final: 0.8077 (t0) REVERT: D 310 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8439 (pm20) REVERT: E 75 GLN cc_start: 0.8945 (tt0) cc_final: 0.8655 (tt0) REVERT: I 23 PHE cc_start: 0.9556 (OUTLIER) cc_final: 0.9257 (m-80) REVERT: I 26 ASN cc_start: 0.9005 (t0) cc_final: 0.8308 (t0) REVERT: K 18 PHE cc_start: 0.9427 (m-80) cc_final: 0.9214 (m-10) REVERT: K 23 ASP cc_start: 0.8326 (m-30) cc_final: 0.8111 (m-30) REVERT: O 126 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: P 64 ASN cc_start: 0.8367 (t0) cc_final: 0.7714 (t0) REVERT: P 107 GLU cc_start: 0.8132 (tt0) cc_final: 0.7916 (tm-30) REVERT: P 122 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8628 (ttmt) REVERT: P 176 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8133 (mm-30) REVERT: U 109 ARG cc_start: 0.8194 (mtt180) cc_final: 0.7691 (mtt180) outliers start: 77 outliers final: 29 residues processed: 395 average time/residue: 0.4839 time to fit residues: 227.3237 Evaluate side-chains 355 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 320 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain O residue 126 GLU Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 122 LYS Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 2 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 217 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 87 ASN D 142 ASN D 186 GLN D 194 ASN F 40 GLN H 79 ASN L 9 GLN ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN P 92 ASN P 197 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.080940 restraints weight = 39067.301| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.94 r_work: 0.2703 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.331 25126 Z= 0.210 Angle : 0.635 16.295 34518 Z= 0.291 Chirality : 0.043 0.239 3449 Planarity : 0.004 0.042 4304 Dihedral : 17.358 121.141 4767 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 4.19 % Allowed : 15.25 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.17), residues: 2576 helix: 1.86 (0.14), residues: 1334 sheet: 0.63 (0.37), residues: 188 loop : -0.17 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 122 TYR 0.024 0.001 TYR A 262 PHE 0.021 0.001 PHE B 246 TRP 0.017 0.001 TRP A 131 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (25090) covalent geometry : angle 0.63539 / 0.29 (34518) hydrogen bonds : bond 0.04663 / 3.16 ( 1182) hydrogen bonds : angle 4.62163 / 3.44 ( 3318) Misc. bond : bond 0.05960 / 3.22 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 327 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9009 (t70) cc_final: 0.8683 (t0) REVERT: B 83 GLU cc_start: 0.7988 (mp0) cc_final: 0.7644 (mp0) REVERT: V 29 ARG cc_start: 0.8444 (mmm160) cc_final: 0.8090 (mmm-85) REVERT: C 165 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9089 (mp) REVERT: C 378 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8634 (ttm170) REVERT: C 460 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7617 (tm) REVERT: D 11 LYS cc_start: 0.9008 (mtmm) cc_final: 0.8566 (ttmm) REVERT: D 16 ASP cc_start: 0.8947 (m-30) cc_final: 0.8302 (m-30) REVERT: D 20 ASP cc_start: 0.8637 (m-30) cc_final: 0.8340 (m-30) REVERT: D 100 ASP cc_start: 0.8749 (t70) cc_final: 0.8137 (t0) REVERT: D 308 ASP cc_start: 0.8512 (t0) cc_final: 0.8106 (t0) REVERT: E 75 GLN cc_start: 0.8913 (tt0) cc_final: 0.8650 (tt0) REVERT: I 26 ASN cc_start: 0.9025 (t0) cc_final: 0.8346 (t0) REVERT: O 158 ARG cc_start: 0.8762 (tpt90) cc_final: 0.8536 (tpt170) REVERT: P 64 ASN cc_start: 0.8426 (t0) cc_final: 0.7801 (t0) REVERT: P 107 GLU cc_start: 0.8129 (tt0) cc_final: 0.7918 (tm-30) REVERT: P 122 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8636 (ttmt) REVERT: P 176 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8107 (mm-30) REVERT: Z 52 PHE cc_start: 0.8797 (m-80) cc_final: 0.8388 (m-80) REVERT: U 109 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7691 (mtt180) REVERT: U 122 ARG cc_start: 0.8543 (tpp80) cc_final: 0.8083 (ttm-80) outliers start: 89 outliers final: 44 residues processed: 381 average time/residue: 0.5231 time to fit residues: 238.5129 Evaluate side-chains 360 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 118 