Starting phenix.real_space_refine on Sun Jul 5 13:27:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mow_48483/07_2026/9mow_48483.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mow_48483/07_2026/9mow_48483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mow_48483/07_2026/9mow_48483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mow_48483/07_2026/9mow_48483.map" model { file = "/net/cci-nas-00/data/ceres_data/9mow_48483/07_2026/9mow_48483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mow_48483/07_2026/9mow_48483.cif" } resolution = 4.9 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= 0.249 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 14 5.49 5 Mg 7 5.21 5 S 174 5.16 5 C 17923 2.51 5 N 4899 2.21 5 O 5640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28660 Number of models: 1 Model: "" Number of chains: 23 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: 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: "H" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1273 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "J" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 643 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Chain: "K" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 795 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain: "L" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1783 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'TRANS': 220} Chain: "M" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1783 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'TRANS': 220} Chain: "N" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "O" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} 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} Chain: "G" 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: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 6.00, per 1000 atoms: 0.21 Number of scatterers: 28660 At special positions: 0 Unit cell: (142.38, 100.344, 420.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 174 16.00 P 14 15.00 Mg 7 11.99 O 5640 8.00 N 4899 7.00 C 17923 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=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 994.1 milliseconds 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 42 sheets defined 58.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.635A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.567A 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: 3.764A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.798A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 4.056A 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: 3.885A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.852A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.222A 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: 3.554A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.603A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.300A 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 370 removed outlier: 3.512A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' 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: 3.634A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.764A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.799A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.057A 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: 3.887A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.855A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.225A 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 306 removed outlier: 3.553A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.600A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.300A 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: 3.512A 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 60 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.634A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.765A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.799A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 4.059A 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 204 through 217 removed outlier: 3.892A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.851A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.557A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.602A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.301A 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 370 removed outlier: 3.511A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 370' 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 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.634A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.567A 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: 3.768A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.792A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 4.057A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' 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: 3.888A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.852A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.556A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.604A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.843A 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: 4.300A 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: 3.512A 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 60 Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.635A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.764A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.795A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 4.053A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 204 through 217 removed outlier: 3.891A 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 257 through 262 Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.854A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.556A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.605A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 355 removed outlier: 4.300A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 370 removed outlier: 3.512A 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: 3.634A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.766A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.798A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 4.053A 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 204 through 217 removed outlier: 3.890A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 273 through 284 removed outlier: 3.854A pdb=" N THR F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 4.224A 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: 3.555A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.604A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) removed outlier: 3.845A 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: 4.300A 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: 3.512A 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 56 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.632A pdb=" N GLU G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 101' Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.764A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.795A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 145 " --> pdb=" O SER G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 removed outlier: 4.056A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 204 through 217 removed outlier: 3.886A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 257 through 262 Processing helix chain 'G' and resid 273 through 284 removed outlier: 3.852A pdb=" N THR G 278 " --> pdb=" O ILE G 274 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR G 279 " --> pdb=" O HIS G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'G' and resid 301 through 306 removed outlier: 3.558A pdb=" N THR G 304 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 removed outlier: 3.603A pdb=" N ARG G 312 " --> pdb=" O GLY G 308 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 350 through 355 removed outlier: 4.301A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 367 through 370 removed outlier: 3.507A pdb=" N VAL G 370 " --> pdb=" O PRO G 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 367 through 370' Processing helix chain 'H' and resid 3 through 12 Processing helix chain 'H' and resid 13 through 28 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 73 through 84 removed outlier: 3.693A pdb=" N CYS H 84 " --> pdb=" O MET H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 113 through 125 removed outlier: 3.581A pdb=" N LEU H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 141 Processing helix chain 'H' and resid 149 through 157 Processing helix chain 'I' and resid 43 through 81 removed outlier: 3.852A pdb=" N LYS I 47 " --> pdb=" O SER I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 138 Processing helix chain 'I' and resid 151 through 161 Processing helix chain 'I' and resid 162 through 164 No H-bonds generated for 'chain 'I' and resid 162 through 164' Processing helix chain 'J' and resid 200 through 216 Processing helix chain 'J' and resid 225 through 271 Processing helix chain 'K' and resid 87 through 175 Processing helix chain 'L' and resid 65 through 283 Processing helix chain 'M' and resid 65 through 283 removed outlier: 3.840A pdb=" N SER M 283 " --> pdb=" O ASN M 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 55 removed outlier: 3.546A pdb=" N SER N 45 " --> pdb=" O ASP N 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 55 removed outlier: 3.578A pdb=" N LYS O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.518A pdb=" N TYR A 53 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 35 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 68 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.717A pdb=" N MET A 132 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.517A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.710A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 155 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 4.481A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (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: 3.520A pdb=" N TYR B 53 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 35 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 68 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.718A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.516A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.710A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 242 removed outlier: 4.482A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 19 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.515A pdb=" N TYR C 53 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 35 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 68 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 103 through 107 removed outlier: 3.716A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.516A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.712A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 242 removed outlier: 4.480A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.520A pdb=" N TYR D 53 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 