Starting phenix.real_space_refine on Wed Nov 19 22:34:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mow_48483/11_2025/9mow_48483.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mow_48483/11_2025/9mow_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_48483/11_2025/9mow_48483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mow_48483/11_2025/9mow_48483.map" model { file = "/net/cci-nas-00/data/ceres_data/9mow_48483/11_2025/9mow_48483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mow_48483/11_2025/9mow_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-2.0-5881/lib/python3.9/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, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.56, per 1000 atoms: 0.23 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: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.12 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: 5.71 Time building geometry restraints manager: 3.37 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 2.510 nonbonded pdb=" OD1 ASN H 143 " pdb="CA CA H 202 " model vdw 1.536 2.510 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 2.510 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.920 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 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 covalent geometry : bond 0.00722 (29145) covalent geometry : angle 0.72319 (39338) hydrogen bonds : bond 0.15760 ( 1632) hydrogen bonds : angle 5.36614 ( 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 : 1.102 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: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.3034 (m-80) cc_final: 0.2634 (m-10) REVERT: A 212 ILE cc_start: 0.7603 (mt) cc_final: 0.7333 (mt) REVERT: A 223 PHE cc_start: 0.6314 (t80) cc_final: 0.6074 (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: 0.4077 (p90) REVERT: A 300 SER cc_start: 0.3607 (OUTLIER) cc_final: 0.3061 (p) REVERT: B 89 THR cc_start: 0.7928 (m) cc_final: 0.7453 (p) REVERT: B 152 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.6063 (p) REVERT: B 185 LEU cc_start: 0.9288 (mt) cc_final: 0.9036 (mp) REVERT: B 189 LEU cc_start: 0.8111 (tp) cc_final: 0.7673 (tp) REVERT: B 217 CYS cc_start: 0.5938 (m) cc_final: 0.5625 (m) REVERT: B 262 PHE cc_start: 0.6892 (m-80) cc_final: 0.6278 (m-10) REVERT: B 323 SER cc_start: 0.8409 (m) cc_final: 0.7997 (p) REVERT: C 31 PHE cc_start: 0.5860 (p90) cc_final: 0.4750 (p90) REVERT: C 81 ASP cc_start: 0.7462 (m-30) cc_final: 0.6798 (t0) REVERT: C 124 PHE cc_start: 0.6377 (m-10) cc_final: 0.5824 (m-80) REVERT: C 140 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7210 (mm) REVERT: C 151 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7612 (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: 0.6187 (t80) REVERT: C 275 HIS cc_start: 0.4677 (p90) cc_final: 0.3485 (p-80) REVERT: C 280 ASN cc_start: 0.7740 (m-40) cc_final: 0.6552 (m110) REVERT: C 309 ILE cc_start: 0.6104 (tt) cc_final: 0.5731 (tt) REVERT: D 81 ASP cc_start: 0.7725 (m-30) cc_final: 0.7230 (m-30) REVERT: D 115 ASN cc_start: 0.7723 (t0) cc_final: 0.7046 (t0) REVERT: D 151 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7200 (tt) REVERT: D 152 VAL cc_start: 0.7434 (OUTLIER) cc_final: 0.6423 (p) REVERT: D 153 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6827 (tt) REVERT: D 233 SER cc_start: 0.5308 (OUTLIER) cc_final: 0.4994 (p) REVERT: D 357 ILE cc_start: 0.8203 (mt) cc_final: 0.7618 (mp) REVERT: E 75 ILE cc_start: 0.5236 (pt) cc_final: 0.4516 (pt) REVERT: E 115 ASN cc_start: 0.7777 (t0) cc_final: 0.7330 (t0) REVERT: E 122 ILE cc_start: 0.7712 (mm) cc_final: 0.7475 (mt) REVERT: E 151 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7693 (tt) REVERT: E 152 VAL cc_start: 0.7052 (OUTLIER) cc_final: 0.6760 (p) REVERT: E 185 LEU cc_start: 0.9175 (mt) cc_final: 0.8715 (tt) REVERT: E 188 TYR cc_start: 0.7751 (t80) cc_final: 0.7266 (t80) REVERT: E 212 ILE cc_start: 0.8298 (mt) cc_final: 0.7980 (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: 0.6583 (m-10) REVERT: E 357 ILE cc_start: 0.8387 (mt) cc_final: 0.7481 (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: 0.6851 (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: 0.6972 (mt) REVERT: F 253 GLU cc_start: 0.8568 (mp0) cc_final: 0.7725 (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: 0.5813 (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: 0.7796 (p0) REVERT: H 88 ASP cc_start: 0.8150 (m-30) cc_final: 0.7676 (t0) REVERT: I 57 ILE cc_start: 0.8160 (mm) cc_final: 0.7941 (tt) REVERT: I 97 LEU cc_start: 0.8342 (mm) cc_final: 0.8053 (mm) REVERT: I 101 LEU cc_start: 0.8547 (mm) cc_final: 0.7350 (mm) REVERT: I 108 VAL cc_start: 0.7435 (t) cc_final: 0.6957 (p) REVERT: J 221 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7850 (pt) REVERT: J 234 LYS cc_start: 0.8326 (tptt) cc_final: 0.7969 (tptp) REVERT: J 253 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6848 (mmmt) REVERT: K 133 GLU cc_start: 0.8979 (pt0) cc_final: 0.8500 (pt0) REVERT: K 138 GLN cc_start: 0.6033 (tp40) cc_final: 0.5639 (tp-100) REVERT: L 131 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8265 (mm-30) REVERT: L 148 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7170 (mt) REVERT: L 196 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.9102 (mm-30) REVERT: L 249 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7131 (tt) REVERT: M 164 GLU cc_start: 0.8853 (tp30) cc_final: 0.8224 (mt-10) REVERT: M 243 GLU cc_start: 0.9003 (tt0) cc_final: 0.8752 (pp20) REVERT: M 246 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7815 (p) REVERT: M 247 THR cc_start: 0.9781 (p) cc_final: 0.8828 (p) REVERT: M 279 ASN cc_start: 0.8959 (m-40) cc_final: 0.8647 (m110) REVERT: N 36 SER cc_start: 0.7395 (OUTLIER) cc_final: 0.6719 (p) outliers start: 250 outliers final: 64 residues processed: 1617 average time/residue: 0.2346 time to fit residues: 558.9933 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 : 1.157 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 18 ASN H 58 GLN H 122 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 238 GLN J 257 GLN ** K 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 ASN L 202 ASN L 263 GLN M 68 GLN M 103 GLN 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.040861 restraints weight = 189639.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.042870 restraints weight = 122449.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044397 restraints weight = 87842.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045585 restraints weight = 67415.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.046464 restraints weight = 54286.822| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29145 Z= 0.197 Angle : 0.779 10.752 39338 Z= 0.396 Chirality : 0.048 0.289 4354 Planarity : 0.006 0.106 5094 Dihedral : 6.629 75.250 4000 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 0.29 % Allowed : 4.88 % Favored : 94.83 % 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: -0.16 (0.14), residues: 3569 helix: 0.76 (0.12), residues: 1848 sheet: -1.86 (0.22), residues: 420 loop : -0.58 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG C 206 TYR 0.038 0.002 TYR D 143 PHE 0.028 0.002 PHE D 124 TRP 0.029 0.002 TRP D 79 HIS 0.012 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00441 (29145) covalent geometry : angle 0.77925 (39338) hydrogen bonds : bond 0.05641 ( 1632) hydrogen bonds : angle 4.62600 ( 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 1073 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1064 time to evaluate : 1.210 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: A 72 GLU cc_start: 0.9574 (pt0) cc_final: 0.9229 (mp0) REVERT: A 122 ILE cc_start: 0.9684 (mm) cc_final: 0.9425 (tt) REVERT: A 253 GLU cc_start: 0.9334 (mp0) cc_final: 0.8437 (mt-10) REVERT: A 269 MET cc_start: 0.6254 (ttt) cc_final: 0.5899 (ttm) REVERT: A 275 HIS cc_start: 0.9786 (p90) cc_final: 0.9477 (p90) REVERT: B 8 LEU cc_start: 0.9854 (mt) cc_final: 0.9613 (mt) REVERT: B 90 PHE cc_start: 0.9629 (m-10) cc_final: 0.9412 (m-10) REVERT: B 128 ASN cc_start: 0.9781 (t0) cc_final: 0.9497 (m110) REVERT: B 178 LEU cc_start: 0.8682 (tp) cc_final: 0.8094 (tt) REVERT: B 179 ASP cc_start: 0.9560 (m-30) cc_final: 0.8931 (m-30) REVERT: B 266 PHE cc_start: 0.9353 (m-80) cc_final: 0.9116 (m-10) REVERT: B 267 ILE cc_start: 0.8298 (pt) cc_final: 0.8096 (pt) REVERT: B 275 HIS cc_start: 0.9316 (p90) cc_final: 0.9012 (p90) REVERT: B 294 TYR cc_start: 0.9009 (m-10) cc_final: 0.8772 (m-10) REVERT: B 305 MET cc_start: 0.7818 (mmp) cc_final: 0.7499 (mmt) REVERT: B 306 TYR cc_start: 0.8252 (m-10) cc_final: 0.7566 (m-10) REVERT: B 313 MET cc_start: 0.9334 (tpp) cc_final: 0.8768 (tpt) REVERT: B 336 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8941 (ttmm) REVERT: C 69 TYR cc_start: 0.8711 (m-10) cc_final: 0.8422 (m-10) REVERT: C 123 MET cc_start: 0.9841 (mmp) cc_final: 0.9638 (mmm) REVERT: C 225 ASN cc_start: 0.9893 (m110) cc_final: 0.9683 (m-40) REVERT: C 261 LEU cc_start: 0.9588 (mp) cc_final: 0.9364 (mt) REVERT: C 274 ILE cc_start: 0.9599 (pt) cc_final: 0.9368 (pt) REVERT: C 311 ASP cc_start: 0.9272 (p0) cc_final: 0.8994 (p0) REVERT: C 313 MET cc_start: 0.9599 (tpp) cc_final: 0.8938 (tpp) REVERT: C 316 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8748 (tm-30) REVERT: C 317 ILE cc_start: 0.9575 (mm) cc_final: 0.9031 (mm) REVERT: D 