VAL Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 84 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 87 ASN F 40 GLN H 79 ASN ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN P 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.081242 restraints weight = 38798.662| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.02 r_work: 0.2691 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.294 25126 Z= 0.164 Angle : 0.606 16.521 34518 Z= 0.278 Chirality : 0.042 0.373 3449 Planarity : 0.004 0.044 4304 Dihedral : 16.989 121.066 4767 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.63 % Allowed : 16.20 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.17), residues: 2576 helix: 1.89 (0.14), residues: 1334 sheet: 0.67 (0.37), residues: 188 loop : -0.16 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 122 TYR 0.021 0.001 TYR A 262 PHE 0.020 0.001 PHE B 246 TRP 0.019 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (25090) covalent geometry : angle 0.60646 / 0.28 (34518) hydrogen bonds : bond 0.04391 / 2.96 ( 1182) hydrogen bonds : angle 4.56235 / 3.39 ( 3318) Misc. bond : bond 0.05375 / 2.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 324 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8034 (pp20) cc_final: 0.7678 (pp20) REVERT: A 59 ASP cc_start: 0.8994 (t70) cc_final: 0.8726 (t0) REVERT: A 227 THR cc_start: 0.6894 (OUTLIER) cc_final: 0.6528 (t) REVERT: B 83 GLU cc_start: 0.7962 (mp0) cc_final: 0.7621 (mp0) REVERT: V 29 ARG cc_start: 0.8497 (mmm160) cc_final: 0.8167 (mmm-85) REVERT: C 165 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9096 (mp) REVERT: C 378 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8613 (ttm170) REVERT: C 460 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7674 (tm) REVERT: D 11 LYS cc_start: 0.9017 (mtmm) cc_final: 0.8571 (ttmm) REVERT: D 16 ASP cc_start: 0.8989 (m-30) cc_final: 0.8345 (m-30) REVERT: D 20 ASP cc_start: 0.8610 (m-30) cc_final: 0.8295 (m-30) REVERT: D 100 ASP cc_start: 0.8719 (t70) cc_final: 0.8102 (t0) REVERT: D 308 ASP cc_start: 0.8517 (t0) cc_final: 0.8076 (t0) REVERT: D 310 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8189 (pp20) REVERT: E 75 GLN cc_start: 0.8921 (tt0) cc_final: 0.8617 (tt0) REVERT: I 23 PHE cc_start: 0.9563 (OUTLIER) cc_final: 0.9179 (m-80) REVERT: I 26 ASN cc_start: 0.9047 (t0) cc_final: 0.8327 (t0) REVERT: P 64 ASN cc_start: 0.8452 (t0) cc_final: 0.7806 (t0) REVERT: P 98 GLU cc_start: 0.7807 (pm20) cc_final: 0.7606 (pm20) REVERT: P 107 GLU cc_start: 0.8148 (tt0) cc_final: 0.7934 (tm-30) REVERT: P 122 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8643 (ttmt) REVERT: P 214 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7701 (tp) REVERT: W 65 MET cc_start: 0.8032 (mmm) cc_final: 0.7769 (mtp) REVERT: U 109 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7698 (mtt180) REVERT: U 122 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8250 (ttm-80) outliers start: 77 outliers final: 45 residues processed: 372 average time/residue: 0.5302 time to fit residues: 235.7343 Evaluate side-chains 365 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 280 MET Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 122 LYS Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 118 VAL Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 198 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 59 optimal weight: 0.0010 chunk 86 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 ASN A 304 GLN B 87 ASN D 61 HIS D 186 GLN F 40 GLN H 79 ASN ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN P 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.079567 restraints weight = 39197.506| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.00 r_work: 0.2665 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.336 25126 Z= 0.215 Angle : 0.643 16.611 34518 Z= 0.295 Chirality : 0.043 0.323 3449 Planarity : 0.004 0.043 4304 Dihedral : 16.811 121.314 4766 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.19 % Allowed : 16.38 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.17), residues: 2576 helix: 1.82 (0.14), residues: 1334 sheet: 0.63 (0.38), residues: 190 loop : -0.21 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 458 TYR 0.022 0.001 TYR A 262 PHE 0.020 0.001 PHE B 246 TRP 0.025 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (25090) covalent geometry : angle 0.64284 / 0.29 (34518) hydrogen bonds : bond 0.04664 / 3.16 ( 1182) hydrogen bonds : angle 4.62316 / 3.43 ( 3318) Misc. bond : bond 0.06044 / 3.