35 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 103 through 107 removed outlier: 3.715A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.518A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.709A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 242 removed outlier: 4.483A pdb=" N LEU D 242 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLN D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.521A pdb=" N TYR E 53 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL E 35 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS E 68 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 103 through 107 removed outlier: 3.719A pdb=" N MET E 132 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.517A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.708A pdb=" N HIS E 161 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER E 155 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 242 removed outlier: 4.481A pdb=" N LEU E 242 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.521A pdb=" N TYR F 53 " --> pdb=" O GLY F 36 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL F 35 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS F 68 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 103 through 107 removed outlier: 3.716A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.519A pdb=" N MET F 176 " --> pdb=" O ASN F 162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.709A pdb=" N HIS F 161 " --> pdb=" O ASP F 154 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER F 155 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 242 removed outlier: 4.481A pdb=" N LEU F 242 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.518A pdb=" N TYR G 53 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL G 35 " --> pdb=" O LYS G 68 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS G 68 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG G 37 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 103 through 107 removed outlier: 3.716A pdb=" N MET G 132 " --> pdb=" O ILE G 357 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.518A pdb=" N MET G 176 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.709A pdb=" N HIS G 161 " --> pdb=" O ASP G 154 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER G 155 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 238 through 242 removed outlier: 4.479A pdb=" N LEU G 242 " --> pdb=" O GLN G 246 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLN G 246 " --> pdb=" O LEU G 242 " (cutoff:3.500A) 1646 hydrogen bonds defined for protein. 4581 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: 5.62 Time building geometry restraints manager: 3.50 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: 9550 1.34 - 1.46: 4562 1.46 - 1.58: 14705 1.58 - 1.69: 21 1.69 - 1.81: 307 Bond restraints: 29145 Sorted by residual: bond pdb=" CA VAL J 218 " pdb=" CB VAL J 218 " ideal model delta sigma weight residual 1.540 1.511 0.029 1.36e-02 5.41e+03 4.56e+00 bond pdb=" CA VAL K 121 " pdb=" CB VAL K 121 " ideal model delta sigma weight residual 1.540 1.517 0.023 1.17e-02 7.31e+03 3.75e+00 bond pdb=" CA ILE K 106 " pdb=" CB ILE K 106 " ideal model delta sigma weight residual 1.539 1.518 0.021 1.20e-02 6.94e+03 3.11e+00 bond pdb=" CD ARG J 201 " pdb=" NE ARG J 201 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.40e-02 5.10e+03 2.65e+00 bond pdb=" CD ARG K 129 " pdb=" NE ARG K 129 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.40e-02 5.10e+03 2.61e+00 ... (remaining 29140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 37409 1.43 - 2.86: 1518 2.86 - 4.29: 287 4.29 - 5.72: 106 5.72 - 7.15: 18 Bond angle restraints: 39338 Sorted by residual: angle pdb=" N LEU L 64 " pdb=" CA LEU L 64 " pdb=" CB LEU L 64 " ideal model delta sigma weight residual 110.50 103.60 6.90 1.70e+00 3.46e-01 1.65e+01 angle pdb=" N LEU M 64 " pdb=" CA LEU M 64 " pdb=" CB LEU M 64 " ideal model delta sigma weight residual 110.50 103.71 6.79 1.70e+00 3.46e-01 1.60e+01 angle pdb=" CA ASP A 211 " pdb=" CB ASP A 211 " pdb=" CG ASP A 211 " ideal model delta sigma weight residual 112.60 109.14 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" CA ASP E 211 " pdb=" CB ASP E 211 " pdb=" CG ASP E 211 " ideal model delta sigma weight residual 112.60 109.19 3.41 1.00e+00 1.00e+00 1.16e+01 angle pdb=" CA ASP B 211 " pdb=" CB ASP B 211 " pdb=" CG ASP B 211 " ideal model delta sigma weight residual 112.60 109.20 3.40 1.00e+00 1.00e+00 1.15e+01 ... (remaining 39333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 16207 17.32 - 34.65: 1265 34.65 - 51.97: 332 51.97 - 69.30: 97 69.30 - 86.62: 30 Dihedral angle restraints: 17931 sinusoidal: 7462 harmonic: 10469 Sorted by residual: dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 1.46 -61.46 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 1.46 -61.45 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 1.34 -61.34 1 2.00e+01 2.50e-03 1.25e+01 ... (remaining 17928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2146 0.028 - 0.056: 1341 0.056 - 0.084: 497 0.084 - 0.112: 277 0.112 - 0.139: 93 Chirality restraints: 4354 Sorted by residual: chirality pdb=" CA ILE G 165 " pdb=" N ILE G 165 " pdb=" C ILE G 165 " pdb=" CB ILE G 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CG LEU G 349 " pdb=" CB LEU G 349 " pdb=" CD1 LEU G 349 " pdb=" CD2 LEU G 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CG LEU K 102 " pdb=" CB LEU K 102 " pdb=" CD1 LEU K 102 " pdb=" CD2 LEU K 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 4351 not shown) Planarity restraints: 5094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO E 243 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO C 243 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO D 243 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.028 5.00e-02 4.00e+02 ... (remaining 5091 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 34 2.20 - 2.88: 11292 2.88 - 3.55: 42035 3.55 - 4.23: 64167 4.23 - 4.90: 113475 Nonbonded interactions: 231003 Sorted by model distance: nonbonded pdb=" OD1 ASP H 65 " pdb="CA CA H 201 " model vdw 1.526 3.250 nonbonded pdb=" OD1 ASN H 143 " pdb="CA CA H 202 " model vdw 1.536 3.250 nonbonded pdb=" OE2 GLU M 273 " pdb=" N MET N 1 " model vdw 1.570 3.120 nonbonded pdb=" OD1 ASP H 141 " pdb="CA CA H 202 " model vdw 1.591 3.250 nonbonded pdb=" OE1 GLN H 58 " pdb=" OE1 GLU L 163 " model vdw 1.639 3.040 ... (remaining 230998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'O' } 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.060 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5330 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 : 0.007 0.041 29145 Z= 0.339 Angle : 0.723 7.147 39338 Z= 0.406 Chirality : 0.046 0.139 4354 Planarity : 0.004 0.052 5094 Dihedral : 14.117 86.621 11175 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 8.13 % Allowed : 10.57 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3569 helix: 1.37 (0.13), residues: 1755 sheet: -2.26 (0.21), residues: 441 loop : -0.73 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 196 TYR 0.010 0.002 TYR D 240 PHE 0.013 0.002 PHE B 375 TRP 0.016 0.003 TRP F 340 HIS 0.006 0.001 HIS J 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.34 (29145) covalent geometry : angle 0.72319 / 0.41 (39338) hydrogen bonds : bond 0.15760 / 10.81 ( 1632) hydrogen bonds : angle 5.36614 / 3.74 ( 4581) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1694 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 1444 time to evaluate : 1.193 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: 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: 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: 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 53 TYR cc_start: 0.3034 (m-80) cc_final: 0.2633 (m-10) REVERT: A 212 ILE cc_start: 0.7603 (mt) cc_final: 0.7334 (mt) REVERT: A 223 PHE cc_start: 0.6314 (t80) cc_final: 0.6075 (t80) REVERT: A 274 ILE cc_start: 0.7270 (pt) cc_final: 0.6694 (mp) REVERT: A 275 HIS cc_start: 0.4298 (p90) cc_final: 0.4078 (p90) REVERT: A 300 SER cc_start: 0.3607 (OUTLIER) cc_final: 0.3059 (p) REVERT: B 89 THR cc_start: 0.7928 (m) cc_final: 0.7457 (p) REVERT: B 152 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.6063 (p) REVERT: B 185 LEU cc_start: 0.9289 (mt) cc_final: 0.9038 (mp) REVERT: B 189 LEU cc_start: 0.8111 (tp) cc_final: 0.7675 (tp) REVERT: B 217 CYS cc_start: 0.5938 (m) cc_final: 0.5624 (m) REVERT: B 262 PHE cc_start: 0.6892 (m-80) cc_final: 0.6272 (m-10) REVERT: B 323 SER cc_start: 0.8409 (m) cc_final: 0.7996 (p) REVERT: C 31 PHE cc_start: 0.5860 (p90) cc_final: 0.4711 (p90) REVERT: C 81 ASP cc_start: 0.7462 (m-30) cc_final: 0.6601 (t0) REVERT: C 124 PHE cc_start: 0.6377 (m-10) cc_final: 0.5826 (m-80) REVERT: C 140 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7229 (mm) REVERT: C 151 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7599 (tt) REVERT: C 153 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6244 (tt) REVERT: C 185 LEU cc_start: 0.9109 (mt) cc_final: 0.8886 (mp) REVERT: C 223 PHE cc_start: 0.6729 (t80) cc_final: 0.6188 (t80) REVERT: C 275 HIS cc_start: 0.4677 (p90) cc_final: 0.3499 (p-80) REVERT: C 280 ASN cc_start: 0.7740 (m-40) cc_final: 0.6554 (m110) REVERT: C 309 ILE cc_start: 0.6104 (tt) cc_final: 0.5748 (tt) REVERT: D 81 ASP cc_start: 0.7725 (m-30) cc_final: 0.7228 (m-30) REVERT: D 89 THR cc_start: 0.7729 (m) cc_final: 0.7525 (p) REVERT: D 115 ASN cc_start: 0.7723 (t0) cc_final: 0.7052 (t0) REVERT: D 151 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7212 (tt) REVERT: D 152 VAL cc_start: 0.7434 (OUTLIER) cc_final: 0.6430 (p) REVERT: D 153 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6836 (tt) REVERT: D 233 SER cc_start: 0.5308 (OUTLIER) cc_final: 0.4995 (p) REVERT: D 357 ILE cc_start: 0.8203 (mt) cc_final: 0.7623 (mp) REVERT: E 75 ILE cc_start: 0.5236 (pt) cc_final: 0.4514 (pt) REVERT: E 115 ASN cc_start: 0.7777 (t0) cc_final: 0.7328 (t0) REVERT: E 122 ILE cc_start: 0.7712 (mm) cc_final: 0.7474 (mt) REVERT: E 151 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7690 (tt) REVERT: E 152 VAL cc_start: 0.7052 (OUTLIER) cc_final: 0.6762 (p) REVERT: E 185 LEU cc_start: 0.9175 (mt) cc_final: 0.8714 (tt) REVERT: E 188 TYR cc_start: 0.7751 (t80) cc_final: 0.7267 (t80) REVERT: E 212 ILE cc_start: 0.8298 (mt) cc_final: 0.7979 (mt) REVERT: E 223 PHE cc_start: 0.6975 (t80) cc_final: 0.6632 (t80) REVERT: E 261 LEU cc_start: 0.7344 (mt) cc_final: 0.7038 (mt) REVERT: E 262 PHE cc_start: 0.7326 (m-80) cc_final: 0.6584 (m-10) REVERT: E 357 ILE cc_start: 0.8387 (mt) cc_final: 0.7482 (mp) REVERT: F 24 ASP cc_start: 0.5574 (OUTLIER) cc_final: 0.4618 (t0) REVERT: F 31 PHE cc_start: 0.5817 (p90) cc_final: 0.4998 (p90) REVERT: F 43 VAL cc_start: 0.7160 (m) cc_final: 0.6853 (m) REVERT: F 152 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.5599 (p) REVERT: F 180 LEU cc_start: 0.7571 (tt) cc_final: 0.7112 (tt) REVERT: F 212 ILE cc_start: 0.7508 (mt) cc_final: 0.6973 (mt) REVERT: F 253 GLU cc_start: 0.8568 (mp0) cc_final: 0.7726 (mt-10) REVERT: F 274 ILE cc_start: 0.6352 (pt) cc_final: 0.5255 (pt) REVERT: F 357 ILE cc_start: 0.8578 (mt) cc_final: 0.8217 (mp) REVERT: G 89 THR cc_start: 0.7984 (m) cc_final: 0.7652 (p) REVERT: G 163 VAL cc_start: 