56 ASP cc_start: 0.9622 (m-30) cc_final: 0.9217 (m-30) REVERT: D 81 ASP cc_start: 0.9126 (m-30) cc_final: 0.8448 (t0) REVERT: D 82 MET cc_start: 0.9186 (ptt) cc_final: 0.8888 (ppp) REVERT: D 85 ILE cc_start: 0.9855 (mm) cc_final: 0.9592 (mm) REVERT: D 123 MET cc_start: 0.9820 (mmp) cc_final: 0.9495 (mmt) REVERT: D 179 ASP cc_start: 0.9470 (m-30) cc_final: 0.9187 (m-30) REVERT: D 236 LEU cc_start: 0.8147 (mt) cc_final: 0.7815 (tp) REVERT: D 250 ILE cc_start: 0.9738 (mm) cc_final: 0.9259 (tt) REVERT: D 257 CYS cc_start: 0.9542 (t) cc_final: 0.9201 (t) REVERT: D 269 MET cc_start: 0.8748 (tpt) cc_final: 0.8428 (tpp) REVERT: D 355 MET cc_start: 0.9588 (mmp) cc_final: 0.9361 (mmm) REVERT: E 8 LEU cc_start: 0.9460 (mm) cc_final: 0.9215 (mm) REVERT: E 86 TRP cc_start: 0.9620 (m-10) cc_final: 0.9419 (m-10) REVERT: E 122 ILE cc_start: 0.9468 (mm) cc_final: 0.9033 (mt) REVERT: E 165 ILE cc_start: 0.9812 (mm) cc_final: 0.9539 (tp) REVERT: E 167 GLU cc_start: 0.9607 (tp30) cc_final: 0.9387 (tm-30) REVERT: E 176 MET cc_start: 0.8974 (mmm) cc_final: 0.8540 (mtp) REVERT: E 178 LEU cc_start: 0.9016 (tp) cc_final: 0.8527 (tp) REVERT: E 179 ASP cc_start: 0.9258 (m-30) cc_final: 0.8800 (m-30) REVERT: E 183 ARG cc_start: 0.9724 (tpp80) cc_final: 0.9407 (mmm-85) REVERT: E 250 ILE cc_start: 0.9427 (tp) cc_final: 0.9161 (tp) REVERT: E 257 CYS cc_start: 0.9113 (t) cc_final: 0.8337 (t) REVERT: E 262 PHE cc_start: 0.9742 (m-80) cc_final: 0.9440 (m-10) REVERT: E 275 HIS cc_start: 0.9704 (p90) cc_final: 0.8842 (p-80) REVERT: E 284 LYS cc_start: 0.9086 (ptpt) cc_final: 0.8800 (pttm) REVERT: E 294 TYR cc_start: 0.9601 (m-80) cc_final: 0.9254 (m-10) REVERT: E 313 MET cc_start: 0.9308 (tpt) cc_final: 0.9085 (tpt) REVERT: E 375 PHE cc_start: 0.9078 (t80) cc_final: 0.8699 (t80) REVERT: F 11 ASP cc_start: 0.9634 (t70) cc_final: 0.9103 (p0) REVERT: F 69 TYR cc_start: 0.9227 (m-10) cc_final: 0.8867 (m-80) REVERT: F 118 LYS cc_start: 0.9338 (tptp) cc_final: 0.8984 (tppt) REVERT: F 167 GLU cc_start: 0.9587 (mp0) cc_final: 0.9270 (mp0) REVERT: F 178 LEU cc_start: 0.8764 (tp) cc_final: 0.8322 (tp) REVERT: F 183 ARG cc_start: 0.9626 (tpp80) cc_final: 0.9356 (ptp-110) REVERT: F 217 CYS cc_start: 0.4845 (p) cc_final: 0.1478 (p) REVERT: F 269 MET cc_start: 0.8621 (ttt) cc_final: 0.8404 (ttm) REVERT: F 277 THR cc_start: 0.9758 (p) cc_final: 0.9509 (p) REVERT: F 303 THR cc_start: 0.9461 (m) cc_final: 0.9076 (p) REVERT: G 180 LEU cc_start: 0.9276 (tt) cc_final: 0.8933 (tp) REVERT: G 269 MET cc_start: 0.9209 (ttm) cc_final: 0.8967 (ttm) REVERT: G 274 ILE cc_start: 0.9850 (pt) cc_final: 0.9595 (pt) REVERT: G 275 HIS cc_start: 0.9727 (p90) cc_final: 0.9520 (p90) REVERT: G 359 LYS cc_start: 0.9662 (tttm) cc_final: 0.9375 (mptt) REVERT: H 115 ASP cc_start: 0.9356 (m-30) cc_final: 0.9124 (m-30) REVERT: I 91 PHE cc_start: 0.9289 (m-80) cc_final: 0.9011 (m-10) REVERT: K 95 MET cc_start: 0.7811 (tpp) cc_final: 0.7575 (tpp) REVERT: L 228 LEU cc_start: 0.9263 (tt) cc_final: 0.8848 (tt) REVERT: M 127 MET cc_start: 0.9145 (mmm) cc_final: 0.8919 (mmm) REVERT: M 139 GLU cc_start: 0.9932 (tm-30) cc_final: 0.9627 (mm-30) REVERT: M 141 MET cc_start: 0.9645 (tmm) cc_final: 0.9429 (tmm) REVERT: M 197 LEU cc_start: 0.9360 (tt) cc_final: 0.8997 (mt) REVERT: M 228 LEU cc_start: 0.9475 (mt) cc_final: 0.9168 (mt) REVERT: M 241 PHE cc_start: 0.9358 (m-80) cc_final: 0.9156 (m-80) REVERT: N 28 ASP cc_start: 0.9579 (t70) cc_final: 0.9319 (t70) outliers start: 9 outliers final: 3 residues processed: 1070 average time/residue: 0.2229 time to fit residues: 354.8733 Evaluate side-chains 689 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 686 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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: 3.9990 chunk 243 optimal weight: 5.9990 chunk 331 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 340 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 320 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS B 353 GLN C 73 HIS ** 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS F 353 GLN ** G 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 122 ASN J 223 HIS ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 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** N 9 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.036252 restraints weight = 210831.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.037970 restraints weight = 137586.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.039259 restraints weight = 99543.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.040269 restraints weight = 77179.