Starting phenix.real_space_refine on Fri Feb 6 09:06:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gnw_51482/02_2026/9gnw_51482.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gnw_51482/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gnw_51482/02_2026/9gnw_51482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gnw_51482/02_2026/9gnw_51482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gnw_51482/02_2026/9gnw_51482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gnw_51482/02_2026/9gnw_51482.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 464 Unusual residues: {' CL': 2, ' NA': 1, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'FE2': 1, 'LHG': 1, 'LMG': 2, 'OEX': 1, 'PHO': 1, 'SQD': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} 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: 5.33, per 1000 atoms: 0.22 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: 2.43 Conformation dependent library (CDL) restraints added in 725.0 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: 0.61 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: 4.02 Time building geometry restraints manager: 2.98 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 - 31.99: 12966 31.99 - 63.98: 726 63.98 - 95.97: 100 95.97 - 127.96: 70 127.96 - 159.95: 1 Dihedral angle restraints: 13863 sinusoidal: 6479 harmonic: 7384 Sorted by residual: dihedral pdb=" C21 3PH B 522 " pdb=" C2 3PH B 522 " pdb=" O21 3PH B 522 " pdb=" C3 3PH B 522 " ideal model delta sinusoidal sigma weight residual 147.58 -12.37 159.95 1 3.00e+01 1.11e-03 2.07e+01 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 ... (remaining 13860 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 20.380 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 20.685 159.955 9163 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 covalent geometry : bond 0.02046 (25090) covalent geometry : angle 1.49240 (34518) hydrogen bonds : bond 0.13100 ( 1182) hydrogen bonds : angle 5.80670 ( 3318) Misc. bond : bond 0.34526 ( 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 : 0.880 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: 0.5591 time to fit residues: 351.2867 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 : 0.830 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3216 r_free = 0.3216 target = 0.105562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.079684 restraints weight = 38981.639| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.96 r_work: 0.2714 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1461 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= 0.191 Angle : 0.694 16.330 34518 Z= 0.311 Chirality : 0.044 0.279 3449 Planarity : 0.005 0.063 4304 Dihedral : 20.667 155.446 4795 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 4.47 % Allowed : 12.99 % Favored : 82.53 % 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 0.032 0.001 TYR A 262 PHE 0.020 0.001 PHE B 246 TRP 0.021 0.001 TRP A 131 HIS 0.007 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00434 (25090) covalent geometry : angle 0.69429 (34518) hydrogen bonds : bond 0.04997 ( 1182) hydrogen bonds : angle 4.85868 ( 3318) Misc. bond : bond 0.05942 ( 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 442 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 347 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9003 (t70) cc_final: 0.8669 (t0) REVERT: B 246 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.9019 (p90) REVERT: C 162 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8715 (tt) REVERT: C 165 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9146 (mp) REVERT: D 11 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8560 (ttmm) REVERT: D 14 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.8239 (p-90) REVERT: D 16 ASP cc_start: 0.8941 (m-30) cc_final: 0.8327 (m-30) REVERT: D 20 ASP cc_start: 0.8508 (m-30) cc_final: 0.8276 (m-30) REVERT: D 100 ASP cc_start: 0.8697 (t70) cc_final: 0.8165 (t0) REVERT: D 302 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8563 (mm-30) REVERT: D 308 ASP cc_start: 0.8657 (t0) cc_final: 0.8323 (t0) REVERT: E 75 GLN cc_start: 0.8964 (tt0) cc_final: 0.8697 (tt0) REVERT: H 84 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8178 (mt) REVERT: I 26 ASN cc_start: 0.8986 (t0) cc_final: 0.8344 (t0) REVERT: M 5 ILE cc_start: 0.8940 (tp) cc_final: 0.8651 (mm) REVERT: O 