0.6596 (t) cc_final: 0.6386 (t) REVERT: G 250 ILE cc_start: 0.6288 (mm) cc_final: 0.5814 (mp) REVERT: G 274 ILE cc_start: 0.6759 (pt) cc_final: 0.4500 (pt) REVERT: G 346 LEU cc_start: 0.7727 (tp) cc_final: 0.7525 (tp) REVERT: H 67 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.7795 (p0) REVERT: H 88 ASP cc_start: 0.8150 (m-30) cc_final: 0.7678 (t0) REVERT: I 97 LEU cc_start: 0.8342 (mm) cc_final: 0.8052 (mm) REVERT: I 101 LEU cc_start: 0.8547 (mm) cc_final: 0.7352 (mm) REVERT: I 108 VAL cc_start: 0.7435 (t) cc_final: 0.6959 (p) REVERT: J 221 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7851 (pt) REVERT: J 234 LYS cc_start: 0.8326 (tptt) cc_final: 0.7972 (tptp) REVERT: J 253 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6846 (mmmt) REVERT: K 133 GLU cc_start: 0.8979 (pt0) cc_final: 0.8502 (pt0) REVERT: K 138 GLN cc_start: 0.6033 (tp40) cc_final: 0.5643 (tp-100) REVERT: L 131 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8259 (mm-30) REVERT: L 148 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7179 (mt) REVERT: L 196 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.9105 (mm-30) REVERT: L 249 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7102 (tt) REVERT: M 164 GLU cc_start: 0.8853 (tp30) cc_final: 0.8219 (mt-10) REVERT: M 243 GLU cc_start: 0.9003 (tt0) cc_final: 0.8735 (pp20) REVERT: M 246 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7831 (p) REVERT: M 247 THR cc_start: 0.9781 (p) cc_final: 0.8886 (p) REVERT: M 279 ASN cc_start: 0.8959 (m-40) cc_final: 0.8652 (m110) REVERT: N 36 SER cc_start: 0.7395 (OUTLIER) cc_final: 0.6717 (p) outliers start: 250 outliers final: 64 residues processed: 1617 average time/residue: 0.2339 time to fit residues: 560.4661 Evaluate side-chains 803 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 717 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN B 111 ASN C 59 GLN C 111 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN C 371 HIS D 111 ASN D 353 GLN E 40 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN F 353 GLN G 78 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS H 58 GLN H 122 GLN I 95 GLN J 238 GLN J 257 GLN J 266 ASN K 138 GLN K 142 ASN K 164 ASN L 202 ASN L 263 GLN M 68 GLN M 103 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.063066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.040825 restraints weight = 189419.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.042827 restraints weight = 122266.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.044333 restraints weight = 87776.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045518 restraints weight = 67453.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046456 restraints weight = 54193.191| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29145 Z= 0.187 Angle : 0.783 10.711 39338 Z= 0.399 Chirality : 0.048 0.319 4354 Planarity : 0.006 0.094 5094 Dihedral : 6.668 75.501 4000 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 0.39 % Allowed : 4.97 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3569 helix: 0.70 (0.12), residues: 1848 sheet: -1.82 (0.22), residues: 420 loop : -0.58 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 206 TYR 0.040 0.002 TYR D 143 PHE 0.027 0.002 PHE D 124 TRP 0.031 0.002 TRP D 79 HIS 0.011 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (29145) covalent geometry : angle 0.78302 / 0.40 (39338) hydrogen bonds : bond 0.05586 / 3.80 ( 1632) hydrogen bonds : angle 4.66288 / 3.25 ( 4581) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1065 time to evaluate : 1.954 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.8882 (m-80) cc_final: 0.8666 (m-10) REVERT: A 72 GLU cc_start: 0.9568 (pt0) cc_final: 0.9269 (mp0) REVERT: A 122 ILE cc_start: 0.9688 (mm) cc_final: 0.9422 (tt) REVERT: A 269 MET cc_start: 0.6249 (ttt) cc_final: 0.5906 (ttm) REVERT: A 275 HIS cc_start: 0.9792 (p90) cc_final: 0.9525 (p90) REVERT: B 128 ASN cc_start: 0.9782 (t0) cc_final: 0.9500 (m110) REVERT: B 178 LEU cc_start: 0.8709 (tp) cc_final: 0.8124 (tt) REVERT: B 179 ASP cc_start: 0.9578 (m-30) cc_final: 0.8981 (m-30) REVERT: B 266 PHE cc_start: 0.9351 (m-80) cc_final: 0.9116 (m-10) REVERT: B 275 HIS cc_start: 0.9326 (p90) cc_final: 0.9035 (p90) REVERT: B 294 TYR cc_start: 0.9023 (m-10) cc_final: 0.8778 (m-10) REVERT: B 305 MET cc_start: 0.7827 (mmp) cc_final: 0.7491 (mmt) REVERT: B 306 TYR cc_start: 0.8172 (m-10) cc_final: 0.7490 (m-10) REVERT: B 311 ASP cc_start: 0.9693 (m-30) cc_final: 0.9412 (m-30) REVERT: B 313 MET cc_start: 0.9349 (tpp) cc_final: 0.8838 (tpt) REVERT: B 336 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8952 (ttmm) REVERT: C 81 ASP cc_start: 0.8991 (m-30) cc_final: 0.8310 (t0) REVERT: C 225 ASN cc_start: 0.9894 (m110) cc_final: 0.9676 (m110) REVERT: C 261 LEU cc_start: 0.9578 (mp) cc_final: 0.9353 (mt) REVERT: C 262 PHE cc_start: 0.9208 (m-80) cc_final: 0.8989 (m-10) REVERT: C 274 ILE cc_start: 0.9600 (pt) cc_final: 0.9374 (pt) REVERT: C 311 ASP cc_start: 0.9232 (p0) cc_final: 0.8936 (p0) REVERT: C 313 MET cc_start: 0.9611 (tpp) cc_final: 0.8778 (tpp) REVERT: C 316 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8674 (tm-30) REVERT: C 317 ILE cc_start: 0.9595 (mm) cc_final: 0.8833 (mm) REVERT: D 56 ASP cc_start: 0.9638 (m-30) cc_final: 0.9257 (m-30) REVERT: D 81 ASP cc_start: 0.9133 (m-30) cc_final: 0.8449 (t0) REVERT: D 82 MET cc_start: 0.9175 (ptt) cc_final: 0.8944 (ppp) REVERT: D 85 ILE cc_start: 0.9842 (mm) cc_final: 0.9610 (mm) REVERT: D 120 THR cc_start: 0.9833 (p) cc_final: 0.9462 (p) REVERT: D 123 MET cc_start: 0.9821 (mmp) cc_final: 0.9527 (mmm) REVERT: D 132 MET cc_start: 0.9614 (ptt) cc_final: 0.9017 (tmm) REVERT: D 134 VAL cc_start: 0.9541 (t) cc_final: 0.8495 (p) REVERT: D 179 ASP cc_start: 0.9464 (m-30) cc_final: 0.9181 (m-30) REVERT: D 236 LEU cc_start: 0.8133 (mt) cc_final: 0.7797 (tp) REVERT: D 250 ILE cc_start: 0.9744 (mm) cc_final: 0.9332 (tp) REVERT: D 257 CYS cc_start: 0.9566 (t) cc_final: 0.9226 (t) REVERT: D 269 MET cc_start: 0.8761 (tpt) cc_final: 0.8441 (tpp) REVERT: D 355 MET cc_start: 0.9582 (mmp) cc_final: 0.9353 (mmm) REVERT: E 51 ASP cc_start: 0.9741 (m-30) cc_final: 0.9541 (t0) REVERT: E 79 TRP cc_start: 0.8480 (m100) cc_final: 0.8234 (m100) REVERT: E 86 TRP cc_start: 0.9618 (m-10) cc_final: 0.9411 (m-10) REVERT: E 122 ILE cc_start: 0.9470 (mm) cc_final: 0.9034 (mt) REVERT: E 165 ILE cc_start: 0.9809 (mm) cc_final: 0.9504 (tp) REVERT: E 176 MET cc_start: 0.8985 (mmm) cc_final: 0.8578 (mtp) REVERT: E 178 LEU cc_start: 0.9011 (tp) cc_final: 0.8529 (tp) REVERT: E 179 ASP cc_start: 0.9241 (m-30) cc_final: 0.8790 (m-30) REVERT: E 183 ARG cc_start: 0.9715 (tpp80) cc_final: 0.9405 (mmm-85) REVERT: E 189 LEU cc_start: 0.9657 (tp) cc_final: 0.9438 (tp) REVERT: E 250 ILE cc_start: 0.9426 (tp) cc_final: 0.9167 (tp) REVERT: E 257 CYS cc_start: 0.9085 (t) cc_final: 0.8306 (t) REVERT: E 262 PHE cc_start: 0.9723 (m-80) cc_final: 0.9451 (m-10) REVERT: E 275 HIS cc_start: 0.9725 (p90) cc_final: 0.8920 (p-80) REVERT: E 284 LYS cc_start: 0.9086 (ptpt) cc_final: 0.8801 (pttm) REVERT: E 294 TYR cc_start: 0.9600 (m-80) cc_final: 0.9248 (m-10) REVERT: E 313 MET cc_start: 0.9323 (tpt) cc_final: 0.9102 (tpt) REVERT: E 375 PHE cc_start: 0.9078 (t80) cc_final: 0.8693 (t80) REVERT: F 11 ASP cc_start: 0.9617 (t70) cc_final: 0.9057 (p0) REVERT: F 69 TYR cc_start: 0.9210 (m-10) cc_final: 0.8872 (m-80) REVERT: F 167 GLU cc_start: 0.9555 (mp0) cc_final: 0.9321 (mp0) REVERT: F 178 LEU cc_start: 0.8839 (tp) cc_final: 0.8427 (tp) REVERT: F 183 ARG cc_start: 0.9607 (tpp80) cc_final: 0.9266 (ptp-110) REVERT: F 217 CYS cc_start: 0.4773 (p) cc_final: 0.1890 (p) REVERT: F 277 THR cc_start: 0.9756 (p) cc_final: 0.9510 (p) REVERT: F 303 THR cc_start: 0.9451 (m) cc_final: 0.9045 (p) REVERT: G 180 LEU cc_start: 0.9277 (tt) cc_final: 0.8925 (tp) REVERT: G 269 MET cc_start: 0.9205 (ttm) cc_final: 0.8964 (ttm) REVERT: G 274 ILE cc_start: 0.9853 (pt) cc_final: 0.9605 (pt) REVERT: G 275 HIS cc_start: 0.9733 (p90) cc_final: 0.9530 (p90) REVERT: G 359 LYS cc_start: 0.9663 (tttm) cc_final: 0.9377 (mptt) REVERT: H 113 ASP cc_start: 0.8781 (t0) cc_final: 0.8572 (t0) REVERT: H 115 ASP cc_start: 0.9390 (m-30) cc_final: 0.9159 (m-30) REVERT: H 136 LEU cc_start: 0.9728 (tt) cc_final: 0.9466 (pp) REVERT: H 156 PHE cc_start: 0.8611 (p90) cc_final: 0.8321 (p90) REVERT: H 157 MET cc_start: 0.8286 (mmt) cc_final: 0.7883 (mmm) REVERT: I 54 MET cc_start: 0.9500 (mmp) cc_final: 0.9281 (mmm) REVERT: I 64 ARG cc_start: 0.9531 (ptm-80) cc_final: 0.9309 (ttp-110) REVERT: I 91 PHE cc_start: 0.9292 (m-80) cc_final: 0.9080 (m-10) REVERT: I 108 VAL cc_start: 0.9019 (t) cc_final: 0.8816 (p) REVERT: I 114 ASP cc_start: 0.9712 (t70) cc_final: 0.9494 (m-30) REVERT: K 95 MET cc_start: 0.7983 (tpp) cc_final: 0.7667 (tpp) REVERT: M 127 MET cc_start: 0.9155 (mmm) cc_final: 0.8844 (mmm) REVERT: M 139 GLU cc_start: 0.9932 (tm-30) cc_final: 0.9624 (mm-30) REVERT: M 141 MET cc_start: 0.9655 (tmm) cc_final: 0.9400 (tmm) REVERT: M 197 LEU cc_start: 0.9358 (tt) cc_final: 0.8996 (mt) REVERT: N 28 ASP cc_start: 0.9579 (t70) cc_final: 0.9297 (t70) REVERT: N 51 LYS cc_start: 0.9265 (tptp) cc_final: 0.9020 (tppt) outliers start: 12 outliers final: 3 residues processed: 1073 average time/residue: 0.2236 time to fit residues: 359.2891 Evaluate side-chains 699 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 696 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 72 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 340 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 320 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS A 275 HIS B 12 ASN B 353 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN E 252 ASN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN F 173 HIS F 353 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN G 353 GLN H 18 ASN I 60 GLN K 150 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 ASN M 103 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.056097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.035941 restraints weight = 213598.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.037631 restraints weight = 138212.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.038931 restraints weight = 99710.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.039922 restraints weight = 77183.