Starting phenix.real_space_refine on Fri Sep 19 03:04:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2e_47449/09_2025/9e2e_47449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2e_47449/09_2025/9e2e_47449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e2e_47449/09_2025/9e2e_47449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2e_47449/09_2025/9e2e_47449.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2e_47449/09_2025/9e2e_47449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2e_47449/09_2025/9e2e_47449.cif" } resolution = 4.0 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= 0.168 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 136 5.16 5 C 14362 2.51 5 N 3908 2.21 5 O 4500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22924 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "E" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "F" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 447 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'TRANS': 54} Chain: "H" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 447 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'TRANS': 54} Chain: "I" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 560 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "J" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 560 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "K" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 670 Classifications: {'peptide': 77} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 72} Chain: "L" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 447 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'TRANS': 54} Chain: "M" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 447 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'TRANS': 54} Chain: "N" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 560 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "O" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 560 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "P" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 670 Classifications: {'peptide': 77} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.00, per 1000 atoms: 0.22 Number of scatterers: 22924 At special positions: 0 Unit cell: (107.124, 115.26, 223.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 12 15.00 Mg 6 11.99 O 4500 8.00 N 3908 7.00 C 14362 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 923.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5412 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 35 sheets defined 58.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.785A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 59' Processing helix chain 'A' and resid 60 through 63 removed outlier: 5.605A pdb=" N GLY A 63 " --> pdb=" O SER A 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 60 through 63' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.992A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.047A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.834A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 4.003A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.822A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.706A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.821A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.506A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.502A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.730A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.301A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.690A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.807A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.866A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.143A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.021A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.505A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.933A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.521A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.831A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.839A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.547A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.755A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.870A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.928A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.781A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.580A pdb=" N ARG C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.680A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.668A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 273 through 285 removed outlier: 4.177A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.109A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.723A pdb=" N PHE C 352 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.586A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.558A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.659A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.150A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.553A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 204 through 217 removed outlier: 3.990A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.543A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.695A pdb=" N ARG D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 257' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.809A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.507A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.577A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.918A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 370 removed outlier: 3.851A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 370' Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.594A pdb=" N SER E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.749A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.780A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.930A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.898A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 217 removed outlier: 4.156A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.856A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 296 removed outlier: 3.570A pdb=" N LEU E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 removed outlier: 4.189A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.536A pdb=" N PHE E 352 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 370 removed outlier: 3.584A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 370' Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.682A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.698A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.825A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.615A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.842A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.690A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 273 through 284 removed outlier: 3.886A pdb=" N THR F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.657A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 4.085A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.723A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 367 through 370 removed outlier: 3.874A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 367 through 370' Processing helix chain 'G' and resid 232 through 282 removed outlier: 3.795A pdb=" N ARG G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU G 243 " --> pdb=" O ALA G 239 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG G 244 " --> pdb=" O GLU G 240 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER G 245 " --> pdb=" O PHE G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 282 removed outlier: 4.101A pdb=" N ARG H 244 " --> pdb=" O GLU H 240 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER H 245 " --> pdb=" O PHE H 241 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR H 247 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS H 251 " --> pdb=" O THR H 247 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER H 252 " --> pdb=" O LYS H 248 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU H 274 " --> pdb=" O ILE H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 69 removed outlier: 3.544A pdb=" N SER I 45 " --> pdb=" O ASP I 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 69 removed outlier: 3.580A pdb=" N LYS J 6 " --> pdb=" O ASP J 2 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU J 64 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS J 65 " --> pdb=" O SER J 61 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP J 66 " --> pdb=" O GLU J 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 152 removed outlier: 4.059A pdb=" N HIS K 94 " --> pdb=" O PHE K 90 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU K 99 " --> pdb=" O ARG K 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS K 100 " --> pdb=" O LYS K 96 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU K 102 " --> pdb=" O VAL K 98 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU K 104 " --> pdb=" O LYS K 100 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU K 122 " --> pdb=" O LYS K 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 282 removed outlier: 4.646A pdb=" N ARG L 238 " --> pdb=" O GLU L 234 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU L 243 " --> pdb=" O ALA L 239 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG L 244 " --> pdb=" O GLU L 240 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER L 245 " --> pdb=" O PHE L 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 282 removed outlier: 3.813A pdb=" N SER M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS M 251 " --> pdb=" O THR M 247 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER M 252 " --> pdb=" O LYS M 248 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU M 273 " --> pdb=" O ALA M 269 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU M 274 " --> pdb=" O ILE M 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 69 Processing helix chain 'O' and resid 2 through 69 removed outlier: 4.049A pdb=" N LYS O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP O 66 " --> pdb=" O GLU O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 153 removed outlier: 4.338A pdb=" N ARG P 95 " --> pdb=" O ASP P 91 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU P 99 " --> pdb=" O ARG P 95 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS P 100 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU P 102 " --> pdb=" O VAL P 98 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU P 121 " --> pdb=" O LYS P 117 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.614A pdb=" N GLY A 20 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 132 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.849A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.896A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 242 removed outlier: 4.748A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.971A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 357 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.524A pdb=" N VAL B 35 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.564A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 242 removed outlier: 4.331A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 8 through 11 removed outlier: 3.565A pdb=" N GLY C 20 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.849A pdb=" N VAL C 35 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 103 through 107 removed outlier: 3.947A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 357 " --> pdb=" O MET C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.730A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 242 removed outlier: 4.351A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 11 removed outlier: 3.701A pdb=" N GLY D 20 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.927A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 103 through 107 removed outlier: 3.802A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 357 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.853A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 242 removed outlier: 4.486A pdb=" N LEU D 242 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 8 through 9 removed outlier: 6.929A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE E 357 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 16 through 19 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.669A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.873A pdb=" N SER E 155 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 238 through 242 removed outlier: 4.377A pdb=" N LEU E 242 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 8 through 9 removed outlier: 3.577A pdb=" N GLY F 20 " --> pdb=" O VAL F 9 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.701A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 103 through 107 Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.816A pdb=" N SER F 155 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 238 through 242 removed outlier: 4.602A pdb=" N LEU F 242 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) 1256 hydrogen bonds defined for protein. 3453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7649 1.34 - 1.46: 4092 1.46 - 1.58: 11331 1.58 - 1.69: 18 1.69 - 1.81: 242 Bond restraints: 23332 Sorted by residual: bond pdb=" N PRO P 83 " pdb=" CD PRO P 83 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.95e+01 bond pdb=" CA ILE K 109 " pdb=" CB ILE K 109 " ideal model delta sigma weight residual 1.540 1.514 0.025 1.29e-02 6.01e+03 3.79e+00 bond pdb=" CA ILE P 82 " pdb=" CB ILE P 82 " ideal model delta sigma weight residual 1.537 1.516 0.022 1.29e-02 6.01e+03 2.81e+00 bond pdb=" CA ILE K 82 " pdb=" CB ILE K 82 " ideal model delta sigma weight residual 1.537 1.516 0.021 1.29e-02 6.01e+03 2.64e+00 bond pdb=" CD ARG P 133 " pdb=" NE ARG P 133 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.40e-02 5.10e+03 2.61e+00 ... (remaining 23327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 31340 3.67 - 7.33: 165 7.33 - 11.00: 1 11.00 - 14.66: 0 14.66 - 18.33: 2 Bond angle restraints: 31508 Sorted by residual: angle pdb=" C ARG K 87 " pdb=" N VAL K 88 " pdb=" CA VAL K 88 " ideal model delta sigma weight residual 121.70 140.03 -18.33 1.80e+00 3.09e-01 1.04e+02 angle pdb=" C ARG P 87 " pdb=" N VAL P 88 " pdb=" CA VAL P 88 " ideal model delta sigma weight residual 121.70 137.18 -15.48 1.80e+00 3.09e-01 7.40e+01 angle pdb=" CA ASP H 275 " pdb=" CB ASP H 275 " pdb=" CG ASP H 275 " ideal model delta sigma weight residual 112.60 109.16 3.44 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA ASP O 34 " pdb=" CB ASP O 34 " pdb=" CG ASP O 34 " ideal model delta sigma weight residual 112.60 109.23 3.37 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CA ASP I 58 " pdb=" CB ASP I 58 " pdb=" CG ASP I 58 " ideal model delta sigma weight residual 112.60 109.24 3.36 1.00e+00 1.00e+00 1.13e+01 ... (remaining 31503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 13185 17.54 - 35.09: 838 35.09 - 52.63: 236 52.63 - 70.17: 67 70.17 - 87.72: 12 Dihedral angle restraints: 14338 sinusoidal: 5954 harmonic: 8384 Sorted by residual: dihedral pdb=" CA GLU P 119 " pdb=" C GLU P 119 " pdb=" N GLU P 120 " pdb=" CA GLU P 120 " ideal model delta harmonic sigma weight residual -180.00 -161.71 -18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 1.39 -61.39 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 1.31 -61.30 1 2.00e+01 2.50e-03 1.25e+01 ... (remaining 14335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2121 0.031 - 0.061: 916 0.061 - 0.092: 273 0.092 - 0.123: 160 0.123 - 0.153: 18 Chirality restraints: 3488 Sorted by residual: chirality pdb=" CG LEU H 232 " pdb=" CB LEU H 232 " pdb=" CD1 LEU H 232 " pdb=" CD2 LEU H 232 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA VAL K 88 " pdb=" N VAL K 88 " pdb=" C VAL K 88 " pdb=" CB VAL K 88 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA VAL P 88 " pdb=" N VAL P 88 " pdb=" C VAL P 88 " pdb=" CB VAL P 88 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 3485 not shown) Planarity restraints: 4064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO B 164 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 163 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO D 164 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO C 164 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.021 5.00e-02 4.00e+02 ... (remaining 4061 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 110 2.38 - 3.01: 12975 3.01 - 3.64: 33644 3.64 - 4.27: 48731 4.27 - 4.90: 83167 Nonbonded interactions: 178627 Sorted by model distance: nonbonded pdb=" O GLY D 146 " pdb=" CB PHE P 90 " model vdw 1.744 3.440 nonbonded pdb=" O LYS D 373 " pdb=" CB PRO P 80 " model vdw 1.792 3.440 nonbonded pdb=" O LYS J 6 " pdb=" SD MET J 10 " model vdw 1.810 3.400 nonbonded pdb=" CD1 TYR M 261 " pdb=" CB LYS P 127 " model vdw 1.823 3.740 nonbonded pdb=" CD2 PHE C 375 " pdb=" CD PRO K 80 " model vdw 1.891 3.740 ... (remaining 178622 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'P' } 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 group one per residue 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: 3.010 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: 0.230 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.490 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.006 0.572 23334 Z= 0.480 Angle : 0.674 18.328 31508 Z= 0.360 Chirality : 0.041 0.153 3488 Planarity : 0.003 0.038 4064 Dihedral : 13.285 87.717 8926 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 6.73 % Allowed : 10.30 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.16), residues: 2848 helix: 1.60 (0.14), residues: 1410 sheet: -1.12 (0.26), residues: 378 loop : -0.30 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 35 TYR 0.013 0.001 TYR H 267 PHE 0.015 0.001 PHE G 241 TRP 0.009 0.001 TRP D 79 HIS 0.006 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00349 (23332) covalent geometry : angle 0.67427 (31508) hydrogen bonds : bond 0.15352 ( 1244) hydrogen bonds : angle 5.81022 ( 3453) Misc. bond : bond 0.48154 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1103 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.8331 (m) cc_final: 0.8005 (p) REVERT: A 111 ASN cc_start: 0.8381 (m-40) cc_final: 0.8107 (m-40) REVERT: A 115 ASN cc_start: 0.7241 (t0) cc_final: 0.6272 (t0) REVERT: A 153 LEU cc_start: 0.9046 (tp) cc_final: 0.8799 (tt) REVERT: A 217 CYS cc_start: 0.7275 (m) cc_final: 0.7047 (m) REVERT: B 11 ASP cc_start: 0.6851 (t70) cc_final: 0.6415 (p0) REVERT: B 81 ASP cc_start: 0.6435 (m-30) cc_final: 0.5443 (m-30) REVERT: B 244 ASP cc_start: 0.8305 (p0) cc_final: 0.7923 (p0) REVERT: B 280 ASN cc_start: 0.7648 (m-40) cc_final: 0.6621 (m-40) REVERT: B 292 ASP cc_start: 0.7179 (m-30) cc_final: 0.6880 (m-30) REVERT: C 43 VAL cc_start: 0.8712 (m) cc_final: 0.8493 (t) REVERT: C 153 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 213 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8290 (tmmt) REVERT: D 104 LEU cc_start: 0.8047 (tp) cc_final: 0.7841 (tp) REVERT: D 111 ASN cc_start: 0.7782 (m-40) cc_final: 0.7061 (m-40) REVERT: D 128 ASN cc_start: 0.8068 (t0) cc_final: 0.6642 (t0) REVERT: D 249 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8948 (p) REVERT: D 325 MET cc_start: 0.8019 (mmp) cc_final: 0.7810 (mmm) REVERT: E 101 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.7096 (m-70) REVERT: E 145 SER cc_start: 0.8651 (p) cc_final: 0.8383 (t) REVERT: E 154 ASP cc_start: 0.7669 (t70) cc_final: 0.7260 (t0) REVERT: E 293 LEU cc_start: 0.8579 (mp) cc_final: 0.8319 (mt) REVERT: F 14 SER cc_start: 0.7017 (t) cc_final: 0.6782 (p) REVERT: F 51 ASP cc_start: 0.7704 (p0) cc_final: 0.7387 (p0) REVERT: F 111 ASN cc_start: 0.7648 (m110) cc_final: 0.7048 (m110) REVERT: F 132 MET cc_start: 0.6606 (ptm) cc_final: 0.6384 (ttp) REVERT: F 162 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8374 (m-40) REVERT: F 178 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7720 (mm) REVERT: F 216 LEU cc_start: 0.9040 (mm) cc_final: 0.8771 (mt) REVERT: F 225 ASN cc_start: 0.7132 (m-40) cc_final: 0.6800 (m-40) REVERT: F 369 ILE cc_start: 0.8493 (tp) cc_final: 0.8256 (tp) REVERT: J 26 GLU cc_start: 0.6276 (mt-10) cc_final: 0.5174 (mt-10) REVERT: K 116 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6253 (mtp85) REVERT: K 149 LYS cc_start: 0.6663 (mtpp) cc_final: 0.6418 (mttm) REVERT: P 103 ASN cc_start: 0.6242 (m-40) cc_final: 0.5844 (m-40) outliers start: 166 outliers final: 50 residues processed: 1203 average time/residue: 0.1544 time to fit residues: 279.0492 Evaluate side-chains 721 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 665 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 250 GLU Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 23 GLU Chi-restraints excluded: chain P residue 113 PHE Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS A 246 GLN A 297 ASN A 353 GLN A 354 GLN A 371 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 88 HIS B 225 ASN B 353 GLN B 371 HIS C 59 GLN C 275 HIS C 360 GLN D 111 ASN D 137 GLN D 246 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 137 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN F 263 GLN I 9 GLN I 47 GLN ** L 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN N 17 ASN N 47 GLN P 112 HIS P 153 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080824 restraints weight = 58135.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.083801 restraints weight = 25517.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085697 restraints weight = 14035.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086909 restraints weight = 8956.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.087683 restraints weight = 6466.445| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23334 Z= 0.179 Angle : 0.735 12.950 31508 Z= 0.367 Chirality : 0.046 0.236 3488 Planarity : 0.005 0.055 4064 Dihedral : 8.227 76.313 3318 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 6.85 % Allowed : 20.68 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.16), residues: 2848 helix: 1.42 (0.14), residues: 1434 sheet: -0.86 (0.26), residues: 378 loop : -0.18 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 372 TYR 0.023 0.001 TYR C 166 PHE 0.019 0.001 PHE G 241 TRP 0.016 0.002 TRP E 356 HIS 0.014 0.002 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00404 (23332) covalent geometry : angle 0.73525 (31508) hydrogen bonds : bond 0.04616 ( 1244) hydrogen bonds : angle 4.55213 ( 3453) Misc. bond : bond 0.00551 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 730 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9349 (m) cc_final: 0.8995 (p) REVERT: A 121 GLN cc_start: 0.9530 (tm-30) cc_final: 0.9140 (tm-30) REVERT: A 167 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 176 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7619 (mtt) REVERT: A 195 GLU cc_start: 0.8509 (tt0) cc_final: 0.8180 (tp30) REVERT: A 217 CYS cc_start: 0.8164 (m) cc_final: 0.7835 (m) REVERT: A 282 ILE cc_start: 0.9289 (mt) cc_final: 0.8900 (tt) REVERT: B 64 ILE cc_start: 0.9681 (OUTLIER) cc_final: 0.9429 (pp) REVERT: B 78 ASN cc_start: 0.7828 (t0) cc_final: 0.7609 (t0) REVERT: B 81 ASP cc_start: 0.8819 (m-30) cc_final: 0.8522 (m-30) REVERT: B 123 MET cc_start: 0.9262 (mmm) cc_final: 0.9046 (tpt) REVERT: B 316 GLU cc_start: 0.9452 (tp30) cc_final: 0.9235 (tp30) REVERT: C 202 THR cc_start: 0.8130 (t) cc_final: 0.7048 (p) REVERT: C 222 ASP cc_start: 0.8390 (t0) cc_final: 0.8103 (t0) REVERT: C 253 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: C 314 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8598 (tm-30) REVERT: C 375 PHE cc_start: 0.8141 (t80) cc_final: 0.7837 (t80) REVERT: D 111 ASN cc_start: 0.8206 (m110) cc_final: 0.7075 (m110) REVERT: D 154 ASP cc_start: 0.8944 (t0) cc_final: 0.8637 (t0) REVERT: D 288 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8167 (t0) REVERT: D 353 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8806 (mp10) REVERT: D 371 HIS cc_start: 0.8497 (m90) cc_final: 0.8287 (m90) REVERT: E 34 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9351 (pt) REVERT: E 92 ASN cc_start: 0.8986 (m110) cc_final: 0.8732 (m-40) REVERT: E 101 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.6924 (m-70) REVERT: E 128 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8170 (t0) REVERT: E 137 GLN cc_start: 0.8134 (mt0) cc_final: 0.7786 (mm-40) REVERT: E 154 ASP cc_start: 0.8325 (t70) cc_final: 0.7720 (t0) REVERT: E 283 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9090 (mmp) REVERT: E 305 MET cc_start: 0.8718 (mmm) cc_final: 0.8382 (tpp) REVERT: F 14 SER cc_start: 0.8212 (t) cc_final: 0.8001 (p) REVERT: F 80 ASP cc_start: 0.8259 (p0) cc_final: 0.7999 (p0) REVERT: F 82 MET cc_start: 0.8612 (tpt) cc_final: 0.7865 (tpp) REVERT: F 86 TRP cc_start: 0.9364 (m-10) cc_final: 0.8898 (m-10) REVERT: F 111 ASN cc_start: 0.8541 (m110) cc_final: 0.6785 (m110) REVERT: F 123 MET cc_start: 0.9488 (tpp) cc_final: 0.8998 (mmt) REVERT: F 128 ASN cc_start: 0.8574 (m-40) cc_final: 0.8325 (m-40) REVERT: F 162 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8764 (m-40) REVERT: F 178 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7808 (mm) REVERT: F 179 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7896 (t0) REVERT: F 305 MET cc_start: 0.8899 (mmm) cc_final: 0.8570 (mmt) REVERT: F 325 MET cc_start: 0.8942 (mmm) cc_final: 0.8549 (mmt) REVERT: G 256 LEU cc_start: 0.9415 (tp) cc_final: 0.9190 (tt) REVERT: G 273 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8407 (mt-10) REVERT: I 42 GLU cc_start: 0.8619 (pt0) cc_final: 0.8332 (pm20) REVERT: J 14 ASP cc_start: 0.8215 (m-30) cc_final: 0.8006 (m-30) REVERT: J 38 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6844 (tm-30) REVERT: J 47 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7193 (mt0) REVERT: K 113 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: K 116 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8021 (mtp-110) REVERT: L 240 GLU cc_start: 0.8934 (tp30) cc_final: 0.8631 (tp30) REVERT: L 268 LYS cc_start: 0.9502 (tptt) cc_final: 0.9291 (tptt) REVERT: M 241 PHE cc_start: 0.9109 (p90) cc_final: 0.8709 (p90) REVERT: M 258 ASP cc_start: 0.8846 (m-30) cc_final: 0.8487 (m-30) REVERT: M 265 LEU cc_start: 0.9415 (mt) cc_final: 0.9192 (mt) REVERT: N 69 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8490 (pp20) REVERT: O 51 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8270 (tppp) REVERT: P 87 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8803 (mmt180) REVERT: P 120 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6623 (mm-30) REVERT: P 139 GLU cc_start: 0.7828 (tp30) cc_final: 0.7278 (tm-30) outliers start: 169 outliers final: 83 residues processed: 832 average time/residue: 0.1563 time to fit residues: 197.2539 Evaluate side-chains 718 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 619 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 113 PHE Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 14 ASP Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 20 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 59 GLN A 246 GLN A 252 ASN A 297 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN H 263 GLN ** L 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078039 restraints weight = 59469.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.080860 restraints weight = 26520.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.082662 restraints weight = 14815.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.083782 restraints weight = 9582.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.084586 restraints weight = 7025.795| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23334 Z= 0.185 Angle : 0.723 11.303 31508 Z= 0.355 Chirality : 0.046 0.240 3488 Planarity : 0.004 0.039 4064 Dihedral : 7.717 79.743 3282 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 6.33 % Allowed : 22.67 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.16), residues: 2848 helix: 1.21 (0.14), residues: 1468 sheet: -0.83 (0.26), residues: 378 loop : -0.26 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 244 TYR 0.019 0.001 TYR E 143 PHE 0.017 0.001 PHE G 241 TRP 0.013 0.002 TRP C 79 HIS 0.010 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00416 (23332) covalent geometry : angle 0.72313 (31508) hydrogen bonds : bond 0.04304 ( 1244) hydrogen bonds : angle 4.44292 ( 3453) Misc. bond : bond 0.01237 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 668 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9334 (m) cc_final: 0.9115 (p) REVERT: A 79 TRP cc_start: 0.8887 (m100) cc_final: 0.8132 (m100) REVERT: A 117 GLU cc_start: 0.8989 (tt0) cc_final: 0.8301 (tp30) REVERT: A 121 GLN cc_start: 0.9560 (tm-30) cc_final: 0.9151 (tm-30) REVERT: A 167 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 176 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7723 (mtm) REVERT: A 205 GLU cc_start: 0.8844 (mp0) cc_final: 0.8537 (pm20) REVERT: A 217 CYS cc_start: 0.8208 (m) cc_final: 0.7925 (m) REVERT: A 282 ILE cc_start: 0.9341 (mt) cc_final: 0.8943 (tt) REVERT: A 372 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.7906 (mtm-85) REVERT: B 78 ASN cc_start: 0.7988 (t0) cc_final: 0.7629 (t0) REVERT: B 106 THR cc_start: 0.8693 (m) cc_final: 0.8168 (p) REVERT: B 123 MET cc_start: 0.9270 (mmm) cc_final: 0.9052 (tpt) REVERT: B 195 GLU cc_start: 0.8444 (tt0) cc_final: 0.8194 (tm-30) REVERT: B 280 ASN