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.041068 restraints weight = 62629.050| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29145 Z= 0.247 Angle : 0.817 11.448 39338 Z= 0.423 Chirality : 0.048 0.232 4354 Planarity : 0.007 0.164 5094 Dihedral : 6.678 79.764 4000 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.81 % Rotamer: Outliers : 0.33 % Allowed : 5.49 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3569 helix: 0.50 (0.12), residues: 1852 sheet: -1.36 (0.23), residues: 441 loop : -0.44 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 182 TYR 0.037 0.002 TYR C 294 PHE 0.035 0.003 PHE E 223 TRP 0.031 0.003 TRP F 86 HIS 0.011 0.002 HIS J 223 Details of bonding type rmsd covalent geometry : bond 0.00516 (29145) covalent geometry : angle 0.81708 (39338) hydrogen bonds : bond 0.05558 ( 1632) hydrogen bonds : angle 4.76387 ( 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 894 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 884 time to evaluate : 1.161 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 269 MET cc_start: 0.6082 (ttt) cc_final: 0.5506 (ttp) REVERT: B 8 LEU cc_start: 0.9795 (mt) cc_final: 0.9582 (mt) REVERT: B 128 ASN cc_start: 0.9736 (t0) cc_final: 0.9467 (m110) REVERT: B 140 LEU cc_start: 0.9646 (mm) cc_final: 0.9389 (mm) REVERT: B 176 MET cc_start: 0.9115 (mtm) cc_final: 0.8809 (mtp) REVERT: B 179 ASP cc_start: 0.9464 (m-30) cc_final: 0.8784 (m-30) REVERT: B 188 TYR cc_start: 0.9504 (t80) cc_final: 0.9002 (t80) REVERT: B 189 LEU cc_start: 0.9653 (tp) cc_final: 0.9444 (tp) REVERT: B 213 LYS cc_start: 0.9515 (ttpp) cc_final: 0.9114 (ttpp) REVERT: B 257 CYS cc_start: 0.9334 (t) cc_final: 0.8657 (t) REVERT: B 266 PHE cc_start: 0.9222 (m-80) cc_final: 0.8762 (m-10) REVERT: B 269 MET cc_start: 0.6607 (ttm) cc_final: 0.6307 (ttm) REVERT: B 311 ASP cc_start: 0.9770 (m-30) cc_final: 0.9299 (t0) REVERT: C 16 LEU cc_start: 0.9300 (mp) cc_final: 0.9075 (mt) REVERT: C 81 ASP cc_start: 0.9576 (m-30) cc_final: 0.8913 (t0) REVERT: C 82 MET cc_start: 0.9848 (tpt) cc_final: 0.9630 (tpp) REVERT: C 85 ILE cc_start: 0.9812 (mm) cc_final: 0.9519 (mt) REVERT: C 122 ILE cc_start: 0.9781 (mm) cc_final: 0.9437 (mt) REVERT: C 253 GLU cc_start: 0.9723 (mp0) cc_final: 0.8826 (mt-10) REVERT: C 262 PHE cc_start: 0.9472 (m-80) cc_final: 0.8765 (m-10) REVERT: C 313 MET cc_start: 0.9524 (tpp) cc_final: 0.8841 (tpt) REVERT: C 316 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8834 (tm-30) REVERT: C 317 ILE cc_start: 0.9692 (mm) cc_final: 0.9123 (mm) REVERT: D 81 ASP cc_start: 0.9276 (m-30) cc_final: 0.8500 (t0) REVERT: D 82 MET cc_start: 0.9356 (ptt) cc_final: 0.8981 (ppp) REVERT: D 85 ILE cc_start: 0.9878 (mm) cc_final: 0.9640 (mm) REVERT: D 123 MET cc_start: 0.9860 (mmp) cc_final: 0.9624 (mmm) REVERT: D 132 MET cc_start: 0.9756 (ptt) cc_final: 0.9342 (ppp) REVERT: D 161 HIS cc_start: 0.9385 (p-80) cc_final: 0.9158 (p-80) REVERT: D 176 MET cc_start: 0.8928 (mtm) cc_final: 0.8129 (mtp) REVERT: D 179 ASP cc_start: 0.9449 (m-30) cc_final: 0.9165 (m-30) REVERT: D 223 PHE cc_start: 0.8803 (t80) cc_final: 0.8342 (t80) REVERT: D 236 LEU cc_start: 0.8473 (mt) cc_final: 0.7944 (tp) REVERT: D 250 ILE cc_start: 0.9828 (mm) cc_final: 0.9495 (tp) REVERT: D 257 CYS cc_start: 0.9632 (t) cc_final: 0.9354 (t) REVERT: D 269 MET cc_start: 0.8845 (tpt) cc_final: 0.8486 (tpp) REVERT: D 313 MET cc_start: 0.9666 (mmm) cc_final: 0.9448 (tpt) REVERT: D 355 MET cc_start: 0.9611 (mmp) cc_final: 0.9359 (mmm) REVERT: E 51 ASP cc_start: 0.9647 (t0) cc_final: 0.9237 (t0) REVERT: E 69 TYR cc_start: 0.9001 (m-10) cc_final: 0.8382 (m-10) REVERT: E 122 ILE cc_start: 0.9557 (mm) cc_final: 0.9284 (mt) REVERT: E 169 TYR cc_start: 0.9840 (m-80) cc_final: 0.9359 (m-80) REVERT: E 176 MET cc_start: 0.9031 (mmm) cc_final: 0.8703 (mtp) REVERT: E 178 LEU cc_start: 0.9208 (tp) cc_final: 0.8749 (tp) REVERT: E 179 ASP cc_start: 0.9122 (m-30) cc_final: 0.8637 (m-30) REVERT: E 183 ARG cc_start: 0.9569 (tpp80) cc_final: 0.9286 (mmm-85) REVERT: E 190 MET cc_start: 0.9744 (ptp) cc_final: 0.9410 (ptp) REVERT: E 213 LYS cc_start: 0.9684 (ptpp) cc_final: 0.9330 (ptpp) REVERT: E 262 PHE cc_start: 0.9750 (m-80) cc_final: 0.9187 (m-80) REVERT: E 294 TYR cc_start: 0.9588 (m-80) cc_final: 0.9336 (m-10) REVERT: E 306 TYR cc_start: 0.8250 (m-10) cc_final: 0.7980 (m-10) REVERT: E 316 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9187 (mm-30) REVERT: E 375 PHE cc_start: 0.9059 (t80) cc_final: 0.8666 (t80) REVERT: F 12 ASN cc_start: 0.9765 (m110) cc_final: 0.9523 (p0) REVERT: F 85 ILE cc_start: 0.9728 (mm) cc_final: 0.9463 (mm) REVERT: F 167 GLU cc_start: 0.9605 (mp0) cc_final: 0.9322 (mp0) REVERT: F 176 MET cc_start: 0.8158 (tmm) cc_final: 0.7638 (tmm) REVERT: F 178 LEU cc_start: 0.8954 (tp) cc_final: 0.8649 (tp) REVERT: F 183 ARG cc_start: 