141 ASP cc_start: 0.8175 (p0) cc_final: 0.7954 (p0) REVERT: P 64 ASN cc_start: 0.8239 (t0) cc_final: 0.7986 (t0) REVERT: P 107 GLU cc_start: 0.8113 (tt0) cc_final: 0.7878 (tm-30) REVERT: P 122 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8616 (ttmt) REVERT: P 137 PHE cc_start: 0.8578 (t80) cc_final: 0.8378 (t80) REVERT: P 176 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8150 (mm-30) REVERT: U 109 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7753 (mtt180) outliers start: 95 outliers final: 31 residues processed: 400 average time/residue: 0.5374 time to fit residues: 255.2206 Evaluate side-chains 363 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 326 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 184 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 151 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 chunk 128 optimal weight: 0.0270 chunk 243 optimal weight: 0.9990 overall best weight: 1.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3261 r_free = 0.3261 target = 0.109822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.084249 restraints weight = 38735.869| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.01 r_work: 0.2743 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.252 25126 Z= 0.117 Angle : 0.598 15.734 34518 Z= 0.270 Chirality : 0.041 0.233 3449 Planarity : 0.004 0.040 4304 Dihedral : 17.895 153.193 4781 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 3.20 % Allowed : 15.16 % Favored : 81.64 % 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: 1.59 (0.17), residues: 2576 helix: 2.03 (0.14), residues: 1325 sheet: 0.68 (0.37), residues: 189 loop : -0.08 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 102 TYR 0.025 0.001 TYR A 262 PHE 0.018 0.001 PHE B 246 TRP 0.018 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00254 (25090) covalent geometry : angle 0.59753 (34518) hydrogen bonds : bond 0.04136 ( 1182) hydrogen bonds : angle 4.55331 ( 3318) Misc. bond : bond 0.04642 ( 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 433 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 365 time to evaluate : 0.797 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: 0.8960 (t70) cc_final: 0.8694 (t0) REVERT: A 223 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7321 (tm) REVERT: B 83 GLU cc_start: 0.7862 (mp0) cc_final: 0.7560 (mp0) REVERT: V 29 ARG cc_start: 0.8465 (mmm160) cc_final: 0.8089 (mmm-85) REVERT: C 165 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9054 (mp) REVERT: C 460 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7676 (tm) REVERT: D 11 LYS cc_start: 0.9051 (mtmm) cc_final: 0.8578 (ttmm) REVERT: D 16 ASP cc_start: 0.8941 (m-30) cc_final: 0.8362 (m-30) REVERT: D 20 ASP cc_start: 0.8542 (m-30) cc_final: 0.8261 (m-30) REVERT: D 100 ASP cc_start: 0.8625 (t70) cc_final: 0.8035 (t0) REVERT: D 302 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8446 (mm-30) REVERT: D 308 ASP cc_start: 0.8581 (t0) cc_final: 0.7971 (t0) REVERT: D 310 GLU cc_start: 0.8629 (pm20) cc_final: 0.8387 (pp20) REVERT: E 75 GLN cc_start: 0.8951 (tt0) cc_final: 0.8664 (tt0) REVERT: H 84 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7961 (mt) REVERT: I 23 PHE cc_start: 0.9539 (OUTLIER) cc_final: 0.9251 (m-80) REVERT: I 26 ASN cc_start: 0.9001 (t0) cc_final: 0.8299 (t0) REVERT: K 18 PHE cc_start: 0.9427 (m-80) cc_final: 0.9220 (m-10) REVERT: K 23 ASP cc_start: 0.8305 (m-30) cc_final: 0.8086 (m-30) REVERT: O 231 LYS cc_start: 0.7655 (mttt) cc_final: 0.7445 (mmtt) REVERT: P 64 ASN cc_start: 0.8395 (t0) cc_final: 0.7756 (t0) REVERT: P 107 GLU cc_start: 0.8131 (tt0) cc_final: 0.7919 (tm-30) REVERT: P 122 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8632 (ttmt) REVERT: P 176 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8147 (mm-30) REVERT: P 239 ASP cc_start: 0.8785 (m-30) cc_final: 0.8564 (m-30) REVERT: U 109 ARG cc_start: 0.8192 (mtt180) cc_final: 0.7697 (mtt180) outliers start: 68 outliers final: 27 residues processed: 407 average time/residue: 0.5124 time to fit residues: 247.7571 Evaluate side-chains 354 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 321 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU 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 168 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 241 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 H residue 84 LEU 