cc_start: 0.8846 (m-40) cc_final: 0.8480 (m110) REVERT: B 316 GLU cc_start: 0.9421 (tp30) cc_final: 0.9212 (tp30) REVERT: B 372 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8285 (ttm-80) REVERT: C 132 MET cc_start: 0.8997 (ppp) cc_final: 0.8486 (ppp) REVERT: C 195 GLU cc_start: 0.8191 (pp20) cc_final: 0.7662 (pp20) REVERT: C 283 MET cc_start: 0.8207 (mmp) cc_final: 0.7938 (mmm) REVERT: C 375 PHE cc_start: 0.8384 (t80) cc_final: 0.8044 (t80) REVERT: D 11 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.7153 (p0) REVERT: D 12 ASN cc_start: 0.9025 (p0) cc_final: 0.8701 (p0) REVERT: D 59 GLN cc_start: 0.9449 (mm-40) cc_final: 0.9245 (mm-40) REVERT: D 72 GLU cc_start: 0.8261 (mp0) cc_final: 0.7797 (mp0) REVERT: D 111 ASN cc_start: 0.8170 (m-40) cc_final: 0.7462 (m-40) REVERT: D 154 ASP cc_start: 0.8892 (t0) cc_final: 0.8619 (t0) REVERT: D 288 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8104 (t0) REVERT: D 371 HIS cc_start: 0.8518 (m90) cc_final: 0.8268 (m90) REVERT: E 34 ILE cc_start: 0.9619 (OUTLIER) cc_final: 0.9372 (pt) REVERT: E 67 LEU cc_start: 0.9384 (mm) cc_final: 0.9059 (mm) REVERT: E 101 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.7103 (m-70) REVERT: E 128 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8157 (t0) REVERT: E 154 ASP cc_start: 0.8374 (t70) cc_final: 0.7802 (t0) REVERT: E 305 MET cc_start: 0.8607 (mmm) cc_final: 0.8249 (tpp) REVERT: E 356 TRP cc_start: 0.8893 (m100) cc_final: 0.8495 (m100) REVERT: F 82 MET cc_start: 0.9085 (tpt) cc_final: 0.8716 (tpp) REVERT: F 86 TRP cc_start: 0.9285 (m-10) cc_final: 0.9017 (m-10) REVERT: F 107 GLU cc_start: 0.8298 (tp30) cc_final: 0.8002 (tp30) REVERT: F 111 ASN cc_start: 0.8049 (m110) cc_final: 0.5874 (m-40) REVERT: F 117 GLU cc_start: 0.8560 (tt0) cc_final: 0.7987 (tp30) REVERT: F 123 MET cc_start: 0.9466 (tpp) cc_final: 0.8975 (mmt) REVERT: F 154 ASP cc_start: 0.8502 (t0) cc_final: 0.8234 (t0) REVERT: F 162 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.8879 (m-40) REVERT: F 178 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7951 (mm) REVERT: F 179 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7907 (t70) REVERT: F 214 GLU cc_start: 0.8670 (mt-10) cc_final: 0.7870 (mt-10) REVERT: F 313 MET cc_start: 0.9164 (tpp) cc_final: 0.8925 (tpp) REVERT: F 325 MET cc_start: 0.8871 (mmm) cc_final: 0.8417 (mmm) REVERT: G 270 ILE cc_start: 0.8601 (mm) cc_final: 0.8396 (mm) REVERT: G 273 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8301 (mt-10) REVERT: J 14 ASP cc_start: 0.8196 (m-30) cc_final: 0.7958 (m-30) REVERT: J 26 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6592 (mp0) REVERT: L 240 GLU cc_start: 0.8948 (tp30) cc_final: 0.8491 (tp30) REVERT: M 265 LEU cc_start: 0.9403 (mt) cc_final: 0.9164 (mt) REVERT: N 6 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8750 (ttpp) REVERT: O 51 LYS cc_start: 0.8448 (mmmm) cc_final: 0.8221 (tppp) REVERT: P 87 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8767 (mmt180) REVERT: P 89 ASP cc_start: 0.8311 (m-30) cc_final: 0.7979 (m-30) REVERT: P 99 GLU cc_start: 0.9108 (pp20) cc_final: 0.8757 (pp20) REVERT: P 126 LEU cc_start: 0.8454 (mt) cc_final: 0.8081 (mm) REVERT: P 139 GLU cc_start: 0.7981 (tp30) cc_final: 0.7774 (tm-30) outliers start: 156 outliers final: 111 residues processed: 763 average time/residue: 0.1614 time to fit residues: 188.3465 Evaluate side-chains 712 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 591 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain M residue 240 GLU Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 14 ASP Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 10 MET Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 47 GLN Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 144 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 264 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 106 optimal weight: 0.0010 chunk 270 optimal weight: 7.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN I 38 GLN ** L 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.080404 restraints weight = 58963.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.083201 restraints weight = 25653.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084970 restraints weight = 14021.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.086105 restraints weight = 8936.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086827 restraints weight = 6439.059| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23334 Z= 0.149 Angle : 0.701 11.703 31508 Z= 0.342 Chirality : 0.045 0.244 3488 Planarity : 0.004 0.051 4064 Dihedral : 7.389 82.547 3272 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 6.12 % Allowed : 23.68 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.16), residues: 2848 helix: 1.24 (0.14), residues: 1468 sheet: -0.81 (0.26), residues: 378 loop : -0.20 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 372 TYR 0.023 0.001 TYR B 362 PHE 0.017 0.001 PHE G 241 TRP 0.012 0.001 TRP C 79 HIS 0.010 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00336 (23332) covalent geometry : angle 0.70139 (31508) hydrogen bonds : bond 0.04046 ( 1244) hydrogen bonds : angle 4.30553 ( 3453) Misc. bond : bond 0.00180 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 639 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9340 (m) cc_final: 0.9116 (p) REVERT: A 79 TRP cc_start: 0.8865 (m100) cc_final: 0.8165 (m100) REVERT: A 118 LYS cc_start: 0.9544 (ttmt) cc_final: 0.8929 (tmtt) REVERT: A 121 GLN cc_start: 0.9570 (tm-30) cc_final: 0.9085 (tm-30) REVERT: A 125 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8808 (mm-30) REVERT: A 167 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 176 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7740 (mtt) REVERT: A 217 CYS cc_start: 0.8220 (m) cc_final: 0.7812 (m) REVERT: A 293 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 316 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8492 (mm-30) REVERT: A 355 MET cc_start: 0.8338 (mmp) cc_final: 0.8065 (mmm) REVERT: A 372 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.7860 (mtm-85) REVERT: B 64 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.9484 (pp) REVERT: B 78 ASN cc_start: 0.7868 (t0) cc_final: 0.7484 (t0) REVERT: B 106 THR cc_start: 0.8625 (m) cc_final: 0.8049 (p) REVERT: B 195 GLU cc_start: 0.8272 (tt0) cc_final: 0.8045 (tm-30) REVERT: B 280 ASN cc_start: 0.8847 (m-40) cc_final: 0.8444 (m110) REVERT: C 111 ASN cc_start: 0.8364 (t0) cc_final: 0.8032 (t0) REVERT: C 132 MET cc_start: 0.9076 (ppp) cc_final: 0.8549 (ppp) REVERT: C 195 GLU cc_start: 0.8190 (pp20) cc_final: 0.7824 (pp20) REVERT: C 222 ASP cc_start: 0.8614 (t0) cc_final: 0.8295 (t0) REVERT: C 375 PHE cc_start: 0.8268 (t80) cc_final: 0.7932 (t80) REVERT: D 59 GLN cc_start: 0.9420 (mm-40) cc_final: 0.9199 (mm-40) REVERT: D 72 GLU cc_start: 0.8286 (mp0) cc_final: 0.7860 (mp0) REVERT: D 154 ASP cc_start: 0.8805 (t0) cc_final: 0.8573 (t0) REVERT: D 176 MET cc_start: 0.8764 (mmm) cc_final: 0.8561 (mmt) REVERT: D 288 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8062 (t0) REVERT: D 371 HIS cc_start: 0.8594 (m90) cc_final: 0.8291 (m90) REVERT: E 34 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9397 (pt) REVERT: E 67 LEU cc_start: 0.9441 (mm) cc_final: 0.9237 (mm) REVERT: E 101 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7172 (m-70) REVERT: E 128 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8098 (t0) REVERT: E 154 ASP cc_start: 0.8414 (t70) cc_final: 0.7882 (t0) REVERT: E 283 MET cc_start: 0.9311 (mmt) cc_final: 0.8999 (mmp) REVERT: E 305 MET cc_start: 0.8643 (mmm) cc_final: 0.8256 (tpp) REVERT: F 82 MET cc_start: 0.8993 (tpt) cc_final: 0.8608 (tpp) REVERT: F 86 TRP cc_start: 0.9283 (m-10) cc_final: 0.8912 (m-10) REVERT: F 107 GLU cc_start: 0.8331 (tp30) cc_final: 0.7992 (tp30) REVERT: F 111 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.5925 (m-40) REVERT: F 117 GLU cc_start: 0.8571 (tt0) cc_final: 0.7953 (tp30) REVERT: F 123 MET cc_start: 0.9434 (tpp) cc_final: 0.9215 (tpp) REVERT: F 154 ASP cc_start: 0.8390 (t0) cc_final: 0.8029 (t0) REVERT: F 162 ASN cc_start: 0.9303 (OUTLIER) cc_final: 0.8954 (m-40) REVERT: F 178 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7900 (mm) REVERT: F 179 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7943 (t70) REVERT: F 214 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7901 (mt-10) REVERT: F 283 MET cc_start: 0.9146 (mmt) cc_final: 0.8825 (mmm) REVERT: F 313 MET cc_start: 0.9138 (tpp) cc_final: 0.8878 (tpp) REVERT: F 325 MET cc_start: 0.8858 (mmm) cc_final: 0.8459 (mmm) REVERT: G 240 GLU cc_start: 0.8820 (tp30) cc_final: 0.8425 (tp30) REVERT: G 266 LYS cc_start: 0.8877 (tttt) cc_final: 0.8673 (ptmt) REVERT: G 273 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8347 (mt-10) REVERT: J 14 ASP cc_start: 0.8126 (m-30) cc_final: 0.7894 (m-30) REVERT: J 26 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6467 (mp0) REVERT: K 116 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8225 (mtp85) REVERT: M 265 LEU cc_start: 0.9369 (mt) cc_final: 0.9143 (mt) REVERT: N 62 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7814 (mm-30) REVERT: O 51 LYS cc_start: 0.8415 (mmmm) cc_final: 0.8208 (tppp) REVERT: P 87 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8505 (mmt-90) REVERT: P 99 GLU cc_start: 0.9132 (pp20) cc_final: 0.8834 (pp20) REVERT: P 120 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6031 (mm-30) outliers start: 151 outliers final: 104 residues processed: 738 average time/residue: 0.1477 time to fit residues: 167.9479 Evaluate side-chains 711 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 593 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 111 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 93 ILE Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 44 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 193 optimal weight: 0.7980 chunk 257 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 297 ASN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077861 restraints weight = 58620.