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.040710 restraints weight = 62667.376| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 29145 Z= 0.266 Angle : 0.826 11.046 39338 Z= 0.429 Chirality : 0.048 0.301 4354 Planarity : 0.007 0.146 5094 Dihedral : 6.763 80.167 4000 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 0.29 % Allowed : 5.56 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3569 helix: 0.45 (0.12), residues: 1868 sheet: -1.31 (0.24), residues: 441 loop : -0.37 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG K 131 TYR 0.037 0.003 TYR C 294 PHE 0.030 0.003 PHE D 352 TRP 0.045 0.003 TRP F 86 HIS 0.010 0.002 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.27 (29145) covalent geometry : angle 0.82597 / 0.43 (39338) hydrogen bonds : bond 0.05559 / 3.79 ( 1632) hydrogen bonds : angle 4.83106 / 3.39 ( 4581) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 897 time to evaluate : 1.149 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: 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: 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 119 MET cc_start: 0.9147 (ppp) cc_final: 0.8946 (ppp) REVERT: A 269 MET cc_start: 0.6214 (ttt) cc_final: 0.5639 (ttp) REVERT: B 128 ASN cc_start: 0.9805 (t0) cc_final: 0.9552 (m110) REVERT: B 140 LEU cc_start: 0.9619 (mm) cc_final: 0.9362 (mm) REVERT: B 176 MET cc_start: 0.9115 (mtm) cc_final: 0.8844 (mtp) REVERT: B 179 ASP cc_start: 0.9456 (m-30) cc_final: 0.8809 (m-30) REVERT: B 188 TYR cc_start: 0.9439 (t80) cc_final: 0.8967 (t80) REVERT: B 189 LEU cc_start: 0.9624 (tp) cc_final: 0.9408 (tp) REVERT: B 213 LYS cc_start: 0.9538 (ttpp) cc_final: 0.9179 (ttpp) REVERT: B 257 CYS cc_start: 0.9318 (t) cc_final: 0.8674 (t) REVERT: B 266 PHE cc_start: 0.9127 (m-80) cc_final: 0.8683 (m-10) REVERT: B 269 MET cc_start: 0.6684 (ttm) cc_final: 0.6393 (ttm) REVERT: B 311 ASP cc_start: 0.9640 (m-30) cc_final: 0.9229 (t0) REVERT: C 16 LEU cc_start: 0.9369 (mp) cc_final: 0.9156 (mt) REVERT: C 69 TYR cc_start: 0.9038 (m-10) cc_final: 0.8700 (m-10) REVERT: C 81 ASP cc_start: 0.9214 (m-30) cc_final: 0.8449 (t0) REVERT: C 85 ILE cc_start: 0.9775 (mm) cc_final: 0.9485 (mt) REVERT: C 122 ILE cc_start: 0.9740 (mm) cc_final: 0.9398 (mt) REVERT: C 176 MET cc_start: 0.8753 (mmm) cc_final: 0.8364 (mtp) REVERT: C 253 GLU cc_start: 0.9739 (mp0) cc_final: 0.8804 (mt-10) REVERT: C 262 PHE cc_start: 0.9450 (m-80) cc_final: 0.8768 (m-10) REVERT: C 313 MET cc_start: 0.9509 (tpp) cc_final: 0.9129 (tpt) REVERT: C 316 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8902 (tm-30) REVERT: C 317 ILE cc_start: 0.9665 (mm) cc_final: 0.9353 (pt) REVERT: D 81 ASP cc_start: 0.9227 (m-30) cc_final: 0.8306 (t0) REVERT: D 82 MET cc_start: 0.9314 (ptt) cc_final: 0.8917 (ptm) REVERT: D 85 ILE cc_start: 0.9885 (mm) cc_final: 0.9644 (mm) REVERT: D 123 MET cc_start: 0.9871 (mmp) cc_final: 0.9661 (mmm) REVERT: D 132 MET cc_start: 0.9773 (ptt) cc_final: 0.9384 (ppp) REVERT: D 176 MET cc_start: 0.8860 (mtm) cc_final: 0.8069 (mtm) REVERT: D 179 ASP cc_start: 0.9434 (m-30) cc_final: 0.9162 (m-30) REVERT: D 213 LYS cc_start: 0.9612 (ttpt) cc_final: 0.9376 (mtpp) REVERT: D 223 PHE cc_start: 0.8784 (t80) cc_final: 0.8333 (t80) REVERT: D 236 LEU cc_start: 0.8311 (mt) cc_final: 0.7802 (tp) REVERT: D 250 ILE cc_start: 0.9790 (mm) cc_final: 0.9477 (tp) REVERT: D 257 CYS cc_start: 0.9586 (t) cc_final: 0.9129 (t) REVERT: D 269 MET cc_start: 0.8877 (tpt) cc_final: 0.8521 (tpp) REVERT: D 313 MET cc_start: 0.9660 (mmm) cc_final: 0.9454 (tpt) REVERT: D 355 MET cc_start: 0.9537 (mmp) cc_final: 0.9323 (mmm) REVERT: E 51 ASP cc_start: 0.9706 (m-30) cc_final: 0.9496 (t0) REVERT: E 69 TYR cc_start: 0.8984 (m-10) cc_final: 0.8377 (m-10) REVERT: E 122 ILE cc_start: 0.9525 (mm) cc_final: 0.9268 (mt) REVERT: E 151 ILE cc_start: 0.8962 (tt) cc_final: 0.8365 (tt) REVERT: E 169 TYR cc_start: 0.9720 (m-80) cc_final: 0.9200 (m-80) REVERT: E 176 MET cc_start: 0.9009 (mmm) cc_final: 0.8694 (mtp) REVERT: E 178 LEU cc_start: 0.9059 (tp) cc_final: 0.8528 (tp) REVERT: E 179 ASP cc_start: 0.9111 (m-30) cc_final: 0.8675 (m-30) REVERT: E 183 ARG cc_start: 0.9547 (tpp80) cc_final: 0.9269 (mmm-85) REVERT: E 190 MET cc_start: 0.9727 (ptp) cc_final: 0.9380 (ptp) REVERT: E 213 LYS cc_start: 0.9683 (ptpp) cc_final: 0.9307 (ptpp) REVERT: E 262 PHE cc_start: 0.9730 (m-80) cc_final: 0.9151 (m-80) REVERT: E 280 ASN cc_start: 0.9715 (m-40) cc_final: 0.9417 (m-40) REVERT: E 294 TYR cc_start: 0.9592 (m-80) cc_final: 0.9280 (m-10) REVERT: E 316 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9173 (mm-30) REVERT: E 375 PHE cc_start: 0.9009 (t80) cc_final: 0.8655 (t80) REVERT: F 12 ASN cc_start: 0.9779 (m110) cc_final: 0.9523 (p0) REVERT: F 82 MET cc_start: 0.9459 (ppp) cc_final: 0.9189 (ppp) REVERT: F 85 ILE cc_start: 0.9729 (mm) cc_final: 0.9326 (mm) REVERT: F 118 LYS cc_start: 0.9434 (tptp) cc_final: 0.9155 (tptp) REVERT: F 167 GLU cc_start: 0.9587 (mp0) cc_final: 0.9322 (mp0) REVERT: F 176 MET cc_start: 0.7988 (tmm) cc_final: 0.7522 (tmm) REVERT: F 180 LEU cc_start: 0.9243 (tt) cc_final: 0.8998 (tt) REVERT: F 183 ARG cc_start: 0.9558 (tpp80) cc_final: 0.9253 (ptp-110) REVERT: F 213 LYS cc_start: 0.9767 (ptpt) cc_final: 0.9356 (ptmm) REVERT: F 269 MET cc_start: 0.8891 (ttt) cc_final: 0.8666 (ttm) REVERT: F 303 THR cc_start: 0.9573 (m) cc_final: 0.9345 (p) REVERT: G 110 LEU cc_start: 0.9114 (mt) cc_final: 0.8657 (mt) REVERT: G 180 LEU cc_start: 0.9224 (tt) cc_final: 0.8908 (tp) REVERT: G 269 MET cc_start: 0.9318 (ttm) cc_final: 0.9111 (ttm) REVERT: H 80 MET cc_start: 0.5121 (tpp) cc_final: 0.4806 (mmm) REVERT: H 88 ASP cc_start: 0.8518 (m-30) cc_final: 0.7928 (t0) REVERT: H 120 MET cc_start: 0.9600 (mtm) cc_final: 0.9374 (mtm) REVERT: I 62 MET cc_start: 0.9615 (ttm) cc_final: 0.9328 (ttp) REVERT: I 91 PHE cc_start: 0.9351 (m-80) cc_final: 0.9007 (m-80) REVERT: J 229 LEU cc_start: 0.8881 (mm) cc_final: 0.6761 (mm) REVERT: K 127 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9354 (mt) REVERT: M 197 LEU cc_start: 0.9423 (tt) cc_final: 0.9071 (mt) REVERT: M 228 LEU cc_start: 0.9633 (mt) cc_final: 0.9375 (tp) REVERT: N 1 MET cc_start: 0.8208 (pmm) cc_final: 0.7504 (pmm) REVERT: O 1 MET cc_start: 0.7411 (mtt) cc_final: 0.7158 (ptt) REVERT: O 10 MET cc_start: 0.7754 (mpp) cc_final: 0.7505 (mpp) outliers start: 9 outliers final: 2 residues processed: 903 average time/residue: 0.2226 time to fit residues: 301.9107 Evaluate side-chains 621 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 618 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 204 optimal weight: 0.0670 chunk 278 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 328 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 290 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 280 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN A 252 ASN A 275 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 314 GLN C 115 ASN D 12 ASN E 225 ASN G 59 GLN G 111 ASN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 122 ASN J 238 GLN L 93 GLN L 202 ASN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 ASN ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.059321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.038154 restraints weight = 195039.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.040021 restraints weight = 121810.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.041425 restraints weight = 86378.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.042528 restraints weight = 66093.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.043393 restraints weight = 53047.244| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 29145 Z= 0.164 Angle : 0.761 12.733 39338 Z= 0.389 Chirality : 0.049 0.362 4354 Planarity : 0.006 0.154 5094 Dihedral : 6.535 83.935 4000 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.20 % Allowed : 4.36 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3569 helix: 0.52 (0.12), residues: 1856 sheet: -0.94 (0.24), residues: 434 loop : -0.24 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 144 TYR 0.050 0.002 TYR B 294 PHE 0.043 0.002 PHE E 223 TRP 0.052 0.003 TRP F 86 HIS 0.013 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (29145) covalent geometry : angle 0.76121 / 0.39 (39338) hydrogen bonds : bond 0.05342 / 3.62 ( 1632) hydrogen bonds : angle 4.74234 / 3.33 ( 4581) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 914 time to evaluate : 1.097 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: 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: 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 119 MET cc_start: 0.8871 (ppp) cc_final: 0.8510 (ppp) REVERT: A 122 ILE cc_start: 0.9010 (mm) cc_final: 0.8750 (tt) REVERT: B 73 HIS cc_start: 0.7760 (m90) cc_final: 0.7556 (m90) REVERT: B 122 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8323 (pt) REVERT: B 140 LEU cc_start: 0.8786 (mm) cc_final: 0.8577 (mm) REVERT: B 179 ASP cc_start: 0.9103 (m-30) cc_final: 0.8741 (m-30) REVERT: B 269 MET cc_start: 0.8282 (ttm) cc_final: 0.7934 (ttm) REVERT: B 274 ILE cc_start: 0.9306 (pt) cc_final: 0.9077 (pt) REVERT: B 275 HIS cc_start: 0.9231 (p90) cc_final: 0.8965 (p90) REVERT: B 311 ASP cc_start: 0.9400 (m-30) cc_final: 0.9131 (t0) REVERT: C 73 HIS cc_start: 0.8256 (m90) cc_final: 0.7908 (m170) REVERT: C 81 ASP cc_start: 0.7856 (m-30) cc_final: 0.7602 (t0) REVERT: C 82 MET cc_start: 0.9474 (tpt) cc_final: 0.9167 (ptt) REVERT: C 179 ASP cc_start: 0.8888 (m-30) cc_final: 0.8577 (m-30) REVERT: C 261 LEU cc_start: 0.9247 (mp) cc_final: 0.9002 (mt) REVERT: C 313 MET cc_start: 0.9062 (tpp) cc_final: 0.8581 (tpt) REVERT: C 316 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7975 (tm-30) REVERT: C 317 ILE cc_start: 0.8768 (mm) cc_final: 0.8165 (pt) REVERT: D 81 ASP cc_start: 0.7892 (m-30) cc_final: 0.7091 (t0) REVERT: D 82 MET cc_start: 0.9415 (ptt) cc_final: 0.8787 (ptm) REVERT: D 85 ILE cc_start: 0.9815 (mm) cc_final: 0.9362 (mm) REVERT: D 104 LEU cc_start: 0.8886 (mm) cc_final: 0.8640 (mm) REVERT: D 115 ASN cc_start: 0.9196 (m110) cc_final: 0.8943 (t0) REVERT: D 132 MET cc_start: 0.9567 (ptt) cc_final: 0.9362 (ppp) REVERT: D 151 ILE cc_start: 0.9316 (tt) cc_final: 0.8628 (tt) REVERT: D 176 MET cc_start: 0.8891 (mtm) cc_final: 0.8503 (mtp) REVERT: D 188 TYR cc_start: 0.7674 (t80) cc_final: 0.7457 (t80) REVERT: D 250 ILE cc_start: 0.8952 (mm) cc_final: 0.8690 (tp) REVERT: D 257 CYS cc_start: 0.9043 (t) cc_final: 0.8768 (t) REVERT: D 269 MET cc_start: 0.8444 (tpt) cc_final: 0.8237 (tpp) REVERT: E 51 ASP cc_start: 0.9785 (m-30) cc_final: 0.9583 (t0) REVERT: E 165 ILE cc_start: 0.9080 (mm) cc_final: 0.8734 (tp) REVERT: E 169 TYR cc_start: 0.9396 (m-80) cc_final: 0.9142 (m-80) REVERT: E 178 LEU cc_start: 0.6735 (tp) cc_final: 0.6086 (tp) REVERT: E 179 ASP cc_start: 0.8618 (m-30) cc_final: 0.8279 (m-30) REVERT: E 257 CYS cc_start: 0.8434 (t) cc_final: 0.7388 (t) REVERT: E 262 PHE cc_start: 0.8318 (m-80) cc_final: 0.7864 (m-80) REVERT: E 274 ILE cc_start: 0.9606 (pt) cc_final: 0.9374 (pt) REVERT: E 316 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8346 (mm-30) REVERT: F 11 ASP cc_start: 0.8930 (t0) cc_final: 0.8525 (t0) REVERT: F 69 TYR cc_start: 0.8158 (m-10) cc_final: 0.7923 (m-10) REVERT: F 176 MET cc_start: 0.5614 (tmm) cc_final: 0.5358 (tmm) REVERT: F 262 PHE cc_start: 0.8110 (m-10) cc_final: 0.7637 (m-10) REVERT: F 274 ILE cc_start: 0.9127 (pt) cc_final: 0.8764 (pt) REVERT: G 178 LEU cc_start: 0.7409 (tp) cc_final: 0.6810 (tp) REVERT: H 103 MET cc_start: 0.6771 (ptp) cc_final: 0.6520 (ptm) REVERT: H 121 LEU cc_start: 0.7819 (mt) cc_final: 0.7579 (mt) REVERT: H 136 LEU cc_start: 0.9573 (tt) cc_final: 0.9310 (pp) REVERT: I 62 MET cc_start: 0.9522 (ttm) cc_final: 0.9231 (ttm) REVERT: I 91 PHE cc_start: 0.8703 (m-80) cc_final: 0.8448 (m-80) REVERT: J 229 LEU cc_start: 0.5210 (mm) cc_final: 0.4041 (mm) REVERT: J 232 LYS cc_start: 0.6671 (ptpp) cc_final: 0.6149 (pttt) REVERT: K 95 MET cc_start: 0.6359 (tpt) cc_final: 0.6123 (tpt) REVERT: K 102 LEU cc_start: 0.7829 (tt) cc_final: 0.7458 (tt) REVERT: L 281 MET cc_start: 0.2978 (ptt) cc_final: 0.2346 (ptt) REVERT: M 127 MET cc_start: 0.8466 (mmm) cc_final: 0.8115 (mmm) REVERT: M 139 GLU cc_start: 0.9865 (tm-30) cc_final: 0.9627 (mt-10) REVERT: M 197 LEU cc_start: 0.8610 (tt) cc_final: 0.8377 (mt) REVERT: M 228 LEU cc_start: 0.9028 (mt) cc_final: 0.8704 (tp) REVERT: M 281 MET cc_start: 0.4097 (ppp) cc_final: 0.3824 (ppp) REVERT: N 8 MET cc_start: 0.4847 (tmm) cc_final: 0.4329 (tmm) outliers start: 6 outliers final: 1 residues processed: 918 average time/residue: 0.2165 time to fit residues: 299.4343 Evaluate side-chains 632 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 630 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 285 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 ASN B 40 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS D 353 GLN E 12 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 GLN ** I 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.052660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033826 restraints weight = 228499.