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 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: 2.9990 chunk 157 optimal weight: 0.4980 chunk 192 optimal weight: 6.9990 chunk 223 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 87 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.080176 restraints weight = 39041.746| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.01 r_work: 0.2677 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.329 25126 Z= 0.206 Angle : 0.633 16.204 34518 Z= 0.290 Chirality : 0.043 0.237 3449 Planarity : 0.004 0.042 4304 Dihedral : 17.426 153.616 4776 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 4.00 % Allowed : 15.58 % Favored : 80.41 % 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: 1.90 (0.14), residues: 1328 sheet: 0.69 (0.37), residues: 187 loop : -0.16 (0.20), residues: 1061 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 Z 33 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00477 (25090) covalent geometry : angle 0.63285 (34518) hydrogen bonds : bond 0.04632 ( 1182) hydrogen bonds : angle 4.60028 ( 3318) Misc. bond : bond 0.05921 ( 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 417 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 332 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8045 (pp20) cc_final: 0.7736 (pp20) REVERT: A 227 THR cc_start: 0.6724 (OUTLIER) cc_final: 0.6343 (t) REVERT: B 83 GLU cc_start: 0.8028 (mp0) cc_final: 0.7701 (mp0) REVERT: V 29 ARG cc_start: 0.8498 (mmm160) cc_final: 0.8151 (mmm-85) REVERT: C 165 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9131 (mp) REVERT: C 378 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8622 (ttm170) REVERT: C 460 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7686 (tm) REVERT: D 11 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8599 (ttmm) REVERT: D 16 ASP cc_start: 0.8986 (m-30) cc_final: 0.8373 (m-30) REVERT: D 20 ASP cc_start: 0.8596 (m-30) cc_final: 0.8310 (m-30) REVERT: D 100 ASP cc_start: 0.8744 (t70) cc_final: 0.8155 (t0) REVERT: D 308 ASP cc_start: 0.8679 (t0) cc_final: 0.8236 (t0) REVERT: E 75 GLN cc_start: 0.8970 (tt0) cc_final: 0.8709 (tt0) REVERT: H 84 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8085 (mt) REVERT: I 26 ASN cc_start: 0.9054 (t0) cc_final: 0.8372 (t0) REVERT: O 158 ARG cc_start: 0.8778 (tpt90) cc_final: 0.8552 (tpt170) REVERT: P 64 ASN cc_start: 0.8464 (t0) cc_final: 0.7855 (t0) REVERT: P 107 GLU cc_start: 0.8206 (tt0) cc_final: 0.7999 (tm-30) REVERT: P 122 LYS cc_start: 0.8937 (ptmt) cc_final: 0.8633 (ttmt) REVERT: Z 52 PHE cc_start: 0.8822 (m-80) cc_final: 0.8423 (m-80) REVERT: U 109 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7704 (mtt180) REVERT: U 122 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8226 (ttm-80) outliers start: 85 outliers final: 44 residues processed: 380 average time/residue: 0.5235 time to fit residues: 236.1239 Evaluate side-chains 363 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 314 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 241 GLU Chi-restraints excluded: chain D residue 294 ARG 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 H residue 84 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 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 W residue 103 LEU Chi-restraints excluded: chain Z residue 3 SER 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: 10.0000 chunk 71 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 87 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.081225 restraints weight = 38824.081| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.01 r_work: 0.2692 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.300 25126 Z= 0.169 Angle : 0.609 16.487 34518 Z= 0.279 Chirality : 0.042 0.368 3449 Planarity : 0.004 0.043 4304 Dihedral : 17.063 150.655 4776 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.63 % Allowed : 16.38 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.17), residues: 2576 helix: 1.89 (0.14), residues: 1335 sheet: 0.64 (0.37), residues: 189 loop : -0.16 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 265 TYR 0.021 0.001 TYR A 262 PHE 0.019 0.001 PHE B 246 TRP 0.020 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00391 (25090) covalent geometry : angle 0.60852 (34518) hydrogen bonds : bond 0.04391 ( 1182) hydrogen bonds : angle 4.54354 ( 3318) Misc. bond : bond 0.05465 ( 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 408 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 331 time to evaluate : 0.911 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: 0.8053 (pp20) cc_final: 0.7734 (pp20) REVERT: A 59 ASP cc_start: 0.8949 (t70) cc_final: 0.8730 (t0) REVERT: A 223 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.6670 (tm) REVERT: A 227 THR cc_start: 0.6807 (OUTLIER) cc_final: 0.6361 (t) REVERT: B 83 GLU cc_start: 0.7997 (mp0) cc_final: 0.7659 (mp0) REVERT: V 29 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8163 (mmm-85) REVERT: C 165 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9108 (mp) REVERT: C 378 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8597 (ttm170) REVERT: C 460 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7693 (tm) REVERT: D 11 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8586 (ttmm) REVERT: D 16 ASP cc_start: 0.8986 (m-30) cc_final: 0.8366 (m-30) REVERT: D 20 ASP cc_start: 0.8598 (m-30) cc_final: 0.8288 (m-30) REVERT: D 100 ASP cc_start: 0.8730 (t70) cc_final: 0.8137 (t0) REVERT: D 308 ASP cc_start: 0.8590 (t0) cc_final: 0.8274 (t0) REVERT: E 75 GLN cc_start: 0.8968 (tt0) cc_final: 0.8669 (tt0) REVERT: H 84 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8030 (mt) REVERT: I 26 ASN cc_start: 0.9067 (t0) cc_final: 0.8354 (t0) REVERT: M 5 ILE cc_start: 0.8953 (tp) cc_final: 0.8748 (tp) REVERT: P 64 ASN cc_start: 0.8492 (t0) cc_final: 0.7862 (t0) REVERT: P 122 LYS cc_start: 0.8955 (ptmt) cc_final: 0.8656 (ttmt) REVERT: P 214 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7760 (tp) REVERT: W 65 MET cc_start: 0.8056 (mmm) cc_final: 0.7801 (mtp) REVERT: Z 52 PHE cc_start: 0.8812 (m-80) cc_final: 0.8450 (m-80) REVERT: U 109 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7728 (mtt180) REVERT: U 122 ARG cc_start: 0.8578 (tpp80) cc_final: 0.8293 (ttm-80) outliers start: 77 outliers final: 45 residues processed: 376 average time/residue: 0.5745 time to fit residues: 255.6663 Evaluate side-chains 364 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 312 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 223 LEU 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 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 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 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 H residue 84 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 198 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 87 ASN D 142 ASN D 186 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.080405 restraints weight = 39118.198| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.01 r_work: 0.2680 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.311 25126 Z= 0.190 Angle : 0.626 16.503 34518 Z= 0.287 Chirality : 0.042 0.317 3449 Planarity : 0.004 0.043 4304 Dihedral : 16.721 147.594 4775 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.24 % Allowed : 16.81 % Favored : 78.95 % 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: 1.41 (0.17), residues: 2576 helix: 1.88 (0.14), residues: 1329 sheet: 0.58 (0.38), residues: 191 loop : -0.15 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 458 TYR 0.021 0.001 TYR A 262 PHE 0.019 0.001 PHE B 246 TRP 0.024 0.001 TRP Z 33 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00440 (25090) covalent geometry : angle 0.62588 (34518) hydrogen bonds : bond 0.04481 ( 1182) hydrogen bonds : angle 4.56676 ( 3318) Misc. bond : bond 0.05640 ( 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: 90 poor density : 324 time to evaluate : 0.917 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: 0.8088 (pp20) cc_final: 0.7751 (pp20) REVERT: A 59 ASP cc_start: 0.8992 (t70) cc_final: 0.8759 (t0) REVERT: A 227 THR cc_start: 0.6793 (OUTLIER) cc_final: 0.6513 (t) REVERT: B 83 GLU cc_start: 0.8036 (mp0) cc_final: 0.7685 (mp0) REVERT: V 29 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8159 (mmm-85) REVERT: C 165 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9135 (mp) REVERT: C 378 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8602 (ttm170) REVERT: C 460 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7688 (tm) REVERT: D 11 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8589 (ttmm) REVERT: D 16 ASP cc_start: 0.8992 (m-30) cc_final: 0.8357 (m-30) REVERT: D 20 ASP cc_start: 0.8618 (m-30) cc_final: 