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080591 restraints weight = 26361.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082296 restraints weight = 14719.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083436 restraints weight = 9601.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.084167 restraints weight = 6988.768| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23334 Z= 0.152 Angle : 0.708 11.268 31508 Z= 0.343 Chirality : 0.045 0.243 3488 Planarity : 0.004 0.047 4064 Dihedral : 7.261 85.708 3270 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 6.61 % Allowed : 24.05 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2848 helix: 1.24 (0.14), residues: 1468 sheet: -0.73 (0.26), residues: 378 loop : -0.12 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 35 TYR 0.018 0.001 TYR B 362 PHE 0.043 0.001 PHE M 241 TRP 0.012 0.001 TRP C 79 HIS 0.009 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00351 (23332) covalent geometry : angle 0.70821 (31508) hydrogen bonds : bond 0.03983 ( 1244) hydrogen bonds : angle 4.27606 ( 3453) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 641 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9418 (m) cc_final: 0.9156 (p) REVERT: A 78 ASN cc_start: 0.8879 (t0) cc_final: 0.8117 (t0) REVERT: A 79 TRP cc_start: 0.8871 (m100) cc_final: 0.8523 (m100) REVERT: A 115 ASN cc_start: 0.8673 (t0) cc_final: 0.8472 (t0) REVERT: A 118 LYS cc_start: 0.9568 (ttmt) cc_final: 0.8827 (tmtt) REVERT: A 121 GLN cc_start: 0.9563 (tm-30) cc_final: 0.8576 (tm-30) REVERT: A 125 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8764 (mm-30) REVERT: A 128 ASN cc_start: 0.9058 (t0) cc_final: 0.8799 (t0) REVERT: A 167 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 176 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7714 (mtt) REVERT: A 217 CYS cc_start: 0.8316 (m) cc_final: 0.7914 (m) REVERT: A 316 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8542 (mm-30) REVERT: A 372 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.7963 (mtm-85) REVERT: B 64 ILE cc_start: 0.9729 (OUTLIER) cc_final: 0.9461 (pp) REVERT: B 78 ASN cc_start: 0.7862 (t0) cc_final: 0.7486 (t0) REVERT: B 106 THR cc_start: 0.8569 (m) cc_final: 0.8014 (p) REVERT: B 190 MET cc_start: 0.8583 (mtp) cc_final: 0.8250 (mtt) REVERT: B 280 ASN cc_start: 0.8858 (m-40) cc_final: 0.8431 (m110) REVERT: B 325 MET cc_start: 0.4360 (mtt) cc_final: 0.3725 (mtt) REVERT: B 372 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8357 (ttm-80) REVERT: C 132 MET cc_start: 0.9064 (ppp) cc_final: 0.8549 (ppp) REVERT: C 222 ASP cc_start: 0.8654 (t0) cc_final: 0.8204 (t0) REVERT: C 292 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8471 (t0) REVERT: C 375 PHE cc_start: 0.8340 (t80) cc_final: 0.7975 (t80) REVERT: D 11 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.7398 (p0) REVERT: D 12 ASN cc_start: 0.9004 (p0) cc_final: 0.8571 (p0) REVERT: D 59 GLN cc_start: 0.9431 (mm-40) cc_final: 0.9179 (mm-40) REVERT: D 72 GLU cc_start: 0.8273 (mp0) cc_final: 0.7862 (mp0) REVERT: D 154 ASP cc_start: 0.8763 (t0) cc_final: 0.8560 (t70) REVERT: D 288 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8007 (t0) REVERT: D 371 HIS cc_start: 0.8610 (m90) cc_final: 0.8382 (m90) REVERT: E 65 LEU cc_start: 0.8696 (mm) cc_final: 0.8401 (mm) REVERT: E 93 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7858 (mp0) REVERT: E 101 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7160 (m-70) REVERT: E 128 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8124 (t0) REVERT: E 154 ASP cc_start: 0.8439 (t70) cc_final: 0.7900 (t0) REVERT: E 185 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9116 (mm) REVERT: E 283 MET cc_start: 0.9303 (mmt) cc_final: 0.9004 (mmp) REVERT: E 305 MET cc_start: 0.8639 (mmm) cc_final: 0.8352 (tpp) REVERT: F 82 MET cc_start: 0.8891 (tpt) cc_final: 0.8508 (tpp) REVERT: F 86 TRP cc_start: 0.9252 (m-10) cc_final: 0.8837 (m-10) REVERT: F 107 GLU cc_start: 0.8362 (tp30) cc_final: 0.7981 (tp30) REVERT: F 111 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.5994 (m-40) REVERT: F 117 GLU cc_start: 0.8547 (tt0) cc_final: 0.7996 (tp30) REVERT: F 123 MET cc_start: 0.9373 (tpp) cc_final: 0.9048 (tpp) REVERT: F 154 ASP cc_start: 0.8390 (t0) cc_final: 0.7981 (t0) REVERT: F 162 ASN cc_start: 0.9379 (OUTLIER) cc_final: 0.9066 (m-40) REVERT: F 178 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7918 (mm) REVERT: F 179 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7939 (t70) REVERT: F 196 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8626 (mpt-90) REVERT: F 214 GLU cc_start: 0.8657 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F 283 MET cc_start: 0.9139 (mmt) cc_final: 0.8830 (mmm) REVERT: F 305 MET cc_start: 0.8910 (mmm) cc_final: 0.8567 (mmt) REVERT: F 325 MET cc_start: 0.8785 (mmm) cc_final: 0.8294 (tpp) REVERT: G 257 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8593 (pp20) REVERT: G 266 LYS cc_start: 0.8959 (tttt) cc_final: 0.8749 (ptmt) REVERT: G 273 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8384 (mt-10) REVERT: I 54 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7492 (mp0) REVERT: J 14 ASP cc_start: 0.8188 (m-30) cc_final: 0.7958 (m-30) REVERT: J 26 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6646 (mp0) REVERT: J 41 ASP cc_start: 0.7875 (t0) cc_final: 0.7600 (m-30) REVERT: K 105 LEU cc_start: 0.8079 (tt) cc_final: 0.7690 (tp) REVERT: K 116 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8258 (mtp85) REVERT: L 240 GLU cc_start: 0.8733 (tp30) cc_final: 0.8533 (tp30) REVERT: M 265 LEU cc_start: 0.9361 (mt) cc_final: 0.9134 (mt) REVERT: O 13 LEU cc_start: 0.9075 (tt) cc_final: 0.8735 (tt) REVERT: O 28 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8396 (p0) REVERT: P 87 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8410 (mmt-90) REVERT: P 99 GLU cc_start: 0.9093 (pp20) cc_final: 0.8803 (pp20) REVERT: P 120 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6084 (mm-30) REVERT: P 140 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7526 (tp-100) outliers start: 163 outliers final: 116 residues processed: 746 average time/residue: 0.1429 time to fit residues: 164.4826 Evaluate side-chains 731 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 597 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 111 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 93 ILE Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 34 optimal weight: 0.0970 chunk 260 optimal weight: 0.7980 chunk 253 optimal weight: 0.0870 chunk 65 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.098243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078562 restraints weight = 58856.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081332 restraints weight = 26343.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083095 restraints weight = 14638.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.084239 restraints weight = 9423.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.084985 restraints weight = 6817.893| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23334 Z= 0.139 Angle : 0.724 13.606 31508 Z= 0.347 Chirality : 0.045 0.302 3488 Planarity : 0.004 0.045 4064 Dihedral : 7.101 84.280 3266 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 6.29 % Allowed : 25.34 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2848 helix: 1.20 (0.14), residues: 1476 sheet: -0.60 (0.27), residues: 378 loop : -0.02 (0.22), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 97 TYR 0.021 0.001 TYR C 198 PHE 0.017 0.001 PHE G 241 TRP 0.011 0.001 TRP E 86 HIS 0.009 0.001 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00319 (23332) covalent geometry : angle 0.72354 (31508) hydrogen bonds : bond 0.03935 ( 1244) hydrogen bonds : angle 4.22153 ( 3453) Misc. bond : bond 0.00208 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 634 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9429 (m) cc_final: 0.9117 (p) REVERT: A 59 GLN cc_start: 0.9494 (tp-100) cc_final: 0.8984 (tp40) REVERT: A 79 TRP cc_start: 0.8807 (m100) cc_final: 0.8516 (m100) REVERT: A 95 ARG cc_start: 0.9103 (mpp80) cc_final: 0.8319 (mpp80) REVERT: A 121 GLN cc_start: 0.9576 (tm-30) cc_final: 0.8760 (tm-30) REVERT: A 125 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8782 (mm-30) REVERT: A 167 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 176 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7703 (mtt) REVERT: A 201 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9184 (t) REVERT: A 217 CYS cc_start: 0.8315 (m) cc_final: 0.7868 (m) REVERT: A 372 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.7993 (mtm-85) REVERT: B 64 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.9460 (pp) REVERT: B 78 ASN cc_start: 0.7786 (t0) cc_final: 0.7265 (t0) REVERT: B 106 THR cc_start: 0.8550 (m) cc_final: 0.7989 (p) REVERT: B 111 ASN cc_start: 0.8292 (m110) cc_final: 0.8035 (m110) REVERT: B 190 MET cc_start: 0.8576 (mtp) cc_final: 0.8238 (mtt) REVERT: B 205 GLU cc_start: 0.8534 (pm20) cc_final: 0.8175 (pm20) REVERT: B 280 ASN cc_start: 0.8861 (m-40) cc_final: 0.8423 (m110) REVERT: B 325 MET cc_start: 0.4420 (mtt) cc_final: 0.3709 (mtt) REVERT: B 372 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8321 (ttm-80) REVERT: C 111 ASN cc_start: 0.8401 (t0) cc_final: 0.7964 (m110) REVERT: C 113 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.7740 (mtmm) REVERT: C 118 LYS cc_start: 0.9175 (ttmm) cc_final: 0.8893 (ttmm) REVERT: C 132 MET cc_start: 0.9046 (ppp) cc_final: 0.8519 (ppp) REVERT: C 222 ASP cc_start: 0.8684 (t0) cc_final: 0.8238 (t0) REVERT: C 349 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9085 (mm) REVERT: C 375 PHE cc_start: 0.8234 (t80) cc_final: 0.7852 (t80) REVERT: D 11 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.7255 (p0) REVERT: D 12 ASN cc_start: 0.8982 (p0) cc_final: 0.8591 (p0) REVERT: D 59 GLN cc_start: 0.9414 (mm-40) cc_final: 0.9146 (mm-40) REVERT: D 72 GLU cc_start: 0.8200 (mp0) cc_final: 0.7775 (mp0) REVERT: D 288 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8508 (m-30) REVERT: D 305 MET cc_start: 0.8114 (ttp) cc_final: 0.7889 (ptp) REVERT: D 371 HIS cc_start: 0.8665 (m90) cc_final: 0.8450 (m90) REVERT: E 93 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7875 (mp0) REVERT: E 101 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7290 (m-70) REVERT: E 128 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8129 (t0) REVERT: E 140 LEU cc_start: 0.9104 (mp) cc_final: 0.8555 (mt) REVERT: E 143 TYR cc_start: 0.8248 (m-80) cc_final: 0.7968 (m-80) REVERT: E 154 ASP cc_start: 0.8451 (t70) cc_final: 0.7917 (t0) REVERT: E 185 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9028 (mm) REVERT: E 198 TYR cc_start: 0.9256 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: E 246 GLN cc_start: 0.8783 (mp10) cc_final: 0.8515 (mp10) REVERT: E 283 MET cc_start: 0.9280 (mmt) cc_final: 0.8975 (mmp) REVERT: E 305 MET cc_start: 0.8634 (mmm) cc_final: 0.8361 (tpp) REVERT: F 82 MET cc_start: 0.8889 (tpt) cc_final: 0.8437 (tpp) REVERT: F 86 TRP cc_start: 0.9250 (m-10) cc_final: 0.8788 (m-10) REVERT: F 111 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.6683 (m-40) REVERT: F 117 GLU cc_start: 0.8644 (tt0) cc_final: 0.8105 (mm-30) REVERT: F 123 MET cc_start: 0.9355 (tpp) cc_final: 0.9046 (tpp) REVERT: F 154 ASP cc_start: 0.8363 (t0) cc_final: 0.7890 (t0) REVERT: F 178 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7810 (mm) REVERT: F 179 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7909 (t0) REVERT: F 196 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8640 (mpt-90) REVERT: F 214 GLU cc_start: 0.8635 (mt-10) cc_final: 0.7889 (mt-10) REVERT: F 313 MET cc_start: 0.9170 (tpp) cc_final: 0.8873 (tpp) REVERT: F 325 MET cc_start: 0.8720 (mmm) cc_final: 0.8213 (tpp) REVERT: G 230 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8760 (p0) REVERT: G 273 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8398 (mt-10) REVERT: J 14 ASP cc_start: 0.8183 (m-30) cc_final: 0.7941 (m-30) REVERT: J 26 GLU cc_start: 0.7249 (mt-10) cc_final: 0.7002 (mp0) REVERT: J 41 ASP cc_start: 0.7848 (t0) cc_final: 0.7622 (m-30) REVERT: K 105 LEU cc_start: 0.8232 (tt) cc_final: 0.7980 (tp) REVERT: K 116 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8202 (mtp85) REVERT: L 240 GLU cc_start: 0.8767 (tp30) cc_final: 0.8543 (tp30) REVERT: M 265 LEU cc_start: 0.9311 (mt) cc_final: 0.9071 (mt) REVERT: N 6 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8497 (ttpp) REVERT: N 7 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8605 (mmmt) REVERT: O 10 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8450 (mmm) REVERT: O 16 GLU cc_start: 0.8887 (pp20) cc_final: 0.8586 (pp20) REVERT: P 99 GLU cc_start: 0.9065 (pp20) cc_final: 0.8811 (pp20) REVERT: P 120 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6036 (mm-30) outliers start: 155 outliers final: 112 residues processed: 739 average time/residue: 0.1455 time to fit residues: 166.2641 Evaluate side-chains 715 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 584 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 111 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 10 MET Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 93 ILE Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 223 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 137 optimal weight: 0.0070 chunk 98 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076148 restraints weight = 59486.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078860 restraints weight = 26561.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.080596 restraints weight = 14860.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.081683 restraints weight = 9631.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082455 restraints weight = 7063.772| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23334 Z= 0.195 Angle : 0.765 16.225 31508 Z= 0.369 Chirality : 0.046 0.239 3488 Planarity : 0.004 0.044 4064 Dihedral : 7.042 84.388 3262 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 7.22 % Allowed : 25.34 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.17), residues: 2848 helix: 1.32 (0.14), residues: 1434 sheet: -0.62 (0.27), residues: 378 loop : -0.05 (0.21), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 129 TYR 0.029 0.001 TYR G 267 PHE 0.020 0.001 PHE M 241 TRP 0.019 0.002 TRP F 356 HIS 0.014 0.001 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00448 (23332) covalent geometry : angle 0.76451 (31508) hydrogen bonds : bond 0.04062 ( 1244) hydrogen bonds : angle 4.30792 ( 3453) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 605 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9452 (m) cc_final: 0.9219 (p) REVERT: A 59 GLN cc_start: 0.9573 (tp-100) cc_final: 0.9198 (tp40) REVERT: A 79 TRP cc_start: 0.8836 (m100) cc_final: 0.8419 (m100) REVERT: A 95 ARG cc_start: 0.9189 (mpp80) cc_final: 0.8429 (mpp80) REVERT: A 121 GLN cc_start: 0.9614 (tm-30) cc_final: 0.9140 (tm-30) REVERT: A 167 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 176 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7793 (mtt) REVERT: A 217 CYS cc_start: 0.8406 (m) cc_final: 0.7962 (m) REVERT: A 293 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8515 (mm) REVERT: A 313 MET cc_start: 0.8885 (ppp) cc_final: 0.8640 (tmm) REVERT: A 372 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.8021 (mtm-85) REVERT: B 64 ILE cc_start: 0.9728 (OUTLIER) cc_final: 0.9450 (pp) REVERT: B 78 ASN cc_start: 0.7986 (t0) cc_final: 0.7506 (t0) REVERT: B 106 THR cc_start: 0.8507 (m) cc_final: 0.7887 (p) REVERT: B 111 ASN cc_start: 0.8212 (m110) cc_final: 0.7957 (m110) REVERT: B 128 ASN cc_start: 0.9303 (m-40) cc_final: 0.8857 (t0) REVERT: B 280 ASN cc_start: 0.8927 (m-40) cc_final: 0.8495 (m110) REVERT: B 325 MET cc_start: 0.4082 (mtt) cc_final: 0.3409 (mtt) REVERT: B 372 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8432 (ttm-80) REVERT: C 113 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8357 (mtpp) REVERT: C 132 MET cc_start: 0.9106 (ppp) cc_final: 0.8677 (ppp) REVERT: C 222 ASP cc_start: 0.8875 (t0) cc_final: 0.8433 (t0) REVERT: C 292 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8497 (t0) REVERT: C 349 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9091 (mm) REVERT: C 375 PHE cc_start: 0.8419 (t80) cc_final: 0.8031 (t80) REVERT: D 11 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.7452 (p0) REVERT: D 12 ASN cc_start: 0.9067 (p0) cc_final: 0.8684 (p0) REVERT: D 59 GLN cc_start: 0.9421 (mm-40) cc_final: 0.9191 (mm-40) REVERT: D 72 GLU cc_start: 0.8300 (mp0) cc_final: 0.7894 (mp0) REVERT: D 288 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8142 (t0) REVERT: D 340 TRP cc_start: 0.9108 (t60) cc_final: 0.8575 (t60) REVERT: D 371 HIS cc_start: 0.8717 (m90) cc_final: 0.8507 (m90) REVERT: E 101 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7394 (m-70) REVERT: E 128 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.7938 (t0) REVERT: E 143 TYR cc_start: 0.8460 (m-80) cc_final: 0.8090 (m-80) REVERT: E 154 ASP cc_start: 0.8467 (t70) cc_final: 0.7934 (t0) REVERT: E 198 TYR cc_start: 0.9296 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: E 283 MET cc_start: 0.9303 (mmt) cc_final: 0.9034 (mmp) REVERT: E 305 MET cc_start: 0.8694 (mmm) cc_final: 0.8450 (tpp) REVERT: E 356 TRP cc_start: 0.8888 (m100) cc_final: 0.8606 (m100) REVERT: F 82 MET cc_start: 0.8968 (tpt) cc_final: 0.8502 (tpp) REVERT: F 86 TRP cc_start: 0.9301 (m-10) cc_final: 0.8856 (m-10) REVERT: F 111 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.6196 (m110) REVERT: F 117 GLU cc_start: 0.8699 (tt0) cc_final: 0.8172 (mm-30) REVERT: F 121 GLN cc_start: 0.9561 (tm-30) cc_final: 0.8679 (tm-30) REVERT: F 123 MET cc_start: 0.9351 (tpp) cc_final: 0.9049 (tpp) REVERT: F 154 ASP cc_start: 0.8382 (t0) cc_final: 0.7883 (t0) REVERT: F 179 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8020 (t0) REVERT: F 196 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8688 (mpt-90) REVERT: F 325 MET cc_start: 0.8737 (mmm) cc_final: 0.8253 (tpp) REVERT: G 273 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8449 (mt-10) REVERT: J 24 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8782 (tm-30) REVERT: K 116 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8244 (mtp85) REVERT: L 240 GLU cc_start: 0.8736 (tp30) cc_final: 0.8508 (tp30) REVERT: M 265 LEU cc_start: 0.9312 (mt) cc_final: 0.9072 (mt) REVERT: M 272 GLU cc_start: 0.7442 (tp30) cc_final: 0.7171 (tp30) REVERT: N 29 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7426 (ttmt) REVERT: O 10 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8343 (mmm) REVERT: O 16 GLU cc_start: 0.9075 (pp20) cc_final: 0.8800 (pp20) REVERT: P 99 GLU cc_start: 0.9098 (pp20) cc_final: 0.8786 (pp20) REVERT: P 120 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.5959 (mm-30) REVERT: P 123 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8245 (mt) outliers start: 178 outliers final: 130 residues processed: 721 average time/residue: 0.1734 time to fit residues: 192.9633 Evaluate side-chains 722 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 573 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 111 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 10 MET Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 93 ILE Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 279 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 275 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 191 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** L 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077234 restraints weight = 58498.