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.035421 restraints weight = 147716.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.036617 restraints weight = 106048.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.037519 restraints weight = 81645.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.038219 restraints weight = 66208.965| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 29145 Z= 0.271 Angle : 0.853 11.439 39338 Z= 0.441 Chirality : 0.049 0.299 4354 Planarity : 0.007 0.128 5094 Dihedral : 6.716 88.975 4000 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 29.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.07 % Allowed : 3.93 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3569 helix: 0.24 (0.11), residues: 1862 sheet: -0.77 (0.25), residues: 434 loop : -0.33 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 206 TYR 0.040 0.003 TYR E 294 PHE 0.041 0.003 PHE E 223 TRP 0.034 0.003 TRP F 86 HIS 0.010 0.002 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.27 (29145) covalent geometry : angle 0.85292 / 0.44 (39338) hydrogen bonds : bond 0.05469 / 3.71 ( 1632) hydrogen bonds : angle 5.17004 / 3.64 ( 4581) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 784 time to evaluate : 1.130 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: 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: 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 25 ASP cc_start: 0.9260 (m-30) cc_final: 0.9031 (p0) REVERT: A 101 HIS cc_start: 0.9244 (m90) cc_final: 0.9038 (m90) REVERT: A 110 LEU cc_start: 0.9552 (tt) cc_final: 0.9263 (mp) REVERT: A 119 MET cc_start: 0.9105 (ppp) cc_final: 0.8868 (ppp) REVERT: A 122 ILE cc_start: 0.9682 (mm) cc_final: 0.9426 (tt) REVERT: A 269 MET cc_start: 0.6250 (ttt) cc_final: 0.5562 (ttp) REVERT: B 73 HIS cc_start: 0.8650 (m90) cc_final: 0.8312 (m-70) REVERT: B 122 ILE cc_start: 0.9464 (mp) cc_final: 0.9082 (pt) REVERT: B 123 MET cc_start: 0.9867 (mmp) cc_final: 0.9613 (mmm) REVERT: B 140 LEU cc_start: 0.9657 (mm) cc_final: 0.9447 (mm) REVERT: B 176 MET cc_start: 0.9201 (mtm) cc_final: 0.8692 (mpp) REVERT: B 179 ASP cc_start: 0.9521 (m-30) cc_final: 0.8870 (m-30) REVERT: B 188 TYR cc_start: 0.9296 (t80) cc_final: 0.8951 (t80) REVERT: B 257 CYS cc_start: 0.9204 (t) cc_final: 0.8815 (t) REVERT: B 269 MET cc_start: 0.6440 (ttm) cc_final: 0.6025 (ttm) REVERT: B 294 TYR cc_start: 0.9399 (m-80) cc_final: 0.9140 (m-80) REVERT: B 311 ASP cc_start: 0.9594 (m-30) cc_final: 0.9379 (t0) REVERT: C 18 LYS cc_start: 0.9184 (mppt) cc_final: 0.8567 (mppt) REVERT: C 69 TYR cc_start: 0.9030 (m-10) cc_final: 0.8773 (m-10) REVERT: C 73 HIS cc_start: 0.9177 (m90) cc_final: 0.8612 (m90) REVERT: C 81 ASP cc_start: 0.9299 (m-30) cc_final: 0.8555 (t0) REVERT: C 82 MET cc_start: 0.9837 (tpt) cc_final: 0.9513 (ptt) REVERT: C 85 ILE cc_start: 0.9798 (mm) cc_final: 0.9597 (mt) REVERT: C 86 TRP cc_start: 0.9554 (m-10) cc_final: 0.9191 (m-10) REVERT: C 262 PHE cc_start: 0.9581 (m-80) cc_final: 0.8881 (m-10) REVERT: C 313 MET cc_start: 0.9520 (tpp) cc_final: 0.9120 (tpt) REVERT: C 316 GLU cc_start: 0.9699 (tp30) cc_final: 0.9377 (tm-30) REVERT: C 317 ILE cc_start: 0.9783 (mm) cc_final: 0.9416 (pt) REVERT: D 21 PHE cc_start: 0.8860 (m-80) cc_final: 0.8584 (m-80) REVERT: D 44 MET cc_start: 0.6596 (tpp) cc_final: 0.6206 (tpp) REVERT: D 47 MET cc_start: 0.8242 (mmp) cc_final: 0.7718 (mmp) REVERT: D 104 LEU cc_start: 0.9355 (mm) cc_final: 0.8864 (mm) REVERT: D 132 MET cc_start: 0.9767 (ptt) cc_final: 0.9420 (ppp) REVERT: D 165 ILE cc_start: 0.9715 (mm) cc_final: 0.9385 (tp) REVERT: D 179 ASP cc_start: 0.9400 (m-30) cc_final: 0.9112 (m-30) REVERT: D 188 TYR cc_start: 0.9359 (t80) cc_final: 0.8714 (t80) REVERT: D 250 ILE cc_start: 0.9820 (mm) cc_final: 0.9586 (tp) REVERT: D 257 CYS cc_start: 0.9602 (t) cc_final: 0.8919 (t) REVERT: D 269 MET cc_start: 0.9015 (tpt) cc_final: 0.8711 (tpp) REVERT: D 355 MET cc_start: 0.9555 (mmp) cc_final: 0.9321 (mmm) REVERT: D 356 TRP cc_start: 0.7440 (m-90) cc_final: 0.6277 (m-90) REVERT: E 16 LEU cc_start: 0.9614 (mp) cc_final: 0.9367 (mp) REVERT: E 51 ASP cc_start: 0.9728 (m-30) cc_final: 0.9502 (t0) REVERT: E 69 TYR cc_start: 0.8928 (m-10) cc_final: 0.8663 (m-10) REVERT: E 86 TRP cc_start: 0.9654 (m-10) cc_final: 0.9441 (m-10) REVERT: E 122 ILE cc_start: 0.9574 (mt) cc_final: 0.9273 (mt) REVERT: E 151 ILE cc_start: 0.9082 (tt) cc_final: 0.8877 (tt) REVERT: E 169 TYR cc_start: 0.9665 (m-80) cc_final: 0.9239 (m-80) REVERT: E 176 MET cc_start: 0.9166 (mmm) cc_final: 0.8595 (mtp) REVERT: E 178 LEU cc_start: 0.9165 (tp) cc_final: 0.8708 (tp) REVERT: E 179 ASP cc_start: 0.9274 (m-30) cc_final: 0.8661 (m-30) REVERT: E 183 ARG cc_start: 0.9477 (tpp80) cc_final: 0.8664 (mtm-85) REVERT: E 207 GLU cc_start: 0.9591 (mp0) cc_final: 0.9135 (mp0) REVERT: E 213 LYS cc_start: 0.9743 (ptpp) cc_final: 0.9381 (ptpp) REVERT: E 236 LEU cc_start: 0.8791 (tp) cc_final: 0.8564 (tt) REVERT: E 294 TYR cc_start: 0.9568 (m-80) cc_final: 0.9337 (m-80) REVERT: E 317 ILE cc_start: 0.9862 (mt) cc_final: 0.9548 (pt) REVERT: E 320 LEU cc_start: 0.9409 (mt) cc_final: 0.8829 (mt) REVERT: E 375 PHE cc_start: 0.9138 (t80) cc_final: 0.8877 (t80) REVERT: F 11 ASP cc_start: 0.9738 (t0) cc_final: 0.9087 (t0) REVERT: F 73 HIS cc_start: 0.9148 (m-70) cc_final: 0.8629 (m-70) REVERT: F 85 ILE cc_start: 0.9794 (mm) cc_final: 0.9554 (mm) REVERT: F 118 LYS cc_start: 0.9676 (tptp) cc_final: 0.9453 (tptp) REVERT: F 167 GLU cc_start: 0.9706 (mp0) cc_final: 0.9428 (mp0) REVERT: F 176 MET cc_start: 0.8458 (tmm) cc_final: 0.7650 (tmm) REVERT: F 180 LEU cc_start: 0.9315 (tt) cc_final: 0.8991 (tt) REVERT: F 191 LYS cc_start: 0.9652 (pptt) cc_final: 0.9445 (pptt) REVERT: F 213 LYS cc_start: 0.9801 (pttm) cc_final: 0.9242 (ptpt) REVERT: F 269 MET cc_start: 0.8891 (ttt) cc_final: 0.8690 (ttm) REVERT: F 305 MET cc_start: 0.9407 (tpp) cc_final: 0.9194 (tpp) REVERT: F 313 MET cc_start: 0.9635 (mmm) cc_final: 0.9420 (mmm) REVERT: F 371 HIS cc_start: 0.9186 (m-70) cc_final: 0.8788 (m90) REVERT: G 132 MET cc_start: 0.9209 (tmm) cc_final: 0.8961 (tmm) REVERT: G 178 LEU cc_start: 0.9303 (tp) cc_final: 0.9100 (tp) REVERT: H 88 ASP cc_start: 0.8824 (m-30) cc_final: 0.8187 (t0) REVERT: H 120 MET cc_start: 0.9531 (mtm) cc_final: 0.9296 (ptp) REVERT: H 156 PHE cc_start: 0.8683 (p90) cc_final: 0.8464 (p90) REVERT: I 91 PHE cc_start: 0.9473 (m-80) cc_final: 0.9114 (m-80) REVERT: J 229 LEU cc_start: 0.8571 (mm) cc_final: 0.7886 (mm) REVERT: K 95 MET cc_start: 0.7775 (tpt) cc_final: 0.7464 (tpt) REVERT: K 102 LEU cc_start: 0.9439 (tt) cc_final: 0.9204 (tt) REVERT: L 221 TYR cc_start: 0.9584 (m-80) cc_final: 0.9352 (m-80) REVERT: M 139 GLU cc_start: 0.9892 (tm-30) cc_final: 0.9616 (mt-10) REVERT: M 197 LEU cc_start: 0.9562 (tt) cc_final: 0.9246 (mt) REVERT: N 1 MET cc_start: 0.8525 (pmm) cc_final: 0.7260 (pmm) REVERT: O 1 MET cc_start: 0.8741 (pmm) cc_final: 0.8340 (pmm) outliers start: 2 outliers final: 0 residues processed: 786 average time/residue: 0.2106 time to fit residues: 250.6734 Evaluate side-chains 578 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 223 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 317 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 345 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 chunk 200 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 115 ASN C 225 ASN C 296 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS F 280 ASN G 59 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 ASN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 ASN ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.054327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.035046 restraints weight = 218661.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.036697 restraints weight = 140829.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.037947 restraints weight = 101034.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.038887 restraints weight = 77715.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.039647 restraints weight = 62904.353| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.7399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29145 Z= 0.169 Angle : 0.764 12.477 39338 Z= 0.393 Chirality : 0.049 0.283 4354 Planarity : 0.005 0.089 5094 Dihedral : 6.575 89.140 4000 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3569 helix: 0.41 (0.12), residues: 1868 sheet: -0.67 (0.25), residues: 420 loop : -0.16 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 206 TYR 0.036 0.002 TYR C 294 PHE 0.046 0.003 PHE E 223 TRP 0.048 0.003 TRP D 86 HIS 0.010 0.001 HIS K 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (29145) covalent geometry : angle 0.76433 / 0.39 (39338) hydrogen bonds : bond 0.05220 / 3.53 ( 1632) hydrogen bonds : angle 4.99172 / 3.51 ( 4581) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 807 time to evaluate : 1.202 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: 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: 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 25 ASP cc_start: 0.9241 (m-30) cc_final: 0.9030 (p0) REVERT: A 82 MET cc_start: 0.9617 (tpt) cc_final: 0.9388 (tpp) REVERT: A 122 ILE cc_start: 0.9649 (mm) cc_final: 0.9402 (tt) REVERT: A 269 MET cc_start: 0.6214 (ttt) cc_final: 0.5513 (ttp) REVERT: B 83 GLU cc_start: 0.9569 (tm-30) cc_final: 0.9114 (pt0) REVERT: B 176 MET cc_start: 0.9162 (mtm) cc_final: 0.8650 (mpp) REVERT: B 179 ASP cc_start: 0.9476 (m-30) cc_final: 0.8926 (m-30) REVERT: B 188 TYR cc_start: 0.9226 (t80) cc_final: 0.8882 (t80) REVERT: B 207 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9308 (mp0) REVERT: B 257 CYS cc_start: 0.9124 (t) cc_final: 0.8492 (t) REVERT: B 269 MET cc_start: 0.6392 (ttm) cc_final: 0.5988 (ttm) REVERT: B 275 HIS cc_start: 0.9302 (p90) cc_final: 0.9040 (p-80) REVERT: B 311 ASP cc_start: 0.9632 (m-30) cc_final: 0.9138 (t0) REVERT: C 18 LYS cc_start: 0.9175 (mppt) cc_final: 0.8540 (mppt) REVERT: C 69 TYR cc_start: 0.8989 (m-10) cc_final: 0.8715 (m-10) REVERT: C 73 HIS cc_start: 0.8984 (m90) cc_final: 0.8244 (m170) REVERT: C 82 MET cc_start: 0.9847 (tpt) cc_final: 0.9523 (ptt) REVERT: C 122 ILE cc_start: 0.9734 (mt) cc_final: 0.9496 (mt) REVERT: C 262 PHE cc_start: 0.9553 (m-80) cc_final: 0.9017 (m-10) REVERT: C 313 MET cc_start: 0.9531 (tpp) cc_final: 0.9239 (tpt) REVERT: C 316 GLU cc_start: 0.9599 (tp30) cc_final: 0.9336 (tm-30) REVERT: C 317 ILE cc_start: 0.9824 (mm) cc_final: 0.9581 (pt) REVERT: C 371 HIS cc_start: 0.9122 (m170) cc_final: 0.8807 (m90) REVERT: D 21 PHE