0.8318 (m-30) REVERT: D 100 ASP cc_start: 0.8759 (t70) cc_final: 0.8169 (t0) REVERT: D 308 ASP cc_start: 0.8577 (t0) cc_final: 0.8270 (t0) REVERT: E 75 GLN cc_start: 0.8972 (tt0) cc_final: 0.8668 (tt0) REVERT: H 84 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8050 (mt) REVERT: I 26 ASN cc_start: 0.9049 (t0) cc_final: 0.8334 (t0) REVERT: O 102 TYR cc_start: 0.8368 (m-80) cc_final: 0.8110 (m-80) REVERT: P 64 ASN cc_start: 0.8486 (t0) cc_final: 0.7861 (t0) REVERT: P 122 LYS cc_start: 0.8962 (ptmt) cc_final: 0.8659 (ttmt) REVERT: P 214 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7767 (tp) REVERT: W 65 MET cc_start: 0.8042 (mmm) cc_final: 0.7791 (mtp) REVERT: Z 52 PHE cc_start: 0.8817 (m-80) cc_final: 0.8447 (m-80) REVERT: U 109 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7746 (mtt180) outliers start: 90 outliers final: 51 residues processed: 380 average time/residue: 0.5237 time to fit residues: 237.0006 Evaluate side-chains 370 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 313 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 241 GLU Chi-restraints excluded: chain D residue 294 ARG 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 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 H residue 84 LEU 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 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 91 THR Chi-restraints excluded: chain Z residue 3 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 115 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 217 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN V 32 ASN D 129 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.080934 restraints weight = 38727.994| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.00 r_work: 0.2689 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.296 25126 Z= 0.172 Angle : 0.615 16.693 34518 Z= 0.283 Chirality : 0.042 0.292 3449 Planarity : 0.004 0.043 4304 Dihedral : 16.465 143.602 4775 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.81 % Allowed : 17.23 % Favored : 78.95 % 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: 1.92 (0.14), residues: 1324 sheet: 0.60 (0.37), residues: 190 loop : -0.14 (0.20), residues: 1062 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 0.019 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 covalent geometry : bond 0.00400 (25090) covalent geometry : angle 0.61471 (34518) hydrogen bonds : bond 0.04395 ( 1182) hydrogen bonds : angle 4.55939 ( 3318) Misc. bond : bond 0.05407 ( 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 408 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 327 time to evaluate : 0.663 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: 0.8086 (pp20) cc_final: 0.7750 (pp20) REVERT: A 59 ASP cc_start: 0.8994 (t70) cc_final: 0.8743 (t0) REVERT: A 227 THR cc_start: 0.6979 (OUTLIER) cc_final: 0.6614 (t) REVERT: B 83 GLU cc_start: 0.8039 (mp0) cc_final: 0.7685 (mp0) REVERT: B 246 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.9089 (p90) REVERT: C 165 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9106 (mp) REVERT: C 378 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8594 (ttm170) REVERT: C 460 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7711 (tm) REVERT: D 11 LYS cc_start: 0.8997 (mtmm) cc_final: 0.8596 (ttmm) REVERT: D 16 ASP cc_start: 0.8977 (m-30) cc_final: 0.8334 (m-30) REVERT: D 20 ASP cc_start: 0.8605 (m-30) cc_final: 0.8278 (m-30) REVERT: D 100 ASP cc_start: 0.8737 (t70) cc_final: 0.8147 (t0) REVERT: D 308 ASP cc_start: 0.8580 (t0) cc_final: 0.8272 (t0) REVERT: D 332 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8737 (mp10) REVERT: E 75 GLN cc_start: 0.8967 (tt0) cc_final: 0.8663 (tt0) REVERT: H 84 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8041 (mt) REVERT: I 26 ASN cc_start: 0.9028 (t0) cc_final: 0.8303 (t0) REVERT: O 158 ARG cc_start: 0.8810 (tpt170) cc_final: 0.8557 (tpt170) REVERT: P 64 ASN cc_start: 0.8494 (t0) cc_final: 0.7909 (t0) REVERT: P 122 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8660 (ttmt) REVERT: P 203 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.6911 (mm110) REVERT: P 214 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7759 (tp) REVERT: W 65 MET cc_start: 0.8051 (mmm) cc_final: 0.7841 (mtp) REVERT: Z 52 PHE cc_start: 0.8802 (m-80) cc_final: 0.8420 (m-80) REVERT: U 109 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7724 (mtt180) outliers start: 81 outliers final: 49 residues processed: 377 average time/residue: 0.4852 time to fit residues: 218.1457 Evaluate side-chains 372 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 313 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE 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 246 PHE 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 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 460 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 332 GLN 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 H residue 84 LEU 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 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 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 203 GLN 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 91 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 208 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 195 optimal weight: 0.0170 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 87 ASN F 40 GLN H 79 ASN O 82 ASN 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 = 0.3276 r_free = 0.3276 target = 0.110907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.085083 restraints weight = 38458.942| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.02 r_work: 0.2761 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.195 25126 Z= 0.108 Angle : 0.572 16.276 34518 Z= 0.265 Chirality : 0.040 0.269 3449 Planarity : 0.004 0.049 4304 Dihedral : 15.828 132.689 4775 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.82 % Allowed : 18.41 % Favored : 78.77 % 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: 1.60 (0.17), residues: 2576 helix: 2.03 (0.14), residues: 1330 sheet: 0.68 (0.38), residues: 189 loop : -0.08 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 458 TYR 0.019 0.001 TYR O 295 PHE 0.016 0.001 PHE B 246 TRP 0.031 0.001 TRP Z 33 HIS 0.005 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00238 (25090) covalent geometry : angle 0.57184 (34518) hydrogen bonds : bond 0.03827 ( 1182) hydrogen bonds : angle 4.42085 ( 3318) Misc. bond : bond 0.03850 ( 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 429 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 369 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8055 (pp20) cc_final: 0.7734 (pp20) REVERT: A 59 ASP cc_start: 0.8941 (t70) cc_final: 0.8715 (t0) REVERT: A 227 THR cc_start: 0.6993 (OUTLIER) cc_final: 0.6597 (t) REVERT: B 83 GLU cc_start: 0.7936 (mp0) cc_final: 0.7584 (mp0) REVERT: C 378 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8551 (ttm170) REVERT: C 448 ASP cc_start: 0.8979 (t0) cc_final: 0.8718 (t0) REVERT: C 460 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7764 (tm) REVERT: D 11 LYS cc_start: 0.9020 (mtmm) cc_final: 0.8623 (ttmm) REVERT: D 16 ASP cc_start: 0.8960 (m-30) cc_final: 0.8334 (m-30) REVERT: D 20 ASP cc_start: 0.8564 (m-30) cc_final: 0.8253 (m-30) REVERT: D 100 ASP cc_start: 0.8658 (t70) cc_final: 0.8089 (t0) REVERT: D 302 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8160 (mm-30) REVERT: D 308 ASP cc_start: 0.8553 (t0) cc_final: 0.8246 (t0) REVERT: E 75 GLN cc_start: 0.8935 (tt0) cc_final: 0.8704 (tt0) REVERT: H 84 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7980 (mt) REVERT: I 26 ASN cc_start: 0.9002 (t0) cc_final: 0.8239 (t0) REVERT: J 10 ILE cc_start: 0.9103 (mm) cc_final: 0.8883 (mp) REVERT: M 23 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8990 (mm) REVERT: O 158 ARG cc_start: 0.8811 (tpt170) cc_final: 0.8580 (tpt170) REVERT: P 64 ASN cc_start: 0.8552 (t0) cc_final: 0.7912 (t0) REVERT: P 122 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8629 (ttmt) REVERT: P 214 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7576 (tp) REVERT: P 239 ASP cc_start: 0.8779 (m-30) cc_final: 0.8499 (m-30) REVERT: W 103 LEU cc_start: 0.5327 (OUTLIER) cc_final: 0.4713 (mt) REVERT: Z 52 PHE cc_start: 0.8767 (m-80) cc_final: 0.8340 (m-80) REVERT: U 109 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7695 (mtt180) outliers start: 60 outliers final: 33 residues processed: 405 average time/residue: 0.5010 time to fit residues: 242.7142 Evaluate side-chains 375 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 334 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE 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 332 