0.9689 (tpp80) cc_final: 0.9298 (ptp-110) REVERT: F 213 LYS cc_start: 0.9767 (ptpt) cc_final: 0.9351 (ptmm) REVERT: F 236 LEU cc_start: 0.8662 (mt) cc_final: 0.8458 (tp) REVERT: F 294 TYR cc_start: 0.9642 (m-10) cc_final: 0.9396 (m-10) REVERT: G 110 LEU cc_start: 0.9124 (mt) cc_final: 0.8672 (mt) REVERT: G 132 MET cc_start: 0.9094 (tmm) cc_final: 0.8765 (tmm) REVERT: G 180 LEU cc_start: 0.9315 (tt) cc_final: 0.9014 (tp) REVERT: G 269 MET cc_start: 0.9250 (ttm) cc_final: 0.9026 (ttm) REVERT: H 88 ASP cc_start: 0.8618 (m-30) cc_final: 0.7994 (t0) REVERT: H 120 MET cc_start: 0.9612 (mtm) cc_final: 0.9279 (mtp) REVERT: H 156 PHE cc_start: 0.8664 (p90) cc_final: 0.8358 (p90) REVERT: I 64 ARG cc_start: 0.9533 (ptm-80) cc_final: 0.9304 (ttp-110) REVERT: I 67 GLU cc_start: 0.9783 (mt-10) cc_final: 0.9398 (mt-10) REVERT: I 91 PHE cc_start: 0.9444 (m-80) cc_final: 0.9164 (m-10) REVERT: J 229 LEU cc_start: 0.8633 (mp) cc_final: 0.7674 (mm) REVERT: M 197 LEU cc_start: 0.9463 (tt) cc_final: 0.9105 (mt) REVERT: N 1 MET cc_start: 0.8168 (pmm) cc_final: 0.7478 (pmm) REVERT: N 8 MET cc_start: 0.7157 (ttt) cc_final: 0.6870 (tmm) REVERT: O 4 ILE cc_start: 0.9625 (pt) cc_final: 0.9423 (pt) outliers start: 10 outliers final: 3 residues processed: 892 average time/residue: 0.2270 time to fit residues: 301.8350 Evaluate side-chains 619 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 616 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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: 0.9990 chunk 278 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 328 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 290 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS A 252 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN C 115 ASN C 173 HIS C 353 GLN D 12 ASN E 225 ASN ** G 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN K 150 ASN L 93 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.057780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.036253 restraints weight = 205309.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.038126 restraints weight = 129945.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.039577 restraints weight = 92751.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.040705 restraints weight = 70942.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.041592 restraints weight = 56928.884| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29145 Z= 0.170 Angle : 0.760 12.273 39338 Z= 0.388 Chirality : 0.048 0.281 4354 Planarity : 0.006 0.173 5094 Dihedral : 6.537 85.154 4000 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.32 % 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: 0.66 (0.12), residues: 1819 sheet: -0.94 (0.24), residues: 434 loop : -0.33 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 372 TYR 0.049 0.002 TYR B 294 PHE 0.042 0.002 PHE E 223 TRP 0.042 0.003 TRP F 86 HIS 0.020 0.002 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00374 (29145) covalent geometry : angle 0.75979 (39338) hydrogen bonds : bond 0.05347 ( 1632) hydrogen bonds : angle 4.74269 ( 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 886 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 881 time to evaluate : 1.170 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: A 119 MET cc_start: 0.8884 (ppp) cc_final: 0.8524 (ppp) REVERT: A 122 ILE cc_start: 0.8964 (mm) cc_final: 0.8697 (tt) REVERT: B 122 ILE cc_start: 0.8757 (mt) cc_final: 0.8488 (pt) REVERT: B 140 LEU cc_start: 0.8742 (mm) cc_final: 0.8522 (mm) REVERT: B 179 ASP cc_start: 0.9100 (m-30) cc_final: 0.8768 (m-30) REVERT: B 269 MET cc_start: 0.8284 (ttm) cc_final: 0.7949 (ttm) REVERT: B 275 HIS cc_start: 0.9195 (p90) cc_final: 0.8950 (p90) REVERT: C 73 HIS cc_start: 0.8289 (m90) cc_final: 0.7942 (m170) REVERT: C 86 TRP cc_start: 0.9471 (m-10) cc_final: 0.9197 (m-10) REVERT: C 107 GLU cc_start: 0.9569 (tt0) cc_final: 0.9344 (tt0) REVERT: C 179 ASP cc_start: 0.8878 (m-30) cc_final: 0.8545 (m-30) REVERT: C 261 LEU cc_start: 0.9265 (mp) cc_final: 0.9029 (mt) REVERT: C 313 MET cc_start: 0.9014 (tpp) cc_final: 0.8482 (tpt) REVERT: C 316 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7854 (tm-30) REVERT: C 317 ILE cc_start: 0.8553 (mm) cc_final: 0.7825 (pt) REVERT: D 64 ILE cc_start: 0.9490 (pt) cc_final: 0.9258 (pt) REVERT: D 81 ASP cc_start: 0.7917 (m-30) cc_final: 0.7342 (t0) REVERT: D 85 ILE cc_start: 0.9824 (mm) cc_final: 0.9419 (mm) REVERT: D 86 TRP cc_start: 0.9394 (m-10) cc_final: 0.8944 (m-10) REVERT: D 104 LEU cc_start: 0.8893 (mm) cc_final: 0.8689 (mm) REVERT: D 106 THR cc_start: 0.4412 (p) cc_final: 0.3937 (p) REVERT: D 122 ILE cc_start: 0.9268 (mm) cc_final: 0.8912 (mm) REVERT: D 151 ILE