cc_start: 0.8877 (m-80) cc_final: 0.8543 (m-80) REVERT: D 44 MET cc_start: 0.6429 (tpp) cc_final: 0.6204 (tpp) REVERT: D 47 MET cc_start: 0.8288 (mmp) cc_final: 0.7825 (mmp) REVERT: D 75 ILE cc_start: 0.9630 (pt) cc_final: 0.9379 (mm) REVERT: D 119 MET cc_start: 0.9828 (ptp) cc_final: 0.9384 (ptt) REVERT: D 122 ILE cc_start: 0.9816 (mm) cc_final: 0.9594 (mm) REVERT: D 132 MET cc_start: 0.9783 (ptt) cc_final: 0.9496 (ppp) REVERT: D 165 ILE cc_start: 0.9704 (mm) cc_final: 0.9350 (tp) REVERT: D 176 MET cc_start: 0.9219 (mtm) cc_final: 0.8934 (mpp) REVERT: D 178 LEU cc_start: 0.9543 (tp) cc_final: 0.9272 (tp) REVERT: D 179 ASP cc_start: 0.9342 (m-30) cc_final: 0.9026 (m-30) REVERT: D 188 TYR cc_start: 0.9295 (t80) cc_final: 0.8660 (t80) REVERT: D 223 PHE cc_start: 0.9146 (t80) cc_final: 0.8700 (t80) REVERT: D 236 LEU cc_start: 0.8438 (mm) cc_final: 0.8091 (pp) REVERT: D 250 ILE cc_start: 0.9812 (mm) cc_final: 0.9535 (tp) REVERT: D 257 CYS cc_start: 0.9553 (t) cc_final: 0.8810 (t) REVERT: D 269 MET cc_start: 0.8937 (tpt) cc_final: 0.8618 (tpp) REVERT: D 297 ASN cc_start: 0.9655 (t0) cc_final: 0.9148 (m110) REVERT: E 51 ASP cc_start: 0.9739 (m-30) cc_final: 0.9496 (t0) REVERT: E 69 TYR cc_start: 0.9089 (m-10) cc_final: 0.8637 (m-10) REVERT: E 122 ILE cc_start: 0.9549 (mt) cc_final: 0.9274 (mt) REVERT: E 151 ILE cc_start: 0.9475 (tt) cc_final: 0.9229 (tt) REVERT: E 165 ILE cc_start: 0.9719 (mm) cc_final: 0.9314 (tp) REVERT: E 169 TYR cc_start: 0.9612 (m-80) cc_final: 0.9224 (m-80) REVERT: E 176 MET cc_start: 0.9091 (mmm) cc_final: 0.8587 (mtp) REVERT: E 179 ASP cc_start: 0.9232 (m-30) cc_final: 0.8479 (m-30) REVERT: E 213 LYS cc_start: 0.9716 (ptpp) cc_final: 0.9329 (ptpp) REVERT: E 248 ILE cc_start: 0.9835 (pt) cc_final: 0.9441 (pt) REVERT: E 257 CYS cc_start: 0.9261 (t) cc_final: 0.9050 (t) REVERT: E 274 ILE cc_start: 0.9512 (pt) cc_final: 0.9301 (pt) REVERT: E 294 TYR cc_start: 0.9557 (m-80) cc_final: 0.9299 (m-80) REVERT: E 352 PHE cc_start: 0.9688 (t80) cc_final: 0.9475 (t80) REVERT: E 375 PHE cc_start: 0.9070 (t80) cc_final: 0.8777 (t80) REVERT: F 73 HIS cc_start: 0.8665 (m-70) cc_final: 0.8213 (m-70) REVERT: F 118 LYS cc_start: 0.9672 (tptp) cc_final: 0.9440 (tptp) REVERT: F 140 LEU cc_start: 0.9212 (mm) cc_final: 0.8768 (mm) REVERT: F 154 ASP cc_start: 0.8676 (m-30) cc_final: 0.8463 (m-30) REVERT: F 167 GLU cc_start: 0.9680 (mp0) cc_final: 0.9442 (mp0) REVERT: F 176 MET cc_start: 0.7875 (tmm) cc_final: 0.7482 (tmm) REVERT: F 213 LYS cc_start: 0.9804 (pttm) cc_final: 0.9329 (ptpt) REVERT: F 262 PHE cc_start: 0.9379 (m-10) cc_final: 0.8675 (m-10) REVERT: F 274 ILE cc_start: 0.9758 (pt) cc_final: 0.9557 (pt) REVERT: F 305 MET cc_start: 0.9450 (tpp) cc_final: 0.9226 (tpp) REVERT: G 53 TYR cc_start: 0.9703 (m-80) cc_final: 0.9499 (m-80) REVERT: G 178 LEU cc_start: 0.9130 (tp) cc_final: 0.8921 (tp) REVERT: H 120 MET cc_start: 0.9541 (mtm) cc_final: 0.9215 (mpp) REVERT: I 54 MET cc_start: 0.9439 (mmp) cc_final: 0.9207 (mmm) REVERT: I 91 PHE cc_start: 0.9523 (m-80) cc_final: 0.9207 (m-80) REVERT: J 224 LEU cc_start: 0.9381 (mm) cc_final: 0.9085 (mm) REVERT: J 229 LEU cc_start: 0.8618 (mm) cc_final: 0.8003 (mm) REVERT: K 95 MET cc_start: 0.7686 (tpt) cc_final: 0.7387 (tpt) REVERT: K 152 LEU cc_start: 0.9275 (mt) cc_final: 0.8763 (mt) REVERT: M 139 GLU cc_start: 0.9852 (tm-30) cc_final: 0.9571 (mt-10) REVERT: M 197 LEU cc_start: 0.9518 (tt) cc_final: 0.9199 (mt) REVERT: N 1 MET cc_start: 0.8652 (pmm) cc_final: 0.7274 (pmm) REVERT: O 1 MET cc_start: 0.8896 (pmm) cc_final: 0.8571 (pmm) REVERT: O 46 LEU cc_start: 0.9575 (tp) cc_final: 0.9346 (tp) outliers start: 1 outliers final: 0 residues processed: 808 average time/residue: 0.2092 time to fit residues: 257.2993 Evaluate side-chains 608 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 608 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 49 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 294 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 chunk 189 optimal weight: 0.0050 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 238 GLN K 149 GLN ** L 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.051562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.032787 restraints weight = 228585.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.034338 restraints weight = 147468.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.035502 restraints weight = 106367.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.036378 restraints weight = 82120.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.037084 restraints weight = 66598.266| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29145 Z= 0.215 Angle : 0.809 12.277 39338 Z= 0.421 Chirality : 0.049 0.283 4354 Planarity : 0.006 0.186 5094 Dihedral : 6.642 87.573 4000 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 28.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3569 helix: 0.25 (0.12), residues: 1876 sheet: -0.77 (0.25), residues: 420 loop : -0.18 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG E 62 TYR 0.040 0.002 TYR B 294 PHE 0.045 0.003 PHE E 223 TRP 0.077 0.003 TRP E 86 HIS 0.010 0.002 HIS E 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (29145) covalent geometry : angle 0.80865 / 0.42 (39338) hydrogen bonds : bond 0.05293 / 3.60 ( 1632) hydrogen bonds : angle 5.21927 / 3.69 ( 4581) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 777 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 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 25 ASP cc_start: 0.9312 (m-30) cc_final: 0.9107 (p0) REVERT: A 82 MET cc_start: 0.9661 (tpt) cc_final: 0.9424 (tpp) REVERT: A 110 LEU cc_start: 0.9622 (tt) cc_final: 0.9324 (mp) REVERT: A 119 MET cc_start: 0.9078 (ppp) cc_final: 0.8858 (ppp) REVERT: A 122 ILE cc_start: 0.9673 (mm) cc_final: 0.9391 (tt) REVERT: A 269 MET cc_start: 0.6468 (ttt) cc_final: 0.5790 (ttp) REVERT: A 325 MET cc_start: 0.4462 (tpt) cc_final: 0.4254 (tpt) REVERT: B 73 HIS cc_start: 0.8342 (m-70) cc_final: 0.8140 (m90) REVERT: B 123 MET cc_start: 0.9891 (mmp) cc_final: 0.9643 (mmm) REVERT: B 176 MET cc_start: 0.9214 (mtm) cc_final: 0.8826 (mpp) REVERT: B 179 ASP cc_start: 0.9423 (m-30) cc_final: 0.8869 (m-30) REVERT: B 188 TYR cc_start: 0.9283 (t80) cc_final: 0.8757 (t80) REVERT: B 269 MET cc_start: 0.6322 (ttm) cc_final: 0.5965 (ttm) REVERT: B 275 HIS cc_start: 0.9361 (p90) cc_final: 0.9142 (p-80) REVERT: B 311 ASP cc_start: 0.9624 (m-30) cc_final: 0.9056 (t0) REVERT: B 313 MET cc_start: 0.9553 (mtm) cc_final: 0.9215 (mmt) REVERT: C 18 LYS cc_start: 0.9198 (mppt) cc_final: 0.8437 (mppt) REVERT: C 73 HIS cc_start: 0.8928 (m90) cc_final: 0.8228 (m90) REVERT: C 82 MET cc_start: 0.9836 (tpt) cc_final: 0.9601 (ptt) REVERT: C 86 TRP cc_start: 0.9546 (m-10) cc_final: 0.9000 (m-10) REVERT: C 262 PHE cc_start: 0.9549 (m-80) cc_final: 0.8965 (m-10) REVERT: C 274 ILE cc_start: 0.9460 (pt) cc_final: 0.9247 (pt) REVERT: C 316 GLU cc_start: 0.9675 (tp30) cc_final: 0.9441 (tm-30) REVERT: D 16 LEU cc_start: 0.9584 (mm) cc_final: 0.9372 (mm) REVERT: D 21 PHE cc_start: 0.8855 (m-80) cc_final: 0.8456 (m-80) REVERT: D 47 MET cc_start: 0.8305 (mmp) cc_final: 0.7973 (mmm) REVERT: D 86 TRP cc_start: 0.9713 (m-90) cc_final: 0.9427 (m-90) REVERT: D 110 LEU cc_start: 0.9503 (mt) cc_final: 0.8984 (mt) REVERT: D 122 ILE cc_start: 0.9808 (mm) cc_final: 0.9509 (mm) REVERT: D 123 MET cc_start: 0.9880 (mmp) cc_final: 0.9591 (mmp) REVERT: D 132 MET cc_start: 0.9795 (ptt) cc_final: 0.9529 (ppp) REVERT: D 165 ILE cc_start: 0.9714 (mm) cc_final: 0.9400 (tp) REVERT: D 176 MET cc_start: 0.9267 (mtm) cc_final: 0.8883 (mpp) REVERT: D 178 LEU cc_start: 0.9592 (tp) cc_final: 0.9358 (tp) REVERT: D 179 ASP cc_start: 0.9329 (m-30) cc_final: 0.8937 (m-30) REVERT: D 188 TYR cc_start: 0.9353 (t80) cc_final: 0.8802 (t80) REVERT: D 223 PHE cc_start: 0.9241 (t80) cc_final: 0.8965 (t80) REVERT: D 236 LEU cc_start: 0.8655 (mm) cc_final: 0.8357 (pp) REVERT: D 250 ILE cc_start: 0.9818 (mm) cc_final: 0.9579 (tp) REVERT: D 269 MET cc_start: 0.9028 (tpt) cc_final: 0.8754 (tpp) REVERT: D 297 ASN cc_start: 0.9668 (t0) cc_final: 0.9186 (m110) REVERT: D 355 MET cc_start: 0.9519 (mmp) cc_final: 0.9258 (mmm) REVERT: E 51 ASP cc_start: 0.9767 (m-30) cc_final: 0.9545 (t0) REVERT: E 69 TYR cc_start: 0.9058 (m-10) cc_final: 0.8744 (m-10) REVERT: E 73 HIS cc_start: 0.9045 (m-70) cc_final: 0.8677 (m90) REVERT: E 122 ILE cc_start: 0.9637 (mt) cc_final: 0.9412 (mt) REVERT: E 151 ILE cc_start: 0.9538 (tt) cc_final: 0.9265 (tt) REVERT: E 165 ILE cc_start: 0.9765 (mm) cc_final: 0.9433 (tp) REVERT: E 169 TYR cc_start: 0.9582 (m-80) cc_final: 0.9286 (m-80) REVERT: E 176 MET cc_start: 0.9128 (mmm) cc_final: 0.8753 (mtp) REVERT: E 179 ASP cc_start: 0.9380 (m-30) cc_final: 0.8724 (m-30) REVERT: E 190 MET cc_start: 0.9751 (ptp) cc_final: 0.9496 (ptp) REVERT: E 206 ARG cc_start: 0.9380 (mpp-170) cc_final: 0.9012 (mpp80) REVERT: E 294 TYR cc_start: 0.9598 (m-80) cc_final: 0.9362 (m-80) REVERT: E 334 GLU cc_start: 0.9438 (pm20) cc_final: 0.8977 (tm-30) REVERT: E 352 PHE cc_start: 0.9721 (t80) cc_final: 0.9486 (t80) REVERT: E 375 PHE cc_start: 0.9115 (t80) cc_final: 0.8827 (t80) REVERT: F 11 ASP cc_start: 0.9266 (t70) cc_final: 0.8944 (t0) REVERT: F 18 LYS cc_start: 0.9470 (mppt) cc_final: 0.9257 (mptt) REVERT: F 73 HIS cc_start: 0.8671 (m-70) cc_final: 0.8242 (m-70) REVERT: F 85 ILE cc_start: 0.9815 (mm) cc_final: 0.9605 (mm) REVERT: F 118 LYS cc_start: 0.9690 (tptp) cc_final: 0.9470 (tptp) REVERT: F 123 MET cc_start: 0.9853 (mmp) cc_final: 0.9653 (mmm) REVERT: F 167 GLU cc_start: 0.9683 (mp0) cc_final: 0.9352 (mp0) REVERT: F 190 MET cc_start: 0.9720 (ptp) cc_final: 0.9500 (ptp) REVERT: F 213 LYS cc_start: 0.9763 (pttm) cc_final: 0.9285 (ptpp) REVERT: F 269 MET cc_start: 0.9349 (ttm) cc_final: 0.9075 (ttm) REVERT: F 294 TYR cc_start: 0.9699 (m-10) cc_final: 0.9389 (m-10) REVERT: F 297 ASN cc_start: 0.9754 (t0) cc_final: 0.9176 (m-40) REVERT: G 53 TYR cc_start: 0.9683 (m-80) cc_final: 0.9481 (m-80) REVERT: H 156 PHE cc_start: 0.8794 (p90) cc_final: 0.8574 (p90) REVERT: I 79 THR cc_start: 0.9869 (p) cc_final: 0.9668 (p) REVERT: I 80 ARG cc_start: 0.9595 (tpm170) cc_final: 0.9333 (mtm110) REVERT: I 91 PHE cc_start: 0.9526 (m-80) cc_final: 0.9213 (m-80) REVERT: J 229 LEU cc_start: 0.8460 (mm) cc_final: 0.7853 (mm) REVERT: K 95 MET cc_start: 0.7815 (tpt) cc_final: 0.7554 (tpt) REVERT: M 139 GLU cc_start: 0.9888 (tm-30) cc_final: 0.9617 (mt-10) REVERT: M 197 LEU cc_start: 0.9635 (tt) cc_final: 0.9342 (mt) REVERT: N 1 MET cc_start: 0.8516 (pmm) cc_final: 0.6716 (ppp) REVERT: O 1 MET cc_start: 0.9094 (pmm) cc_final: 0.8750 (pmm) REVERT: O 46 LEU cc_start: 0.9529 (tp) cc_final: 0.9275 (tp) outliers start: 2 outliers final: 1 residues processed: 779 average time/residue: 0.2117 time to fit residues: 251.6598 Evaluate side-chains 571 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 570 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 137 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 260 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 338 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS C 59 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 ASN M 216 GLN ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.063483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.044582 restraints weight = 223735.