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.079925 restraints weight = 26362.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.081662 restraints weight = 14784.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082773 restraints weight = 9569.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083529 restraints weight = 6970.964| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23334 Z= 0.161 Angle : 0.771 16.566 31508 Z= 0.371 Chirality : 0.046 0.245 3488 Planarity : 0.004 0.061 4064 Dihedral : 6.931 87.390 3258 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 6.20 % Allowed : 26.16 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.17), residues: 2848 helix: 1.27 (0.14), residues: 1440 sheet: -0.56 (0.27), residues: 378 loop : -0.01 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG P 116 TYR 0.025 0.001 TYR H 267 PHE 0.039 0.001 PHE M 241 TRP 0.016 0.001 TRP E 86 HIS 0.011 0.001 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00369 (23332) covalent geometry : angle 0.77095 (31508) hydrogen bonds : bond 0.03978 ( 1244) hydrogen bonds : angle 4.29501 ( 3453) Misc. bond : bond 0.00123 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 606 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8672 (mmt) cc_final: 0.8458 (mmm) REVERT: A 59 GLN cc_start: 0.9585 (tp-100) cc_final: 0.9164 (tp40) REVERT: A 79 TRP cc_start: 0.8861 (m100) cc_final: 0.8425 (m100) REVERT: A 95 ARG cc_start: 0.9155 (mpp80) cc_final: 0.8415 (mpp80) REVERT: A 121 GLN cc_start: 0.9605 (tm-30) cc_final: 0.8782 (tm-30) REVERT: A 125 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8777 (mm-30) REVERT: A 132 MET cc_start: 0.8286 (tmm) cc_final: 0.7838 (tmm) REVERT: A 167 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 176 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7748 (mtt) REVERT: A 217 CYS cc_start: 0.8368 (m) cc_final: 0.7916 (m) REVERT: A 372 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8055 (mtm-85) REVERT: B 64 ILE cc_start: 0.9718 (OUTLIER) cc_final: 0.9435 (pp) REVERT: B 78 ASN cc_start: 0.7751 (t0) cc_final: 0.7225 (t0) REVERT: B 106 THR cc_start: 0.8462 (m) cc_final: 0.7839 (p) REVERT: B 111 ASN cc_start: 0.8249 (m110) cc_final: 0.8000 (m110) REVERT: B 128 ASN cc_start: 0.9249 (m-40) cc_final: 0.8840 (t0) REVERT: B 190 MET cc_start: 0.8547 (mtp) cc_final: 0.8231 (mtt) REVERT: B 280 ASN cc_start: 0.8900 (m-40) cc_final: 0.8483 (m110) REVERT: B 325 MET cc_start: 0.4162 (mtt) cc_final: 0.3509 (mtt) REVERT: B 330 ILE cc_start: 0.9180 (mm) cc_final: 0.8972 (mm) REVERT: B 372 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8317 (ttm-80) REVERT: C 113 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8343 (mtpp) REVERT: C 118 LYS cc_start: 0.9171 (ttmm) cc_final: 0.8856 (ttmm) REVERT: C 132 MET cc_start: 0.9050 (ppp) cc_final: 0.8598 (ppp) REVERT: C 222 ASP cc_start: 0.8866 (t0) cc_final: 0.8398 (t0) REVERT: C 283 MET cc_start: 0.8492 (mmp) cc_final: 0.8159 (mmm) REVERT: C 325 MET cc_start: 0.8671 (mmm) cc_final: 0.8448 (mmm) REVERT: C 349 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9058 (mm) REVERT: C 375 PHE cc_start: 0.8300 (t80) cc_final: 0.7950 (t80) REVERT: D 11 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.7487 (p0) REVERT: D 12 ASN cc_start: 0.9040 (p0) cc_final: 0.8687 (p0) REVERT: D 72 GLU cc_start: 0.8269 (mp0) cc_final: 0.7877 (mp0) REVERT: D 184 ASP cc_start: 0.8805 (t70) cc_final: 0.8470 (t70) REVERT: D 288 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8530 (m-30) REVERT: D 305 MET cc_start: 0.8101 (ttp) cc_final: 0.7872 (ptp) REVERT: D 325 MET cc_start: 0.8868 (mmp) cc_final: 0.8531 (mmt) REVERT: D 340 TRP cc_start: 0.9074 (t60) cc_final: 0.8559 (t60) REVERT: E 93 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7965 (mp0) REVERT: E 101 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7508 (m-70) REVERT: E 128 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8028 (t0) REVERT: E 154 ASP cc_start: 0.8480 (t70) cc_final: 0.7946 (t0) REVERT: E 198 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: E 283 MET cc_start: 0.9255 (mmt) cc_final: 0.8997 (mmp) REVERT: E 305 MET cc_start: 0.8663 (mmm) cc_final: 0.8401 (tpp) REVERT: F 82 MET cc_start: 0.8914 (tpt) cc_final: 0.8420 (tpp) REVERT: F 86 TRP cc_start: 0.9254 (m-10) cc_final: 0.8792 (m-10) REVERT: F 107 GLU cc_start: 0.8337 (tp30) cc_final: 0.8013 (tp30) REVERT: F 111 ASN cc_start: 0.8375 (m-40) cc_final: 0.7697 (m-40) REVERT: F 121 GLN cc_start: 0.9571 (tm-30) cc_final: 0.8737 (tm-30) REVERT: F 123 MET cc_start: 0.9331 (tpp) cc_final: 0.9036 (tpp) REVERT: F 154 ASP cc_start: 0.8267 (t0) cc_final: 0.7748 (t0) REVERT: F 179 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7978 (t0) REVERT: F 325 MET cc_start: 0.8705 (mmm) cc_final: 0.8214 (tpp) REVERT: G 255 ASP cc_start: 0.9418 (m-30) cc_final: 0.8946 (p0) REVERT: J 24 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8853 (tm-30) REVERT: K 116 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8235 (mtp85) REVERT: L 240 GLU cc_start: 0.8709 (tp30) cc_final: 0.8489 (tp30) REVERT: M 281 MET cc_start: 0.7075 (tpp) cc_final: 0.6790 (tpp) REVERT: N 8 MET cc_start: 0.7893 (tmm) cc_final: 0.7491 (tmm) REVERT: O 10 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: O 13 LEU cc_start: 0.8959 (tt) cc_final: 0.8684 (tt) REVERT: O 16 GLU cc_start: 0.9073 (pp20) cc_final: 0.8807 (pp20) REVERT: P 99 GLU cc_start: 0.9091 (pp20) cc_final: 0.8787 (pp20) REVERT: P 120 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6393 (mm-30) REVERT: P 123 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8370 (mt) REVERT: P 132 LYS cc_start: 0.9523 (mmmt) cc_final: 0.9248 (mmmt) outliers start: 153 outliers final: 118 residues processed: 708 average time/residue: 0.1633 time to fit residues: 177.8309 Evaluate side-chains 710 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 578 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain O residue 10 MET Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 113 PHE Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 183 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 106 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 240 optimal weight: 0.7980 chunk 283 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.078478 restraints weight = 59030.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081267 restraints weight = 26245.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083046 restraints weight = 14589.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084111 restraints weight = 9410.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084857 restraints weight = 6953.221| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23334 Z= 0.144 Angle : 0.800 16.645 31508 Z= 0.385 Chirality : 0.046 0.240 3488 Planarity : 0.004 0.058 4064 Dihedral : 6.758 88.669 3253 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 5.27 % Allowed : 27.37 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.17), residues: 2848 helix: 1.23 (0.14), residues: 1442 sheet: -0.48 (0.27), residues: 378 loop : 0.02 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 129 TYR 0.020 0.001 TYR H 267 PHE 0.033 0.001 PHE A 352 TRP 0.018 0.001 TRP E 86 HIS 0.010 0.001 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00332 (23332) covalent geometry : angle 0.80024 (31508) hydrogen bonds : bond 0.03977 ( 1244) hydrogen bonds : angle 4.32118 ( 3453) Misc. bond : bond 0.00173 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 620 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.9580 (tp-100) cc_final: 0.9156 (tp40) REVERT: A 95 ARG cc_start: 0.9181 (mpp80) cc_final: 0.8424 (mpp80) REVERT: A 118 LYS cc_start: 0.9576 (ttmt) cc_final: 0.9005 (mtpt) REVERT: A 121 GLN cc_start: 0.9596 (tm-30) cc_final: 0.8777 (tm-30) REVERT: A 125 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8722 (mm-30) REVERT: A 132 MET cc_start: 0.8339 (tmm) cc_final: 0.7896 (tmm) REVERT: A 167 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 176 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7817 (mtt) REVERT: A 217 CYS cc_start: 0.8350 (m) cc_final: 0.7885 (m) REVERT: A 372 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8042 (mtm-85) REVERT: B 64 ILE cc_start: 0.9732 (OUTLIER) cc_final: 0.9487 (pp) REVERT: B 78 ASN cc_start: 0.7766 (t0) cc_final: 0.7227 (t0) REVERT: B 106 THR cc_start: 0.8406 (m) cc_final: 0.7763 (p) REVERT: B 111 ASN cc_start: 0.8297 (m110) cc_final: 0.7974 (m110) REVERT: B 128 ASN cc_start: 0.9309 (m-40) cc_final: 0.8882 (t0) REVERT: B 154 ASP cc_start: 0.8784 (t70) cc_final: 0.8529 (t0) REVERT: B 165 ILE cc_start: 0.9720 (mt) cc_final: 0.9506 (mm) REVERT: B 190 MET cc_start: 0.8538 (mtp) cc_final: 0.8229 (mtt) REVERT: B 280 ASN cc_start: 0.8899 (m-40) cc_final: 0.8465 (m110) REVERT: B 325 MET cc_start: 0.4536 (mtt) cc_final: 0.3916 (mmt) REVERT: B 330 ILE cc_start: 0.9157 (mm) cc_final: 0.8934 (mm) REVERT: B 372 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8301 (ttm-80) REVERT: C 49 GLN cc_start: 0.8536 (mm110) cc_final: 0.8317 (mm-40) REVERT: C 113 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8373 (mtpp) REVERT: C 118 LYS cc_start: 0.9043 (ttmm) cc_final: 0.8716 (ttmm) REVERT: C 132 MET cc_start: 0.9095 (ppp) cc_final: 0.8601 (ppp) REVERT: C 222 ASP cc_start: 0.8870 (t0) cc_final: 0.8373 (t0) REVERT: C 283 MET cc_start: 0.8456 (mmp) cc_final: 0.8148 (mmm) REVERT: C 292 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8449 (t0) REVERT: C 335 ARG cc_start: 0.9207 (mtm-85) cc_final: 0.8319 (mtm180) REVERT: C 349 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9076 (mm) REVERT: C 375 PHE cc_start: 0.8261 (t80) cc_final: 0.7906 (t80) REVERT: D 11 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.7234 (p0) REVERT: D 12 ASN cc_start: 0.9041 (p0) cc_final: 0.8803 (p0) REVERT: D 72 GLU cc_start: 0.8215 (mp0) cc_final: 