cc_start: 0.9245 (tt) cc_final: 0.8621 (tt) REVERT: D 176 MET cc_start: 0.8867 (mtm) cc_final: 0.8502 (mtp) REVERT: D 213 LYS cc_start: 0.8331 (pttm) cc_final: 0.8008 (pttp) REVERT: D 250 ILE cc_start: 0.8899 (mm) cc_final: 0.8644 (tp) REVERT: D 257 CYS cc_start: 0.9179 (t) cc_final: 0.8572 (t) REVERT: D 284 LYS cc_start: 0.8024 (ptpp) cc_final: 0.7823 (pttp) REVERT: E 165 ILE cc_start: 0.9293 (mm) cc_final: 0.8965 (tp) REVERT: E 178 LEU cc_start: 0.6671 (tp) cc_final: 0.6166 (tp) REVERT: E 179 ASP cc_start: 0.8597 (m-30) cc_final: 0.8234 (m-30) REVERT: E 190 MET cc_start: 0.8750 (ptp) cc_final: 0.8524 (ptp) REVERT: E 213 LYS cc_start: 0.7974 (ptpp) cc_final: 0.7177 (ptpp) REVERT: E 257 CYS cc_start: 0.8443 (t) cc_final: 0.7674 (t) REVERT: E 262 PHE cc_start: 0.8495 (m-80) cc_final: 0.8049 (m-80) REVERT: E 274 ILE cc_start: 0.9595 (pt) cc_final: 0.9369 (pt) REVERT: E 294 TYR cc_start: 0.9336 (m-10) cc_final: 0.9106 (m-10) REVERT: E 316 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8290 (mm-30) REVERT: F 11 ASP cc_start: 0.8926 (t0) cc_final: 0.8668 (t0) REVERT: F 73 HIS cc_start: 0.7497 (m-70) cc_final: 0.6923 (m-70) REVERT: F 82 MET cc_start: 0.9219 (ppp) cc_final: 0.8936 (ppp) REVERT: F 262 PHE cc_start: 0.8266 (m-10) cc_final: 0.7751 (m-10) REVERT: F 274 ILE cc_start: 0.8987 (pt) cc_final: 0.8725 (pt) REVERT: H 120 MET cc_start: 0.6963 (mtm) cc_final: 0.6225 (mtp) REVERT: I 83 PRO cc_start: 0.7188 (Cg_exo) cc_final: 0.6038 (Cg_endo) REVERT: I 91 PHE cc_start: 0.8640 (m-80) cc_final: 0.8381 (m-80) REVERT: J 229 LEU cc_start: 0.4170 (mp) cc_final: 0.2797 (mp) REVERT: J 232 LYS cc_start: 0.6533 (ptpp) cc_final: 0.6222 (pttt) REVERT: K 102 LEU cc_start: 0.7267 (tt) cc_final: 0.6876 (tt) REVERT: M 197 LEU cc_start: 0.8590 (tt) cc_final: 0.8369 (mt) REVERT: N 35 ARG cc_start: 0.9060 (tmm160) cc_final: 0.8726 (tmt170) REVERT: O 43 LEU cc_start: 0.7957 (tp) cc_final: 0.7693 (tp) outliers start: 5 outliers final: 1 residues processed: 885 average time/residue: 0.2262 time to fit residues: 299.0629 Evaluate side-chains 628 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 627 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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: 0.8980 chunk 10 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 304 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN E 12 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 150 ASN ** 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 = 0.3136 r_free = 0.3136 target = 0.052618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.033589 restraints weight = 223807.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.035152 restraints weight = 145869.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.036329 restraints weight = 105554.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.037223 restraints weight = 81758.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.037925 restraints weight = 66540.989| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 29145 Z= 0.273 Angle : 0.858 11.797 39338 Z= 0.445 Chirality : 0.049 0.306 4354 Planarity : 0.007 0.138 5094 Dihedral : 6.688 87.380 4000 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 30.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % 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: -0.08 (0.14), residues: 3569 helix: 0.47 (0.12), residues: 1789 sheet: -0.85 (0.24), residues: 434 loop : -0.29 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 116 TYR 0.042 0.003 TYR B 294 PHE 0.041 0.004 PHE E 223 TRP 0.039 0.003 TRP F 86 HIS 0.012 0.002 HIS K 91 Details of bonding type rmsd covalent geometry : bond 0.00568 (29145) covalent geometry : angle 0.85784 (39338) hydrogen bonds : bond 0.05496 ( 1632) hydrogen bonds : angle 5.13363 ( 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 789 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 788 time to evaluate : 1.183 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: A 25 ASP cc_start: 0.9263 (m-30) cc_final: 0.9037 (p0) REVERT: A 82 MET cc_start: 0.9678 (tpt) cc_final: 0.9474 (tpp) REVERT: A 92 ASN cc_start: 0.9882 (m110) cc_final: 0.9448 (m110) REVERT: A 101 HIS cc_start: 0.9271 (m90) cc_final: 0.9044 (m90) REVERT: A 188 TYR cc_start: 0.9522 (t80) cc_final: 0.9277 (t80) REVERT: A 208 ILE cc_start: 0.8987 (mt) cc_final: 0.8766 (tp) REVERT: A 269 MET cc_start: 0.6288 (ttt) cc_final: 0.5602 (ttp) REVERT: B 92 ASN cc_start: 0.9627 (m110) cc_final: 0.9338 (m110) REVERT: B 122 ILE cc_start: 0.9560 (mt) cc_final: 0.9344 (mt) REVERT: B 140 LEU cc_start: 0.9673 (mm) cc_final: 0.9471 (mm) REVERT: B 179 ASP cc_start: 0.9499 (m-30) cc_final: 0.8932 (m-30) REVERT: B 188 TYR cc_start: 0.9226 (t80) cc_final: 0.9018 (t80) REVERT: B 257 CYS cc_start: 0.9234 (t) cc_final: 0.8737 (t) REVERT: B 269 MET cc_start: 0.6333 (ttm) cc_final: 0.5980 (ttm) REVERT: B 294 TYR cc_start: 0.9370 (m-80) cc_final: 0.9169 (m-80) REVERT: C 73 HIS cc_start: 0.9105 (m90) cc_final: 0.8581 (m90) REVERT: C 132 MET cc_start: 0.9583 (tmm) cc_final: 0.9321 (tmm) REVERT: C 313 MET cc_start: 0.9525 (tpp) cc_final: 0.9321 (tpt) REVERT: C 316 GLU cc_start: 0.9730 (tp30) cc_final: 0.9525 (tm-30) REVERT: D 44 MET cc_start: 0.6746 (tpp) cc_final: 0.6308 (tpp) REVERT: D 47 MET cc_start: 0.8078 (mmp) cc_final: 0.7574 (mmp) REVERT: D 132 MET cc_start: 0.9504 (ppp) cc_final: 0.9264 (ppp) REVERT: D 165 ILE cc_start: 0.9731 (mm) cc_final: 0.9347 (tp) REVERT: D 176 MET cc_start: 0.9130 (mtm) cc_final: 0.8290 (mtp) REVERT: D 178 LEU cc_start: 0.9606 (tp) cc_final: 0.9339 (tp) REVERT: D 179 ASP cc_start: 0.9420 (m-30) cc_final: 0.9160 (m-30) REVERT: D 213 LYS cc_start: 0.9723 (pttm) cc_final: 0.9422 (pttp) REVERT: D 223 PHE cc_start: 0.8967 (t80) cc_final: 0.8570 (t80) REVERT: D 250 ILE cc_start: 0.9821 (mm) cc_final: 0.9589 (tp) REVERT: D 269 MET cc_start: 0.9173 (tpt) cc_final: 0.8777 (tpt) REVERT: D 284 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8374 (pttp) REVERT: D 355 MET cc_start: 0.9497 (mmp) cc_final: 0.9283 (mmm) REVERT: E 16 LEU cc_start: 0.9631 (mp) cc_final: 0.9376 (mp) REVERT: E 69 TYR cc_start: 0.9035 (m-10) cc_final: 0.8550 (m-10) REVERT: E 73 HIS cc_start: 0.9515 (m90) cc_final: 0.9187 (m90) REVERT: E 122 ILE cc_start: 0.9572 (mt) cc_final: 0.9269 (mt) REVERT: E 151 ILE cc_start: 0.9117 (tt) cc_final: 0.8576 (tt) REVERT: E 169 TYR cc_start: 0.9807 (m-80) cc_final: 0.9171 (m-80) REVERT: E 176 MET cc_start: 0.9206 (mmm) cc_final: 0.8702 (mtp) REVERT: E 178 LEU cc_start: 0.9144 (tp) cc_final: 0.8703 (tp) REVERT: E 179 ASP cc_start: 0.9295 (m-30) cc_final: 0.8678 (m-30) REVERT: E 183 ARG cc_start: 0.9559 (tpp80) cc_final: 0.9184 (tpp80) REVERT: E 213 LYS cc_start: 0.9690 (ptpp) cc_final: 0.9242 (ptpp) REVERT: E 375 PHE cc_start: 0.9118 (t80) cc_final: 0.8841 (t80) REVERT: F 11 ASP cc_start: 0.9747 (t0) cc_final: 0.9342 (t0) REVERT: F 82 MET cc_start: 0.9653 (ppp) cc_final: 0.9431 (ppp) REVERT: F 85 ILE cc_start: 0.9820 (mm) cc_final: 0.9562 (mm) REVERT: F 122 ILE cc_start: 0.9629 (mm) cc_final: 0.9300 (mt) REVERT: F 123 MET cc_start: 0.9859 (mmp) cc_final: 0.9608 (mmm) REVERT: F 133 TYR cc_start: 0.9235 (t80) cc_final: 0.8611 (t80) REVERT: F 167 GLU cc_start: 0.9692 (mp0) cc_final: 0.9417 (mp0) REVERT: F 178 LEU cc_start: 0.9011 (tp) cc_final: 0.8700 (tp) REVERT: F 190 MET cc_start: 0.9490 (ptp) cc_final: 0.9245 (ptp) REVERT: F 213 LYS cc_start: 0.9803 (pttm) cc_final: 0.9301 (pttm) REVERT: F 262 PHE cc_start: 0.9443 (m-10) cc_final: 0.8865 (m-10) REVERT: F 274 ILE cc_start: 0.9661 (pt) cc_final: 0.9439 (pt) REVERT: F 313 MET cc_start: 0.9642 (mmm) cc_final: 0.9404 (mmm) REVERT: F 371 HIS cc_start: 0.9121 (m-70) cc_final: 0.8700 (m90) REVERT: G 132 MET cc_start: 0.9232 (tmm) cc_final: 0.9015 (tmm) REVERT: G 178 LEU cc_start: 0.9423 (tp) cc_final: 0.9123 (tp) REVERT: I 91 PHE cc_start: 0.9458 (m-80) cc_final: 0.9060 (m-80) REVERT: J 229 LEU cc_start: 0.8604 (mp) cc_final: 0.7350 (mp) REVERT: K 102 LEU cc_start: 0.9469 (tt) cc_final: 0.9268 (tt) REVERT: M 127 MET cc_start: 0.8987 (mmm) cc_final: 0.8743 (mmm) REVERT: M 139 GLU cc_start: 0.9868 (tm-30) cc_final: 0.9515 (mt-10) REVERT: M 197 LEU cc_start: 0.9558 (tt) cc_final: 0.9226 (mt) REVERT: M 238 ARG cc_start: 0.9555 (mmp-170) cc_final: 0.9158 (tmt-80) REVERT: N 1 MET cc_start: 0.8371 (pmm) cc_final: 0.6805 (pmm) REVERT: O 1 MET cc_start: 0.8672 (pmm) cc_final: 0.8107 (pmm) outliers start: 1 outliers final: 0 residues processed: 789 average time/residue: 0.2231 time to fit residues: 264.0391 Evaluate side-chains 567 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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: 8.9990 chunk 156 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 111 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 GLN L 202 ASN L 216 GLN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.059334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.038350 restraints weight = 189269.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.039945 restraints weight = 125490.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.041117 restraints weight = 92544.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.041965 restraints weight = 73960.