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.046166 restraints weight = 144274.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.047361 restraints weight = 104144.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.048278 restraints weight = 80434.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.049011 restraints weight = 65228.779| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.7940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 29145 Z= 0.172 Angle : 0.781 12.294 39338 Z= 0.406 Chirality : 0.049 0.313 4354 Planarity : 0.005 0.085 5094 Dihedral : 6.546 88.125 4000 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3569 helix: 0.42 (0.12), residues: 1822 sheet: -0.65 (0.25), residues: 420 loop : -0.12 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 177 TYR 0.044 0.002 TYR B 294 PHE 0.050 0.003 PHE E 223 TRP 0.070 0.003 TRP E 86 HIS 0.010 0.001 HIS E 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (29145) covalent geometry : angle 0.78096 / 0.41 (39338) hydrogen bonds : bond 0.05232 / 3.55 ( 1632) hydrogen bonds : angle 5.19887 / 3.68 ( 4581) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 792 time to evaluate : 1.266 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: 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: 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 82 MET cc_start: 0.9665 (tpt) cc_final: 0.9428 (tpp) REVERT: A 110 LEU cc_start: 0.9590 (tt) cc_final: 0.9288 (mp) REVERT: A 119 MET cc_start: 0.9050 (ppp) cc_final: 0.8776 (ppp) REVERT: A 122 ILE cc_start: 0.9651 (mm) cc_final: 0.9360 (tt) REVERT: A 132 MET cc_start: 0.9081 (mtm) cc_final: 0.8542 (mpp) REVERT: A 269 MET cc_start: 0.6421 (ttt) cc_final: 0.5780 (ttt) REVERT: B 165 ILE cc_start: 0.9860 (mp) cc_final: 0.9573 (tt) REVERT: B 176 MET cc_start: 0.9220 (mtm) cc_final: 0.8831 (mpp) REVERT: B 179 ASP cc_start: 0.9409 (m-30) cc_final: 0.8910 (m-30) REVERT: B 213 LYS cc_start: 0.9490 (pttp) cc_final: 0.9029 (pttm) REVERT: B 269 MET cc_start: 0.6431 (ttm) cc_final: 0.6013 (ttm) REVERT: B 311 ASP cc_start: 0.9610 (m-30) cc_final: 0.9080 (t0) REVERT: B 313 MET cc_start: 0.9529 (mtm) cc_final: 0.9172 (mmt) REVERT: C 18 LYS cc_start: 0.9216 (mppt) cc_final: 0.8482 (mppt) REVERT: C 73 HIS cc_start: 0.8883 (m90) cc_final: 0.8197 (m90) REVERT: C 269 MET cc_start: 0.9409 (mpp) cc_final: 0.9198 (mpp) REVERT: D 12 ASN cc_start: 0.9769 (m110) cc_final: 0.9279 (p0) REVERT: D 21 PHE cc_start: 0.8816 (m-80) cc_final: 0.8554 (m-80) REVERT: D 47 MET cc_start: 0.8387 (mmp) cc_final: 0.7870 (mmp) REVERT: D 104 LEU cc_start: 0.9324 (mm) cc_final: 0.9003 (mm) REVERT: D 119 MET cc_start: 0.9714 (ptp) cc_final: 0.9501 (ptt) REVERT: D 132 MET cc_start: 0.9795 (ptt) cc_final: 0.9503 (ppp) REVERT: D 165 ILE cc_start: 0.9694 (mm) cc_final: 0.9375 (tp) REVERT: D 179 ASP cc_start: 0.8934 (m-30) cc_final: 0.8508 (m-30) REVERT: D 188 TYR cc_start: 0.9279 (t80) cc_final: 0.8751 (t80) REVERT: D 223 PHE cc_start: 0.9213 (t80) cc_final: 0.8808 (t80) REVERT: D 236 LEU cc_start: 0.8402 (mm) cc_final: 0.8023 (pp) REVERT: D 240 TYR cc_start: 0.8648 (t80) cc_final: 0.7978 (t80) REVERT: D 241 GLU cc_start: 0.9858 (pm20) cc_final: 0.9564 (tp30) REVERT: D 250 ILE cc_start: 0.9792 (mm) cc_final: 0.9512 (tp) REVERT: D 269 MET cc_start: 0.9020 (tpt) cc_final: 0.8714 (tpp) REVERT: D 297 ASN cc_start: 0.9641 (t0) cc_final: 0.9160 (m110) REVERT: D 355 MET cc_start: 0.9542 (mmp) cc_final: 0.9283 (mmm) REVERT: D 356 TRP cc_start: 0.6757 (m-90) cc_final: 0.5954 (t-100) REVERT: E 10 CYS cc_start: 0.8550 (t) cc_final: 0.8288 (t) REVERT: E 51 ASP cc_start: 0.9806 (m-30) cc_final: 0.9593 (t0) REVERT: E 69 TYR cc_start: 0.9050 (m-10) cc_final: 0.8711 (m-10) REVERT: E 73 HIS cc_start: 0.9035 (m-70) cc_final: 0.8535 (m-70) REVERT: E 151 ILE cc_start: 0.9504 (tt) cc_final: 0.9268 (tt) REVERT: E 165 ILE cc_start: 0.9705 (mm) cc_final: 0.9366 (tp) REVERT: E 169 TYR cc_start: 0.9591 (m-80) cc_final: 0.9302 (m-80) REVERT: E 176 MET cc_start: 0.9185 (mmm) cc_final: 0.8866 (mtt) REVERT: E 179 ASP cc_start: 0.9275 (m-30) cc_final: 0.8529 (m-30) REVERT: E 190 MET cc_start: 0.9714 (ptp) cc_final: 0.9414 (ptp) REVERT: E 206 ARG cc_start: 0.9303 (mpp-170) cc_final: 0.8817 (mpp80) REVERT: E 213 LYS cc_start: 0.9684 (ptpp) cc_final: 0.9369 (ptpp) REVERT: E 274 ILE cc_start: 0.9472 (pt) cc_final: 0.9247 (pt) REVERT: E 294 TYR cc_start: 0.9596 (m-80) cc_final: 0.9312 (m-80) REVERT: E 334 GLU cc_start: 0.9454 (pm20) cc_final: 0.8952 (tm-30) REVERT: E 352 PHE cc_start: 0.9702 (t80) cc_final: 0.9464 (t80) REVERT: E 375 PHE cc_start: 0.9027 (t80) cc_final: 0.8769 (t80) REVERT: F 11 ASP cc_start: 0.9427 (t70) cc_final: 0.8925 (t0) REVERT: F 73 HIS cc_start: 0.8546 (m-70) cc_final: 0.8103 (m-70) REVERT: F 118 LYS cc_start: 0.9696 (tptp) cc_final: 0.9460 (tptp) REVERT: F 167 GLU cc_start: 0.9697 (mp0) cc_final: 0.9478 (mp0) REVERT: F 176 MET cc_start: 0.8299 (tmm) cc_final: 0.7877 (tmm) REVERT: F 178 LEU cc_start: 0.8878 (tp) cc_final: 0.8450 (tp) REVERT: F 190 MET cc_start: 0.9753 (ptp) cc_final: 0.9541 (ptp) REVERT: F 213 LYS cc_start: 0.9819 (pttm) cc_final: 0.9348 (ptpp) REVERT: F 262 PHE cc_start: 0.9486 (m-10) cc_final: 0.9185 (m-80) REVERT: F 294 TYR cc_start: 0.9651 (m-10) cc_final: 0.9359 (m-10) REVERT: F 297 ASN cc_start: 0.9724 (t0) cc_final: 0.9182 (m-40) REVERT: G 119 MET cc_start: 0.9412 (ppp) cc_final: 0.9186 (ppp) REVERT: G 178 LEU cc_start: 0.9047 (tp) cc_final: 0.8803 (tp) REVERT: H 120 MET cc_start: 0.9564 (mtp) cc_final: 0.9275 (mtm) REVERT: I 54 MET cc_start: 0.9295 (mmp) cc_final: 0.8979 (mmm) REVERT: I 80 ARG cc_start: 0.9613 (tpm170) cc_final: 0.9356 (mtm110) REVERT: I 91 PHE cc_start: 0.9554 (m-80) cc_final: 0.9257 (m-80) REVERT: J 229 LEU cc_start: 0.8459 (mm) cc_final: 0.7913 (mm) REVERT: J 249 ASP cc_start: 0.9943 (t0) cc_final: 0.9717 (m-30) REVERT: M 172 ILE cc_start: 0.9231 (mm) cc_final: 0.8892 (tt) REVERT: M 197 LEU cc_start: 0.9609 (tt) cc_final: 0.9297 (mt) REVERT: N 1 MET cc_start: 0.8566 (pmm) cc_final: 0.7531 (pmm) REVERT: O 1 MET cc_start: 0.9085 (pmm) cc_final: 0.8818 (pmm) REVERT: O 10 MET cc_start: 0.8455 (mpp) cc_final: 0.8120 (mpp) REVERT: O 46 LEU cc_start: 0.9566 (tp) cc_final: 0.9326 (tp) outliers start: 0 outliers final: 0 residues processed: 792 average time/residue: 0.2055 time to fit residues: 248.8436 Evaluate side-chains 584 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 205 optimal weight: 0.8980 chunk 278 optimal weight: 0.9990 chunk 337 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 240 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 208 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 115 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 111 ASN E 173 HIS ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 HIS L 202 ASN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.043813 restraints weight = 219676.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.045389 restraints weight = 142582.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.046627 restraints weight = 103022.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.047572 restraints weight = 79546.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.048295 restraints weight = 64348.295| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.8126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29145 Z= 0.166 Angle : 0.798 12.849 39338 Z= 0.419 Chirality : 0.050 0.332 4354 Planarity : 0.005 0.157 5094 Dihedral : 6.522 86.677 4000 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3569 helix: 0.54 (0.12), residues: 1919 sheet: -0.56 (0.26), residues: 420 loop : -0.14 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 62 TYR 0.043 0.002 TYR B 294 PHE 0.049 0.003 PHE B 223 TRP 0.076 0.004 TRP D 86 HIS 0.006 0.001 HIS E 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (29145) covalent geometry : angle 0.79817 / 0.42 (39338) hydrogen bonds : bond 0.05249 / 3.57 ( 1632) hydrogen bonds : angle 5.24974 / 3.70 ( 4581) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 794 time to evaluate : 1.179 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: 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 82 MET cc_start: 0.9668 (tpt) cc_final: 0.9448 (tpp) REVERT: A 110 LEU cc_start: 0.9589 (tt) cc_final: 0.9285 (mp) REVERT: A 188 TYR cc_start: 0.9501 (t80) cc_final: 0.9263 (t80) REVERT: A 269 MET cc_start: 0.6346 (ttt) cc_final: 0.5704 (ttt) REVERT: B 165 ILE cc_start: 0.9855 (mp) cc_final: 0.9587 (tt) REVERT: B 176 MET cc_start: 0.9228 (mtm) cc_final: 0.8827 (mpp) REVERT: B 179 ASP cc_start: 0.9459 (m-30) cc_final: 0.8830 (m-30) REVERT: B 269 MET cc_start: 0.6485 (ttm) cc_final: 0.6033 (ttm) REVERT: B 311 ASP cc_start: 0.9617 (m-30) cc_final: 0.9062 (t0) REVERT: B 313 MET cc_start: 0.9513 (mtm) cc_final: 0.9186 (mmt) REVERT: C 18 LYS cc_start: 0.9248 (mppt) cc_final: 0.8555 (mppt) REVERT: C 73 HIS cc_start: 0.8961 (m90) cc_final: 0.8323 (m90) REVERT: C 115 ASN cc_start: 0.9545 (m110) cc_final: 0.9102 (t0) REVERT: C 137 GLN cc_start: 0.9675 (mt0) cc_final: 0.9368 (mt0) REVERT: C 165 ILE cc_start: 0.9609 (mm) cc_final: 0.9358 (tp) REVERT: C 171 LEU cc_start: 0.9594 (mt) cc_final: 0.9383 (mp) REVERT: C 269 MET cc_start: 0.9365 (mpp) cc_final: 0.9161 (mpp) REVERT: C 274 ILE cc_start: 0.9432 (pt) cc_final: 0.9227 (pt) REVERT: C 297 ASN cc_start: 0.9656 (t0) cc_final: 0.9252 (m110) REVERT: C 313 MET cc_start: 0.9787 (mmm) cc_final: 0.9263 (mmm) REVERT: D 16 LEU cc_start: 0.9600 (mm) cc_final: 0.9399 (mm) REVERT: D 21 PHE cc_start: 0.8822 (m-80) cc_final: 0.8588 (m-80) REVERT: D 47 MET cc_start: 0.8534 (mmp) cc_final: 0.8080 (mmp) REVERT: D 75 ILE cc_start: 0.9779 (pt) cc_final: 0.9489 (mm) REVERT: D 86 TRP cc_start: 0.9692 (m-90) cc_final: 0.9450 (m-90) REVERT: D 104 LEU cc_start: 0.9310 (mm) cc_final: 0.9007 (mm) REVERT: D 115 ASN cc_start: 0.9650 (t0) cc_final: 0.9404 (t0) REVERT: D 132 MET cc_start: 0.9742 (ptt) cc_final: 0.9532 (ppp) REVERT: D 165 ILE cc_start: 0.9710 (mm) cc_final: 0.9395 (tp) REVERT: D 178 LEU cc_start: 0.9665 (tp) cc_final: 0.9339 (tp) REVERT: D 179 ASP cc_start: 0.8973 (m-30) cc_final: 0.8520 (m-30) REVERT: D 188 TYR cc_start: 0.9281 (t80) cc_final: 0.8836 (t80) REVERT: D 223 PHE cc_start: 0.9239 (t80) cc_final: 0.8829 (t80) REVERT: D 236 LEU cc_start: 0.8417 (mm) cc_final: 0.8080 (pp) REVERT: D 240 TYR cc_start: 0.8640 (t80) cc_final: 0.7709 (t80) REVERT: D 241 GLU cc_start: 0.9859 (pm20) cc_final: 0.9545 (tp30) REVERT: D 250 ILE cc_start: 0.9788 (mm) cc_final: 0.9489 (tp) REVERT: D 269 MET cc_start: 0.8959 (tpt) cc_final: 0.8668 (tpp) REVERT: D 274 ILE cc_start: 0.9649 (pt) cc_final: 0.9413 (pt) REVERT: D 297 ASN cc_start: 0.9594 (t0) cc_final: 0.9190 (m110) REVERT: D 355 MET cc_start: 0.9489 (mmp) cc_final: 0.9158 (mmm) REVERT: D 356 TRP cc_start: 0.6519 (m-90) cc_final: 0.5981 (t-100) REVERT: E 10 CYS cc_start: 0.8332 (t) cc_final: 0.8072 (t) REVERT: E 51 ASP cc_start: 0.9820 (m-30) cc_final: 0.9605 (t0) REVERT: E 69 TYR cc_start: 0.9007 (m-10) cc_final: 0.8705 (m-10) REVERT: E 73 HIS cc_start: 0.8984 (m-70) cc_final: 0.8471 (m-70) REVERT: E 151 ILE cc_start: 0.9531 (tt) cc_final: 0.9088 (tt) REVERT: E 165 ILE cc_start: 0.9723 (mm) cc_final: 0.9391 (tp) REVERT: E 169 TYR cc_start: 0.9593 (m-80) cc_final: 0.9265 (m-80) REVERT: E 176 MET cc_start: 0.9233 (mmm) cc_final: 