0.7797 (mp0) REVERT: D 121 GLN cc_start: 0.9341 (tt0) cc_final: 0.9096 (tp40) REVERT: D 154 ASP cc_start: 0.8982 (t70) cc_final: 0.8654 (t70) REVERT: D 184 ASP cc_start: 0.8845 (t70) cc_final: 0.8516 (t70) REVERT: D 288 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8541 (m-30) REVERT: D 305 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7816 (ptp) REVERT: D 325 MET cc_start: 0.8876 (mmp) cc_final: 0.8620 (mmm) REVERT: D 340 TRP cc_start: 0.9026 (t60) cc_final: 0.8490 (t60) REVERT: D 371 HIS cc_start: 0.8692 (m90) cc_final: 0.8367 (m90) REVERT: E 93 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8015 (mp0) REVERT: E 101 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7527 (m-70) REVERT: E 128 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8018 (t0) REVERT: E 154 ASP cc_start: 0.8498 (t70) cc_final: 0.7955 (t0) REVERT: E 198 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: E 283 MET cc_start: 0.9244 (mmt) cc_final: 0.8976 (mmp) REVERT: E 305 MET cc_start: 0.8692 (mmm) cc_final: 0.8468 (tpp) REVERT: F 82 MET cc_start: 0.8913 (tpt) cc_final: 0.8495 (tpp) REVERT: F 86 TRP cc_start: 0.9223 (m-10) cc_final: 0.8828 (m-10) REVERT: F 111 ASN cc_start: 0.8360 (m-40) cc_final: 0.7707 (m-40) REVERT: F 117 GLU cc_start: 0.8845 (tt0) cc_final: 0.8567 (tp30) REVERT: F 123 MET cc_start: 0.9355 (tpp) cc_final: 0.9098 (tpp) REVERT: F 154 ASP cc_start: 0.8321 (t0) cc_final: 0.7758 (t0) REVERT: F 155 SER cc_start: 0.9401 (t) cc_final: 0.9068 (t) REVERT: G 240 GLU cc_start: 0.8708 (tp30) cc_final: 0.8462 (tp30) REVERT: K 116 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8159 (mtp85) REVERT: L 240 GLU cc_start: 0.8697 (tp30) cc_final: 0.8497 (tp30) REVERT: M 258 ASP cc_start: 0.8465 (m-30) cc_final: 0.8179 (m-30) REVERT: M 261 TYR cc_start: 0.8556 (t80) cc_final: 0.8156 (t80) REVERT: N 8 MET cc_start: 0.7886 (tmm) cc_final: 0.7552 (tmm) REVERT: O 16 GLU cc_start: 0.9108 (pp20) cc_final: 0.8769 (pp20) REVERT: P 99 GLU cc_start: 0.9102 (pp20) cc_final: 0.8805 (pp20) REVERT: P 120 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: P 123 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8325 (mt) REVERT: P 132 LYS cc_start: 0.9519 (mmmt) cc_final: 0.9246 (mmmt) outliers start: 130 outliers final: 97 residues processed: 703 average time/residue: 0.1505 time to fit residues: 164.0472 Evaluate side-chains 697 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 586 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 20 ASP Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 114 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 281 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.097298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.077472 restraints weight = 58944.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080211 restraints weight = 26351.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081948 restraints weight = 14667.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083074 restraints weight = 9485.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083799 restraints weight = 6912.402| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23334 Z= 0.170 Angle : 0.824 16.858 31508 Z= 0.401 Chirality : 0.047 0.344 3488 Planarity : 0.004 0.057 4064 Dihedral : 6.691 88.256 3247 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 4.83 % Allowed : 28.18 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2848 helix: 0.96 (0.14), residues: 1478 sheet: -0.54 (0.27), residues: 372 loop : -0.05 (0.22), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 129 TYR 0.020 0.001 TYR H 267 PHE 0.046 0.001 PHE M 241 TRP 0.077 0.002 TRP A 79 HIS 0.015 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00394 (23332) covalent geometry : angle 0.82381 (31508) hydrogen bonds : bond 0.04103 ( 1244) hydrogen bonds : angle 4.42824 ( 3453) Misc. bond : bond 0.00162 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 590 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.9571 (tp-100) cc_final: 0.9159 (tp40) REVERT: A 95 ARG cc_start: 0.9226 (mpp80) cc_final: 0.8477 (mpp80) REVERT: A 132 MET cc_start: 0.8302 (tmm) cc_final: 0.7921 (tmm) REVERT: A 167 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 176 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7839 (mtt) REVERT: A 217 CYS cc_start: 0.8397 (m) cc_final: 0.7941 (m) REVERT: A 372 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8047 (mtm-85) REVERT: B 64 ILE cc_start: 0.9731 (OUTLIER) cc_final: 0.9465 (pp) REVERT: B 78 ASN cc_start: 0.7684 (t0) cc_final: 0.7156 (t0) REVERT: B 106 THR cc_start: 0.8355 (m) cc_final: 0.7736 (p) REVERT: B 128 ASN cc_start: 0.9306 (m-40) cc_final: 0.8885 (t0) REVERT: B 154 ASP cc_start: 0.8847 (t70) cc_final: 0.8607 (t0) REVERT: B 165 ILE cc_start: 0.9713 (mt) cc_final: 0.9504 (mm) REVERT: B 190 MET cc_start: 0.8532 (mtp) cc_final: 0.8234 (mtt) REVERT: B 280 ASN cc_start: 0.8915 (m-40) cc_final: 0.8494 (m110) REVERT: B 288 ASP cc_start: 0.8971 (p0) cc_final: 0.8580 (p0) REVERT: B 325 MET cc_start: 0.4188 (mtt) cc_final: 0.3610 (mmt) REVERT: B 330 ILE cc_start: 0.9176 (mm) cc_final: 0.8952 (mm) REVERT: C 118 LYS cc_start: 0.9170 (ttmm) cc_final: 0.8830 (ttmm) REVERT: C 132 MET cc_start: 0.9084 (ppp) cc_final: 0.8602 (ppp) REVERT: C 222 ASP cc_start: 0.8904 (t0) cc_final: 0.8370 (t0) REVERT: C 283 MET cc_start: 0.8470 (mmp) cc_final: 0.8161 (mmm) REVERT: C 292 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8502 (t0) REVERT: C 335 ARG cc_start: 0.9205 (mtm-85) cc_final: 0.8285 (mtm180) REVERT: C 349 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.8942 (mm) REVERT: C 375 PHE cc_start: 0.8334 (t80) cc_final: 0.8001 (t80) REVERT: D 11 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.7341 (p0) REVERT: D 12 ASN cc_start: 0.9097 (p0) cc_final: 0.8859 (p0) REVERT: D 72 GLU cc_start: 0.8210 (mp0) cc_final: 0.7795 (mp0) REVERT: D 184 ASP cc_start: 0.8858 (t70) cc_final: 0.8520 (t70) REVERT: D 283 MET cc_start: 0.8898 (mmm) cc_final: 0.8550 (mmm) REVERT: D 288 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8479 (m-30) REVERT: D 305 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7860 (ptp) REVERT: D 340 TRP cc_start: 0.9076 (t60) cc_final: 0.8548 (t60) REVERT: D 371 HIS cc_start: 0.8749 (m90) cc_final: 0.8481 (m170) REVERT: E 93 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8000 (mp0) REVERT: E 101 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7458 (m-70) REVERT: E 128 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8039 (t0) REVERT: E 154 ASP cc_start: 0.8532 (t70) cc_final: 0.8006 (t0) REVERT: E 283 MET cc_start: 0.9210 (mmt) cc_final: 0.8979 (mmp) REVERT: F 82 MET cc_start: 0.8948 (tpt) cc_final: 0.8529 (tpp) REVERT: F 86 TRP cc_start: 0.9249 (m-10) cc_final: 0.8820 (m-10) REVERT: F 117 GLU cc_start: 0.8882 (tt0) cc_final: 0.8445 (tp30) REVERT: F 123 MET cc_start: 0.9329 (tpp) cc_final: 0.9064 (tpp) REVERT: F 154 ASP cc_start: 0.8296 (t0) cc_final: 0.7739 (t0) REVERT: F 155 SER cc_start: 0.9507 (t) cc_final: 0.9081 (t) REVERT: G 240 GLU cc_start: 0.8754 (tp30) cc_final: 0.8482 (tp30) REVERT: J 38 GLN cc_start: 0.7227 (tp40) cc_final: 0.7017 (tp40) REVERT: L 240 GLU cc_start: 0.8674 (tp30) cc_final: 0.7654 (tp30) REVERT: M 258 ASP cc_start: 0.8408 (m-30) cc_final: 0.8114 (m-30) REVERT: M 281 MET cc_start: 0.6729 (tpp) cc_final: 0.6465 (tpp) REVERT: N 8 MET cc_start: 0.7882 (tmm) cc_final: 0.7439 (tmm) REVERT: N 42 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8733 (tt0) REVERT: O 16 GLU cc_start: 0.9061 (pp20) cc_final: 0.8725 (pp20) REVERT: P 99 GLU cc_start: 0.9112 (pp20) cc_final: 0.8772 (pp20) REVERT: P 120 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6561 (mm-30) REVERT: P 123 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8285 (mt) REVERT: P 132 LYS cc_start: 0.9561 (mmmt) cc_final: 0.9262 (mmmt) outliers start: 119 outliers final: 101 residues processed: 670 average time/residue: 0.1587 time to fit residues: 162.8542 Evaluate side-chains 677 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 565 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 20 ASP Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 20 ASP Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 51 optimal weight: 0.7980 chunk 221 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 171 optimal weight: 0.0050 chunk 107 optimal weight: 3.9990 chunk 166 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 92 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 GLN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.098832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.078925 restraints weight = 58739.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081685 restraints weight = 26213.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083444 restraints weight = 14612.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.084595 restraints weight = 9457.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085348 restraints weight = 6873.335| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23334 Z= 0.149 Angle : 0.839 16.900 31508 Z= 0.406 Chirality : 0.047 0.322 3488 Planarity : 0.004 0.054 4064 Dihedral : 6.606 84.804 3247 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 4.58 % Allowed : 28.95 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.16), residues: 2848 helix: 1.07 (0.14), residues: 1430 sheet: -0.45 (0.27), residues: 372 loop : -0.05 (0.21), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 244 TYR 0.022 0.001 TYR E 143 PHE 0.046 0.001 PHE M 241 TRP 0.073 0.002 TRP A 79 HIS 0.018 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00345 (23332) covalent geometry : angle 0.83938 (31508) hydrogen bonds : bond 0.04014 ( 1244) hydrogen bonds : angle 4.41823 ( 3453) Misc. bond : bond 0.00153 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4459.50 seconds wall clock time: 77 minutes 39.06 seconds (4659.06 seconds total)