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 325 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8105 (pp20) cc_final: 0.7803 (pp20) REVERT: A 227 THR cc_start: 0.6863 (OUTLIER) cc_final: 0.6498 (t) REVERT: B 83 GLU cc_start: 0.8053 (mp0) cc_final: 0.7707 (mp0) REVERT: V 29 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8168 (mmm-85) REVERT: C 165 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9138 (mp) REVERT: C 378 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8619 (ttm170) REVERT: C 460 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7683 (tm) REVERT: D 11 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8592 (ttmm) REVERT: D 16 ASP cc_start: 0.9001 (m-30) cc_final: 0.8357 (m-30) REVERT: D 20 ASP cc_start: 0.8617 (m-30) cc_final: 0.8308 (m-30) REVERT: D 100 ASP cc_start: 0.8790 (t70) cc_final: 0.8233 (t0) REVERT: D 308 ASP cc_start: 0.8556 (t0) cc_final: 0.8145 (t0) REVERT: D 310 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8221 (pp20) REVERT: E 75 GLN cc_start: 0.8966 (tt0) cc_final: 0.8698 (tt0) REVERT: I 26 ASN cc_start: 0.9048 (t0) cc_final: 0.8341 (t0) REVERT: P 64 ASN cc_start: 0.8496 (t0) cc_final: 0.7902 (t0) REVERT: P 122 LYS cc_start: 0.8947 (ptmt) cc_final: 0.8643 (ttmt) REVERT: P 214 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7766 (tp) REVERT: W 65 MET cc_start: 0.8037 (mmm) cc_final: 0.7782 (mtp) REVERT: Z 10 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8214 (tm) REVERT: U 109 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7731 (mtt180) outliers start: 89 outliers final: 49 residues processed: 379 average time/residue: 0.5150 time to fit residues: 234.7669 Evaluate side-chains 369 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 118 VAL Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 115 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 217 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN F 40 GLN H 79 ASN ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN P 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.081667 restraints weight = 38583.469| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.01 r_work: 0.2702 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.268 25126 Z= 0.145 Angle : 0.602 16.805 34518 Z= 0.276 Chirality : 0.041 0.280 3449 Planarity : 0.004 0.043 4304 Dihedral : 16.424 120.645 4766 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.00 % Allowed : 16.76 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.17), residues: 2576 helix: 1.91 (0.14), residues: 1331 sheet: 0.64 (0.38), residues: 190 loop : -0.14 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 122 TYR 0.020 0.001 TYR A 262 PHE 0.018 0.001 PHE B 246 TRP 0.027 0.001 TRP Z 33 HIS 0.005 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (25090) covalent geometry : angle 0.60153 / 0.28 (34518) hydrogen bonds : bond 0.04257 / 2.88 ( 1182) hydrogen bonds : angle 4.53904 / 3.37 ( 3318) Misc. bond : bond 0.04956 / 2.74 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 335 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8079 (pp20) cc_final: 0.7766 (pp20) REVERT: A 227 THR cc_start: 0.6949 (OUTLIER) cc_final: 0.6494 (t) REVERT: B 83 GLU cc_start: 0.8008 (mp0) cc_final: 0.7650 (mp0) REVERT: B 440 ASP cc_start: 0.8919 (p0) cc_final: 0.8609 (p0) REVERT: C 165 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9099 (mp) REVERT: C 378 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8597 (ttm170) REVERT: C 447 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9236 (mm) REVERT: C 460 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7715 (tm) REVERT: D 11 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8584 (ttmm) REVERT: D 16 ASP cc_start: 0.8965 (m-30) cc_final: 0.8311 (m-30) REVERT: D 20 ASP cc_start: 0.8599 (m-30) cc_final: 