SER Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 287 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 241 GLU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 22 ILE 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 H residue 84 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain M residue 23 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 P residue 72 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 87 ASN V 32 ASN D 194 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.081422 restraints weight = 39076.032| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.02 r_work: 0.2700 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.281 25126 Z= 0.174 Angle : 0.619 16.452 34518 Z= 0.287 Chirality : 0.042 0.270 3449 Planarity : 0.004 0.044 4304 Dihedral : 15.879 126.156 4775 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.45 % Allowed : 19.63 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.17), residues: 2576 helix: 2.00 (0.14), residues: 1325 sheet: 0.78 (0.38), residues: 178 loop : -0.09 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 458 TYR 0.020 0.001 TYR A 262 PHE 0.020 0.001 PHE B 246 TRP 0.036 0.001 TRP Z 33 HIS 0.005 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00405 (25090) covalent geometry : angle 0.61920 (34518) hydrogen bonds : bond 0.04330 ( 1182) hydrogen bonds : angle 4.51736 ( 3318) Misc. bond : bond 0.05140 ( 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 381 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 329 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8092 (pp20) cc_final: 0.7746 (pp20) REVERT: A 59 ASP cc_start: 0.9010 (t70) cc_final: 0.8775 (t0) REVERT: A 227 THR cc_start: 0.7054 (OUTLIER) cc_final: 0.6613 (t) REVERT: B 83 GLU cc_start: 0.8018 (mp0) cc_final: 0.7657 (mp0) REVERT: C 165 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9053 (mp) REVERT: C 448 ASP cc_start: 0.8940 (t0) cc_final: 0.8695 (t0) REVERT: C 460 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7698 (tm) REVERT: D 11 LYS cc_start: 0.8990 (mtmm) cc_final: 0.8582 (ttmm) REVERT: D 16 ASP cc_start: 0.8975 (m-30) cc_final: 0.8347 (m-30) REVERT: D 20 ASP cc_start: 0.8602 (m-30) cc_final: 0.8278 (m-30) REVERT: D 100 ASP cc_start: 0.8729 (t70) cc_final: 0.8182 (t0) REVERT: D 308 ASP cc_start: 0.8563 (t0) cc_final: 0.8269 (t0) REVERT: E 75 GLN cc_start: 0.8959 (tt0) cc_final: 0.8689 (tt0) REVERT: H 84 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8088 (mt) REVERT: I 26 ASN cc_start: 0.8994 (t0) cc_final: 0.8241 (t0) REVERT: J 27 LEU cc_start: 0.8966 (tp) cc_final: 0.8649 (mm) REVERT: M 23 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9018 (mm) REVERT: O 158 ARG cc_start: 0.8817 (tpt170) cc_final: 0.8593 (tmt170) REVERT: P 64 ASN cc_start: 0.8528 (t0) cc_final: 0.7928 (t0) REVERT: P 122 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8615 (tppt) REVERT: P 214 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7635 (tp) REVERT: P 239 ASP cc_start: 0.8817 (m-30) cc_final: 0.8512 (m-30) REVERT: W 103 LEU cc_start: 0.5457 (OUTLIER) cc_final: 0.5160 (mt) REVERT: Z 52 PHE cc_start: 0.8801 (m-80) cc_final: 0.8417 (m-80) REVERT: U 109 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7727 (mtt180) outliers start: 52 outliers final: 34 residues processed: 360 average time/residue: 0.5120 time to fit residues: 219.1087 Evaluate side-chains 363 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 321 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 329 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain V residue 32 ASN 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 398 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 22 ILE 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 H residue 84 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 42 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN V 32 ASN H 79 ASN O 68 GLN ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3259 r_free = 0.3259 target = 0.109657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.083661 restraints weight = 38898.542| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.03 r_work: 0.2736 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.228 25126 Z= 0.122 Angle : 0.589 16.876 34518 Z= 0.275 Chirality : 0.041 0.270 3449 Planarity : 0.004 0.044 4304 Dihedral : 15.629 119.617 4775 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.21 % Allowed : 20.10 % Favored : 77.68 % 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: 1.59 (0.17), residues: 2576 helix: 2.01 (0.14), residues: 1332 sheet: 0.94 (0.39), residues: 171 loop : -0.11 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 458 TYR 0.020 0.001 TYR O 295 PHE 0.021 0.001 PHE B 246 TRP 0.040 0.001 TRP Z 33 HIS 0.005 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00275 (25090) covalent geometry : angle 0.58864 (34518) hydrogen bonds : bond 0.04022 ( 1182) hydrogen bonds : angle 4.45554 ( 3318) Misc. bond : bond 0.04374 ( 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 388 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 341 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8073 (pp20) cc_final: 0.7724 (pp20) REVERT: A 59 ASP cc_start: 0.8959 (t70) cc_final: 0.8727 (t0) REVERT: A 227 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6623 (t) REVERT: B 83 GLU cc_start: 0.7954 (mp0) cc_final: 0.7597 (mp0) REVERT: B 440 ASP cc_start: 0.8908 (p0) cc_final: 0.8588 (p0) REVERT: C 336 GLU cc_start: 0.9250 (mp0) cc_final: 0.8937 (mp0) REVERT: C 448 ASP cc_start: 0.8894 (t0) cc_final: 0.8661 (t0) REVERT: C 460 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7708 (tm) REVERT: D 11 LYS cc_start: 0.8993 (mtmm) cc_final: 0.8601 (ttmm) REVERT: D 16 ASP cc_start: 0.8948 (m-30) cc_final: 0.8318 (m-30) REVERT: D 20 ASP cc_start: 0.8571 (m-30) cc_final: 0.8239 (m-30) REVERT: D 100 ASP cc_start: 0.8684 (t70) cc_final: 0.8111 (t0) REVERT: D 308 ASP cc_start: 0.8572 (t0) cc_final: 0.8289 (t0) REVERT: E 75 GLN cc_start: 0.8941 (tt0) cc_final: 0.8636 (tt0) REVERT: H 84 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8047 (mt) REVERT: I 26 ASN cc_start: 0.8978 (t0) cc_final: 0.8208 (t0) REVERT: J 10 ILE cc_start: 0.9124 (mm) cc_final: 0.8903 (mp) REVERT: L 10 VAL cc_start: 0.9282 (t) cc_final: 0.8947 (m) REVERT: M 23 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8998 (mm) REVERT: O 158 ARG cc_start: 0.8815 (tpt170) cc_final: 0.8570 (tpt170) REVERT: P 64 ASN cc_start: 0.8557 (t0) cc_final: 0.7965 (t0) REVERT: P 122 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8625 (tppt) REVERT: P 214 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7610 (tp) REVERT: P 239 ASP cc_start: 0.8810 (m-30) cc_final: 0.8516 (m-30) REVERT: Z 52 PHE cc_start: 0.8774 (m-80) cc_final: 0.8353 (m-80) REVERT: U 109 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7701 (mtt180) outliers start: 47 outliers final: 37 residues processed: 370 average time/residue: 0.4965 time to fit residues: 219.1703 Evaluate side-chains 373 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 330 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE 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 298 VAL 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 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 150 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 22 ILE 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 H residue 84 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 42 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 91 optimal weight: 0.6980 chunk 162 optimal weight: 0.0770 chunk 38 optimal weight: 0.1980 chunk 149 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN C 193 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.086704 restraints weight = 38565.253| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.01 r_work: 0.2792 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 25126 Z= 0.105 Angle : 0.570 16.602 34518 Z= 0.266 Chirality : 0.040 0.271 3449 Planarity : 0.004 0.045 4304 Dihedral : 15.073 119.156 4773 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 2.17 % Allowed : 20.29 % Favored : 77.54 % 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: 1.67 (0.17), residues: 2576 helix: 2.09 (0.14), residues: 1331 sheet: 0.88 (0.38), residues: 178 loop : -0.06 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG U 102 TYR 0.021 0.001 TYR O 295 PHE 0.020 0.001 PHE B 246 TRP 0.040 0.001 TRP Z 33 HIS 0.005 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00230 (25090) covalent geometry : angle 0.56974 (34518) hydrogen bonds : bond 0.03705 ( 1182) hydrogen bonds : angle 4.35652 ( 3318) Misc. bond : bond 0.03523 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7756.19 seconds wall clock time: 133 minutes 6.77 seconds (7986.77 seconds total)