0.8733 (mtp) REVERT: E 179 ASP cc_start: 0.9225 (m-30) cc_final: 0.8488 (m-30) REVERT: E 190 MET cc_start: 0.9669 (ptp) cc_final: 0.9373 (ptp) REVERT: E 206 ARG cc_start: 0.9176 (mpp-170) cc_final: 0.8945 (mpp80) REVERT: E 274 ILE cc_start: 0.9464 (pt) cc_final: 0.9238 (pt) REVERT: E 294 TYR cc_start: 0.9601 (m-80) cc_final: 0.9333 (m-80) REVERT: E 334 GLU cc_start: 0.9453 (pm20) cc_final: 0.8956 (tm-30) REVERT: E 352 PHE cc_start: 0.9688 (t80) cc_final: 0.9452 (t80) REVERT: E 375 PHE cc_start: 0.8975 (t80) cc_final: 0.8699 (t80) REVERT: F 11 ASP cc_start: 0.9454 (t70) cc_final: 0.9102 (t0) REVERT: F 73 HIS cc_start: 0.8682 (m-70) cc_final: 0.8296 (m-70) REVERT: F 82 MET cc_start: 0.9690 (ppp) cc_final: 0.9365 (ppp) REVERT: F 86 TRP cc_start: 0.9790 (m-90) cc_final: 0.9577 (m-90) REVERT: F 118 LYS cc_start: 0.9695 (tptp) cc_final: 0.9443 (tptp) REVERT: F 123 MET cc_start: 0.9848 (mmp) cc_final: 0.9513 (mmm) REVERT: F 167 GLU cc_start: 0.9684 (mp0) cc_final: 0.9451 (mp0) REVERT: F 176 MET cc_start: 0.8395 (tmm) cc_final: 0.8180 (tmm) REVERT: F 178 LEU cc_start: 0.9026 (tp) cc_final: 0.8781 (tp) REVERT: F 190 MET cc_start: 0.9708 (ptp) cc_final: 0.9413 (mtp) REVERT: F 213 LYS cc_start: 0.9832 (pttm) cc_final: 0.9384 (ptpp) REVERT: F 262 PHE cc_start: 0.9430 (m-10) cc_final: 0.9100 (m-80) REVERT: G 53 TYR cc_start: 0.9703 (m-80) cc_final: 0.9502 (m-80) REVERT: G 119 MET cc_start: 0.9445 (ppp) cc_final: 0.9222 (ppp) REVERT: G 269 MET cc_start: 0.8782 (ttt) cc_final: 0.8573 (ttm) REVERT: H 156 PHE cc_start: 0.8727 (p90) cc_final: 0.8245 (p90) REVERT: H 157 MET cc_start: 0.7690 (mmp) cc_final: 0.7423 (mmm) REVERT: I 62 MET cc_start: 0.9407 (mmt) cc_final: 0.9140 (mmt) REVERT: I 91 PHE cc_start: 0.9631 (m-80) cc_final: 0.9329 (m-80) REVERT: I 139 LYS cc_start: 0.7894 (mppt) cc_final: 0.6579 (mmmm) REVERT: J 224 LEU cc_start: 0.9187 (mm) cc_final: 0.8985 (mm) REVERT: J 229 LEU cc_start: 0.8438 (mm) cc_final: 0.7667 (mm) REVERT: L 141 MET cc_start: 0.8476 (mpp) cc_final: 0.8171 (mpp) REVERT: M 172 ILE cc_start: 0.9205 (mm) cc_final: 0.8872 (tt) REVERT: M 197 LEU cc_start: 0.9593 (tt) cc_final: 0.9296 (mt) REVERT: N 1 MET cc_start: 0.8274 (pmm) cc_final: 0.7088 (pmm) REVERT: O 1 MET cc_start: 0.9084 (pmm) cc_final: 0.8734 (pmm) REVERT: O 46 LEU cc_start: 0.9569 (tp) cc_final: 0.9347 (tp) outliers start: 0 outliers final: 0 residues processed: 794 average time/residue: 0.2098 time to fit residues: 255.2828 Evaluate side-chains 568 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 41 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 339 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 184 optimal weight: 0.0870 chunk 95 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN C 59 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 ASN ** M 263 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 = 0.3087 r_free = 0.3087 target = 0.050676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.032177 restraints weight = 229379.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.033635 restraints weight = 151239.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.034753 restraints weight = 110615.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035608 restraints weight = 86363.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.036282 restraints weight = 70663.797| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.8464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29145 Z= 0.211 Angle : 0.846 12.080 39338 Z= 0.445 Chirality : 0.050 0.363 4354 Planarity : 0.006 0.112 5094 Dihedral : 6.620 85.277 4000 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 28.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3569 helix: 0.34 (0.11), residues: 1941 sheet: -0.61 (0.26), residues: 420 loop : -0.14 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 206 TYR 0.038 0.002 TYR B 294 PHE 0.048 0.003 PHE B 223 TRP 0.093 0.004 TRP C 86 HIS 0.013 0.002 HIS K 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (29145) covalent geometry : angle 0.84575 / 0.45 (39338) hydrogen bonds : bond 0.05331 / 3.62 ( 1632) hydrogen bonds : angle 5.42892 / 3.82 ( 4581) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 754 time to evaluate : 0.905 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: 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 82 MET cc_start: 0.9693 (tpt) cc_final: 0.9481 (tpp) REVERT: A 110 LEU cc_start: 0.9608 (tt) cc_final: 0.9331 (mp) REVERT: A 119 MET cc_start: 0.9078 (ppp) cc_final: 0.8814 (ppp) REVERT: A 132 MET cc_start: 0.9078 (mtm) cc_final: 0.8736 (mpp) REVERT: B 165 ILE cc_start: 0.9866 (mp) cc_final: 0.9613 (tt) REVERT: B 176 MET cc_start: 0.9249 (mtm) cc_final: 0.8845 (mpp) REVERT: B 179 ASP cc_start: 0.9495 (m-30) cc_final: 0.8876 (m-30) REVERT: B 269 MET cc_start: 0.6440 (ttm) cc_final: 0.5990 (ttm) REVERT: B 311 ASP cc_start: 0.9633 (m-30) cc_final: 0.9103 (t0) REVERT: B 313 MET cc_start: 0.9496 (mtm) cc_final: 0.9150 (mmt) REVERT: C 18 LYS cc_start: 0.9220 (mppt) cc_final: 0.8438 (mppt) REVERT: C 73 HIS cc_start: 0.9185 (m90) cc_final: 0.8595 (m90) REVERT: C 115 ASN cc_start: 0.9631 (m110) cc_final: 0.9293 (t0) REVERT: C 165 ILE cc_start: 0.9628 (mm) cc_final: 0.9391 (tp) REVERT: C 269 MET cc_start: 0.9379 (mpp) cc_final: 0.9177 (mpp) REVERT: C 297 ASN cc_start: 0.9694 (t0) cc_final: 0.9298 (m-40) REVERT: D 16 LEU cc_start: 0.9586 (mm) cc_final: 0.9353 (mp) REVERT: D 47 MET cc_start: 0.8629 (mmp) cc_final: 0.8226 (mmp) REVERT: D 104 LEU cc_start: 0.9374 (mm) cc_final: 0.9042 (mm) REVERT: D 106 THR cc_start: 0.8380 (p) cc_final: 0.7821 (p) REVERT: D 122 ILE cc_start: 0.9834 (mm) cc_final: 0.9496 (pt) REVERT: D 123 MET cc_start: 0.9885 (mmp) cc_final: 0.9520 (mmm) REVERT: D 132 MET cc_start: 0.9739 (ptt) cc_final: 0.9379 (tmm) REVERT: D 165 ILE cc_start: 0.9722 (mm) cc_final: 0.9413 (tp) REVERT: D 169 TYR cc_start: 0.9786 (m-80) cc_final: 0.9556 (m-80) REVERT: D 178 LEU cc_start: 0.9686 (tp) cc_final: 0.9388 (tp) REVERT: D 179 ASP cc_start: 0.9028 (m-30) cc_final: 0.8602 (m-30) REVERT: D 188 TYR cc_start: 0.9332 (t80) cc_final: 0.8789 (t80) REVERT: D 236 LEU cc_start: 0.8677 (mm) cc_final: 0.8243 (pp) REVERT: D 240 TYR cc_start: 0.8789 (t80) cc_final: 0.7785 (t80) REVERT: D 241 GLU cc_start: 0.9852 (pm20) cc_final: 0.9549 (tp30) REVERT: D 250 ILE cc_start: 0.9806 (mm) cc_final: 0.9550 (tp) REVERT: D 269 MET cc_start: 0.9021 (tpt) cc_final: 0.8714 (tpp) REVERT: D 274 ILE cc_start: 0.9563 (pt) cc_final: 0.9313 (pt) REVERT: D 297 ASN cc_start: 0.9620 (t0) cc_final: 0.9339 (m110) REVERT: D 355 MET cc_start: 0.9514 (mmp) cc_final: 0.9161 (mmm) REVERT: D 356 TRP cc_start: 0.6768 (m-90) cc_final: 0.6084 (t-100) REVERT: E 51 ASP cc_start: 0.9821 (m-30) cc_final: 0.9597 (t0) REVERT: E 69 TYR cc_start: 0.9028 (m-10) cc_final: 0.8721 (m-10) REVERT: E 73 HIS cc_start: 0.9050 (m-70) cc_final: 0.8570 (m90) REVERT: E 151 ILE cc_start: 0.9569 (tt) cc_final: 0.9198 (tt) REVERT: E 165 ILE cc_start: 0.9769 (mm) cc_final: 0.9471 (tp) REVERT: E 176 MET cc_start: 0.9220 (mmm) cc_final: 0.8923 (mtp) REVERT: E 178 LEU cc_start: 0.9100 (tp) cc_final: 0.8644 (tp) REVERT: E 179 ASP cc_start: 0.9299 (m-30) cc_final: 0.8695 (m-30) REVERT: E 190 MET cc_start: 0.9784 (ptp) cc_final: 0.9505 (ptp) REVERT: E 213 LYS cc_start: 0.9623 (ptpp) cc_final: 0.9312 (pttm) REVERT: E 236 LEU cc_start: 0.8576 (tp) cc_final: 0.8375 (tp) REVERT: E 257 CYS cc_start: 0.9179 (t) cc_final: 0.8975 (t) REVERT: E 274 ILE cc_start: 0.9482 (pt) cc_final: 0.9255 (pt) REVERT: E 294 TYR cc_start: 0.9634 (m-80) cc_final: 0.9379 (m-80) REVERT: E 352 PHE cc_start: 0.9730 (t80) cc_final: 0.9511 (t80) REVERT: E 375 PHE cc_start: 0.8967 (t80) cc_final: 0.8706 (t80) REVERT: F 11 ASP cc_start: 0.9508 (t70) cc_final: 0.9207 (t0) REVERT: F 73 HIS cc_start: 0.8736 (m-70) cc_final: 0.8381 (m-70) REVERT: F 82 MET cc_start: 0.9705 (ppp) cc_final: 0.9353 (ppp) REVERT: F 118 LYS cc_start: 0.9723 (tptp) cc_final: 0.9496 (tptp) REVERT: F 123 MET cc_start: 0.9848 (mmp) cc_final: 0.9550 (mmm) REVERT: F 167 GLU cc_start: 0.9686 (mp0) cc_final: 0.9426 (mp0) REVERT: F 176 MET cc_start: 0.8494 (tmm) cc_final: 0.8229 (tmm) REVERT: F 178 LEU cc_start: 0.9110 (tp) cc_final: 0.8854 (tp) REVERT: F 213 LYS cc_start: 0.9814 (pttm) cc_final: 0.9433 (ptpp) REVERT: F 274 ILE cc_start: 0.9694 (pt) cc_final: 0.9374 (pt) REVERT: F 294 TYR cc_start: 0.9732 (m-10) cc_final: 0.9492 (m-10) REVERT: F 297 ASN cc_start: 0.9742 (t0) cc_final: 0.9194 (m-40) REVERT: G 53 TYR cc_start: 0.9729 (m-80) cc_final: 0.9524 (m-80) REVERT: H 88 ASP cc_start: 0.8899 (m-30) cc_final: 0.8201 (t0) REVERT: I 54 MET cc_start: 0.9339 (mmp) cc_final: 0.8790 (mmm) REVERT: I 62 MET cc_start: 0.9410 (mmt) cc_final: 0.8821 (mmm) REVERT: I 91 PHE cc_start: 0.9627 (m-80) cc_final: 0.9334 (m-80) REVERT: I 139 LYS cc_start: 0.7813 (mppt) cc_final: 0.6468 (mmmm) REVERT: I 163 ARG cc_start: 0.9125 (mtm-85) cc_final: 0.8770 (ptt90) REVERT: J 229 LEU cc_start: 0.8413 (mm) cc_final: 0.7882 (mm) REVERT: M 127 MET cc_start: 0.8267 (mmp) cc_final: 0.8033 (mmp) REVERT: M 172 ILE cc_start: 0.9173 (mm) cc_final: 0.8843 (tt) REVERT: M 197 LEU cc_start: 0.9625 (tt) cc_final: 0.9318 (mt) REVERT: N 1 MET cc_start: 0.8577 (pmm) cc_final: 0.7289 (ppp) REVERT: O 1 MET cc_start: 0.9179 (pmm) cc_final: 0.8731 (pmm) REVERT: O 46 LEU cc_start: 0.9569 (tp) cc_final: 0.9336 (tp) outliers start: 0 outliers final: 0 residues processed: 754 average time/residue: 0.1973 time to fit residues: 228.5297 Evaluate side-chains 551 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 226 optimal weight: 0.0570 chunk 325 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 316 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 2 optimal weight: 0.0470 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 111 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 ASN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 263 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 = 0.3146 r_free = 0.3146 target = 0.052620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.033978 restraints weight = 223326.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.035540 restraints weight = 145265.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.036713 restraints weight = 105087.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.037642 restraints weight = 81347.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.038349 restraints weight = 65933.043| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.8502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29145 Z= 0.165 Angle : 0.817 14.025 39338 Z= 0.428 Chirality : 0.051 0.532 4354 Planarity : 0.005 0.102 5094 Dihedral : 6.567 87.700 4000 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3569 helix: 0.55 (0.12), residues: 1915 sheet: -0.63 (0.24), residues: 455 loop : -0.13 (0.19), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 372 TYR 0.042 0.002 TYR C 294 PHE 0.049 0.003 PHE B 223 TRP 0.098 0.004 TRP C 86 HIS 0.014 0.001 HIS K 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (29145) covalent geometry : angle 0.81728 / 0.43 (39338) hydrogen bonds : bond 0.05209 / 3.52 ( 1632) hydrogen bonds : angle 5.31497 / 3.73 ( 4581) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6794.55 seconds wall clock time: 118 minutes 7.79 seconds (7087.79 seconds total)