0.8279 (m-30) REVERT: D 100 ASP cc_start: 0.8733 (t70) cc_final: 0.8186 (t0) REVERT: D 308 ASP cc_start: 0.8556 (t0) cc_final: 0.8136 (t0) REVERT: D 310 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8208 (pp20) REVERT: E 75 GLN cc_start: 0.8945 (tt0) cc_final: 0.8652 (tt0) REVERT: I 26 ASN cc_start: 0.9053 (t0) cc_final: 0.8317 (t0) REVERT: O 102 TYR cc_start: 0.8354 (m-80) cc_final: 0.8150 (m-80) REVERT: O 158 ARG cc_start: 0.8797 (tpt170) cc_final: 0.8577 (tpt170) REVERT: P 64 ASN cc_start: 0.8492 (t0) cc_final: 0.7893 (t0) REVERT: P 122 LYS cc_start: 0.8959 (ptmt) cc_final: 0.8655 (ttmt) REVERT: P 214 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7738 (tp) REVERT: W 65 MET cc_start: 0.8043 (mmm) cc_final: 0.7810 (mtp) REVERT: Z 52 PHE cc_start: 0.8799 (m-80) cc_final: 0.8419 (m-80) REVERT: U 102 ARG cc_start: 0.7559 (tpm-80) cc_final: 0.7341 (tpm-80) REVERT: U 109 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7715 (mtt180) outliers start: 85 outliers final: 50 residues processed: 387 average time/residue: 0.5175 time to fit residues: 240.1743 Evaluate side-chains 377 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 280 MET Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 118 VAL Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 208 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 247 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 195 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 87 ASN D 129 GLN F 40 GLN H 79 ASN O 68 GLN ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN P 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.081603 restraints weight = 38739.360| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.01 r_work: 0.2703 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.268 25126 Z= 0.154 Angle : 0.606 16.712 34518 Z= 0.280 Chirality : 0.042 0.275 3449 Planarity : 0.004 0.043 4304 Dihedral : 16.265 120.542 4766 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.48 % Allowed : 17.80 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.17), residues: 2576 helix: 1.92 (0.14), residues: 1330 sheet: 0.71 (0.38), residues: 190 loop : -0.13 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 458 TYR 0.019 0.001 TYR A 262 PHE 0.018 0.001 PHE B 246 TRP 0.029 0.001 TRP Z 33 HIS 0.006 0.001 HIS D 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (25090) covalent geometry : angle 0.60587 / 0.28 (34518) hydrogen bonds : bond 0.04279 / 2.89 ( 1182) hydrogen bonds : angle 4.54038 / 3.37 ( 3318) Misc. bond : bond 0.04939 / 2.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 325 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8099 (pp20) cc_final: 0.7782 (pp20) REVERT: A 227 THR cc_start: 0.6891 (OUTLIER) cc_final: 0.6503 (t) REVERT: B 83 GLU cc_start: 0.8038 (mp0) cc_final: 0.7687 (mp0) REVERT: B 246 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.9073 (p90) REVERT: C 165 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9100 (mp) REVERT: C 447 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9231 (mm) REVERT: C 458 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8175 (ttp-110) REVERT: C 460 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7709 (tm) REVERT: D 11 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8591 (ttmm) REVERT: D 16 ASP cc_start: 0.8973 (m-30) cc_final: 0.8318 (m-30) REVERT: D 20 ASP cc_start: 0.8596 (m-30) cc_final: 0.8275 (m-30) REVERT: D 100 ASP cc_start: 0.8737 (t70) cc_final: 0.8268 (t0) REVERT: D 308 ASP cc_start: 0.8557 (t0) cc_final: 0.8142 (t0) REVERT: D 310 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8216 (pp20) REVERT: E 75 GLN cc_start: 0.8954 (tt0) cc_final: 0.8690 (tt0) REVERT: I 26 ASN cc_start: 0.9026 (t0) cc_final: 0.8281 (t0) REVERT: O 102 TYR cc_start: 0.8353 (m-80) cc_final: 0.8147 (m-80) REVERT: O 158 ARG cc_start: 0.8808 (tpt170) cc_final: 0.8537 (tpt170) REVERT: P 64 ASN cc_start: 0.8494 (t0) cc_final: 0.7884 (t0) REVERT: P 122 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8665 (ttmt) REVERT: P 214 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7712 (tp) REVERT: W 65 MET cc_start: 0.8022 (mmm) cc_final: 0.7798 (mtp) REVERT: W 103 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.4823 (mt) REVERT: Z 52 PHE cc_start: 0.8794 (m-80) cc_final: 0.8411 (m-80) REVERT: U 109 ARG cc_start: 0.8262 (mtt180) cc_final: 0.7740 (mtt180) outliers start: 74 outliers final: 48 residues processed: 372 average time/residue: 0.5354 time to fit residues: 237.6855 Evaluate side-chains 374 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 317 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 280 MET Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 122 LYS Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 118 VAL Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN V 32 ASN D 142 ASN F 40 GLN H 79 ASN O 68 GLN ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN P 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.078626 restraints weight = 39305.294| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.00 r_work: 0.2652 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.345 25126 Z= 0.259 Angle : 0.680 17.232 34518 Z= 0.315 Chirality : 0.045 0.283 3449 Planarity : 0.005 0.044 4304 Dihedral : 16.580 121.379 4766 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.58 % Allowed : 17.98 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2576 helix: 1.75 (0.14), residues: 1335 sheet: 0.65 (0.38), residues: 190 loop : -0.19 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 122 TYR 0.022 0.002 TYR A 262 PHE 0.020 0.002 PHE B 246 TRP 0.038 0.002 TRP Z 33 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (25090) covalent geometry : angle 0.68042 / 0.31 (34518) hydrogen bonds : bond 0.04893 / 3.32 ( 1182) hydrogen bonds : angle 4.70846 / 3.48 ( 3318) Misc. bond : bond 0.06211 / 3.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 327 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8133 (pp20) cc_final: 0.7820 (pp20) REVERT: A 227 THR cc_start: 0.7000 (OUTLIER) cc_final: 0.6535 (t) REVERT: B 83 GLU cc_start: 0.8072 (mp0) cc_final: 0.7701 (mp0) REVERT: B 440 ASP cc_start: 0.8916 (p0) cc_final: 0.8607 (p0) REVERT: C 165 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9154 (mp) REVERT: C 378 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8608 (ttm170) REVERT: C 447 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9262 (mm) REVERT: C 460 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7692 (tm) REVERT: D 11 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8587 (ttmm) REVERT: D 16 ASP cc_start: 0.9013 (m-30) cc_final: 0.8369 (m-30) REVERT: D 20 ASP cc_start: 0.8620 (m-30) cc_final: 0.8291 (m-30) REVERT: D 100 ASP cc_start: 0.8834 (t70) cc_final: 0.8275 (t0) REVERT: D 308 ASP cc_start: 0.8562 (t0) cc_final: 0.8152 (t0) REVERT: D 310 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8215 (pp20) REVERT: E 75 GLN cc_start: 0.8959 (tt0) cc_final: 0.8682 (tt0) REVERT: I 26 ASN cc_start: 0.9013 (t0) cc_final: 0.8293 (t0) REVERT: M 23 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9034 (mm) REVERT: O 102 TYR cc_start: 0.8378 (m-80) cc_final: 0.8085 (m-80) REVERT: O 158 ARG cc_start: 0.8846 (tpt170) cc_final: 0.8604 (tpt170) REVERT: P 64 ASN cc_start: 0.8507 (t0) cc_final: 0.7919 (t0) REVERT: P 122 LYS cc_start: 0.8965 (ptmt) cc_final: 0.8662 (ttmt) REVERT: P 214 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7796 (tp) REVERT: T 28 ARG cc_start: 0.7711 (mmm160) cc_final: 0.7457 (mmm160) REVERT: W 65 MET cc_start: 0.8058 (mmm) cc_final: 0.7819 (mtp) REVERT: U 109 ARG cc_start: 0.8288 (mtt180) cc_final: 0.7776 (mtt180) outliers start: 76 outliers final: 46 residues processed: 373 average time/residue: 0.5276 time to fit residues: 235.2414 Evaluate side-chains 371 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 118 VAL Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 163 optimal weight: 0.0770 chunk 169 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN V 32 ASN D 129 GLN H 79 ASN O 68 GLN O 82 ASN O 297 GLN P 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.081772 restraints weight = 38988.877| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.99 r_work: 0.2706 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.255 25126 Z= 0.138 Angle : 0.615 17.315 34518 Z= 0.286 Chirality : 0.042 0.274 3449 Planarity : 0.004 0.049 4304 Dihedral : 16.254 120.523 4764 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.45 % Allowed : 19.16 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.17), residues: 2576 helix: 1.87 (0.14), residues: 1330 sheet: 0.63 (0.38), residues: 190 loop : -0.15 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG U 102 TYR 0.019 0.001 TYR O 295 PHE 0.017 0.001 PHE B 246 TRP 0.039 0.001 TRP Z 33 HIS 0.006 0.001 HIS D 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (25090) covalent geometry : angle 0.61547 / 0.29 (34518) hydrogen bonds : bond 0.04292 / 2.90 ( 1182) hydrogen bonds : angle 4.58079 / 3.39 ( 3318) Misc. bond : bond 0.04829 / 2.72 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8079 (pp20) cc_final: 0.7790 (pp20) REVERT: A 227 THR cc_start: 0.6987 (OUTLIER) cc_final: 0.6582 (t) REVERT: B 83 GLU cc_start: 0.8001 (mp0) cc_final: 0.7622 (mp0) REVERT: C 165 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9110 (mp) REVERT: C 378 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8571 (ttm170) REVERT: C 447 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9238 (mm) REVERT: C 460 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7700 (tm) REVERT: D 11 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8603 (ttmm) REVERT: D 16 ASP cc_start: 0.8954 (m-30) cc_final: 0.8296 (m-30) REVERT: D 20 ASP cc_start: 0.8557 (m-30) cc_final: 0.8222 (m-30) REVERT: D 100 ASP cc_start: 0.8727 (t70) cc_final: 0.8263 (t0) REVERT: D 308 ASP cc_start: 0.8544 (t0) cc_final: 0.8134 (t0) REVERT: D 310 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8205 (pp20) REVERT: E 75 GLN cc_start: 0.8945 (tt0) cc_final: 0.8689 (tt0) REVERT: I 26 ASN cc_start: 0.9014 (t0) cc_final: 0.8270 (t0) REVERT: O 102 TYR cc_start: 0.8313 (m-80) cc_final: 0.8084 (m-80) REVERT: O 158 ARG cc_start: 0.8827 (tpt170) cc_final: 0.8618 (tmt170) REVERT: P 64 ASN cc_start: 0.8508 (t0) cc_final: 0.7916 (t0) REVERT: P 122 LYS cc_start: 0.8947 (ptmt) cc_final: 0.8648 (ttmt) REVERT: P 203 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.6956 (mm110) REVERT: P 214 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7680 (tp) REVERT: W 65 MET cc_start: 0.8030 (mmm) cc_final: 0.7795 (mtp) REVERT: U 109 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7712 (mtt180) outliers start: 52 outliers final: 39 residues processed: 356 average time/residue: 0.5475 time to fit residues: 232.2510 Evaluate side-chains 364 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 222 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 203 GLN Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain U residue 118 VAL Chi-restraints excluded: chain U residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 91 optimal weight: 0.0040 chunk 162 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 149 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 overall best weight: 0.7734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN C 193 ASN H 79 ASN O 68 GLN O 238 GLN O 297 GLN P 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.085245 restraints weight = 38554.759| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.00 r_work: 0.2765 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.178 25126 Z= 0.110 Angle : 0.581 16.756 34518 Z= 0.270 Chirality : 0.040 0.269 3449 Planarity : 0.004 0.055 4304 Dihedral : 15.662 119.663 4764 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.21 % Allowed : 19.63 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.17), residues: 2576 helix: 1.99 (0.14), residues: 1337 sheet: 0.83 (0.38), residues: 184 loop : -0.11 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 458 TYR 0.020 0.001 TYR O 295 PHE 0.016 0.001 PHE B 246 TRP 0.034 0.001 TRP Z 33 HIS 0.005 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (25090) covalent geometry : angle 0.58105 / 0.27 (34518) hydrogen bonds : bond 0.03799 / 2.56 ( 1182) hydrogen bonds : angle 4.42440 / 3.27 ( 3318) Misc. bond : bond 0.03604 / 2.12 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7756.85 seconds wall clock time: 133 minutes 28.69 seconds (8008.69 seconds total)