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.042630 restraints weight = 62114.010| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29145 Z= 0.195 Angle : 0.789 12.893 39338 Z= 0.410 Chirality : 0.048 0.314 4354 Planarity : 0.006 0.141 5094 Dihedral : 6.575 82.373 4000 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3569 helix: 0.60 (0.12), residues: 1834 sheet: -0.76 (0.25), residues: 420 loop : -0.27 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 116 TYR 0.045 0.002 TYR E 294 PHE 0.044 0.003 PHE E 223 TRP 0.066 0.003 TRP E 86 HIS 0.010 0.002 HIS J 223 Details of bonding type rmsd covalent geometry : bond 0.00423 (29145) covalent geometry : angle 0.78925 (39338) hydrogen bonds : bond 0.05305 ( 1632) hydrogen bonds : angle 5.12051 ( 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 799 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 797 time to evaluate : 1.070 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: A 119 MET cc_start: 0.9089 (ppp) cc_final: 0.8853 (ppp) REVERT: A 122 ILE cc_start: 0.9617 (mm) cc_final: 0.9334 (tt) REVERT: A 305 MET cc_start: 0.9196 (mpp) cc_final: 0.8947 (mpp) REVERT: B 176 MET cc_start: 0.9218 (mtm) cc_final: 0.8881 (mpp) REVERT: B 179 ASP cc_start: 0.9405 (m-30) cc_final: 0.9036 (m-30) REVERT: B 188 TYR cc_start: 0.9380 (t80) cc_final: 0.8794 (t80) REVERT: B 207 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9371 (mp0) REVERT: B 269 MET cc_start: 0.6706 (ttm) cc_final: 0.6320 (ttm) REVERT: C 69 TYR cc_start: 0.8701 (m-10) cc_final: 0.8485 (m-10) REVERT: C 73 HIS cc_start: 0.8717 (m90) cc_final: 0.8039 (m90) REVERT: C 132 MET cc_start: 0.9527 (tmm) cc_final: 0.9268 (tmm) REVERT: C 262 PHE cc_start: 0.9488 (m-10) cc_final: 0.8928 (m-10) REVERT: C 313 MET cc_start: 0.9504 (tpp) cc_final: 0.9013 (tpt) REVERT: C 316 GLU cc_start: 0.9640 (tp30) cc_final: 0.9372 (tm-30) REVERT: C 317 ILE cc_start: 0.9825 (mm) cc_final: 0.9392 (pt) REVERT: D 44 MET cc_start: 0.6419 (tpp) cc_final: 0.6216 (tpp) REVERT: D 47 MET cc_start: 0.8012 (mmp) cc_final: 0.7576 (mmp) REVERT: D 110 LEU cc_start: 0.9603 (mt) cc_final: 0.9164 (mt) REVERT: D 132 MET cc_start: 0.9592 (ppp) cc_final: 0.9308 (ppp) REVERT: D 165 ILE cc_start: 0.9705 (mm) cc_final: 0.9391 (tp) REVERT: D 176 MET cc_start: 0.9123 (mtm) cc_final: 0.8544 (mtp) REVERT: D 178 LEU cc_start: 0.9465 (tp) cc_final: 0.9164 (tp) REVERT: D 179 ASP cc_start: 0.9346 (m-30) cc_final: 0.9010 (m-30) REVERT: D 213 LYS cc_start: 0.9662 (pttm) cc_final: 0.9412 (pttp) REVERT: D 236 LEU cc_start: 0.8058 (mm) cc_final: 0.7790 (pp) REVERT: D 250 ILE cc_start: 0.9663 (mm) cc_final: 0.9356 (tp) REVERT: D 257 CYS cc_start: 0.9576 (t) cc_final: 0.9260 (t) REVERT: D 269 MET cc_start: 0.9134 (tpt) cc_final: 0.8840 (tpp) REVERT: D 284 LYS cc_start: 0.8531 (ptpp) cc_final: 0.8190 (pttp) REVERT: D 294 TYR cc_start: 0.9650 (m-10) cc_final: 0.9278 (m-10) REVERT: D 297 ASN cc_start: 0.9644 (t0) cc_final: 0.9175 (m110) REVERT: E 69 TYR cc_start: 0.9207 (m-10) cc_final: 0.8590 (m-10) REVERT: E 73 HIS cc_start: 0.9403 (m90) cc_final: 0.8958 (m90) REVERT: E 86 TRP cc_start: 0.9696 (m-90) cc_final: 0.9406 (m-90) REVERT: E 122 ILE cc_start: 0.9608 (mt) cc_final: 0.9324 (mt) REVERT: E 151 ILE cc_start: 0.9408 (tt) cc_final: 0.9071 (tt) REVERT: E 165 ILE cc_start: 0.9786 (mm) cc_final: 0.9450 (tp) REVERT: E 169 TYR cc_start: 0.9818 (m-80) cc_final: 0.9262 (m-80) REVERT: E 176 MET cc_start: 0.9155 (mmm) cc_final: 0.8773 (mtp) REVERT: E 179 ASP cc_start: 0.9141 (m-30) cc_final: 0.8569 (m-30) REVERT: E 190 MET cc_start: 0.9640 (ptp) cc_final: 0.9426 (ptp) REVERT: E 213 LYS cc_start: 0.9630 (ptpp) cc_final: 0.9179 (ptpp) REVERT: E 236 LEU cc_start: 0.8070 (tp) cc_final: 0.7865 (tp) REVERT: E 294 TYR cc_start: 0.9529 (m-80) cc_final: 0.9301 (m-80) REVERT: E 352 PHE cc_start: 0.9647 (t80) cc_final: 0.9402 (t80) REVERT: E 375 PHE cc_start: 0.8930 (t80) cc_final: 0.8665 (t80) REVERT: F 73 HIS cc_start: 0.9026 (m-70) cc_final: 0.8626 (m-70) REVERT: F 85 ILE cc_start: 0.9828 (mm) cc_final: 0.9589 (mm) REVERT: F 167 GLU cc_start: 0.9666 (mp0) cc_final: 0.9323 (mp0) REVERT: F 180 LEU cc_start: 0.8982 (tt) cc_final: 0.8697 (tt) REVERT: F 213 LYS cc_start: 0.9751 (pttm) cc_final: 0.9245 (ptpp) REVERT: F 255 PHE cc_start: 0.9531 (p90) cc_final: 0.7792 (p90) REVERT: F 262 PHE cc_start: 0.9464 (m-10) cc_final: 0.8886 (m-10) REVERT: G 132 MET cc_start: 0.9167 (tmm) cc_final: 0.8937 (tmm) REVERT: G 178 LEU cc_start: 0.9165 (tp) cc_final: 0.8848 (tp) REVERT: I 79 THR cc_start: 0.9833 (p) cc_final: 0.9471 (p) REVERT: I 80 ARG cc_start: 0.9608 (tpm170) cc_final: 0.9306 (mtm180) REVERT: I 91 PHE cc_start: 0.9493 (m-80) cc_final: 0.9192 (m-80) REVERT: J 229 LEU cc_start: 0.8405 (mp) cc_final: 0.7175 (mp) REVERT: J 232 LYS cc_start: 0.8824 (ptpp) cc_final: 0.8561 (pttm) REVERT: J 237 TRP cc_start: 0.8761 (t60) cc_final: 0.8494 (t60) REVERT: K 148 ARG cc_start: 0.9517 (pmt-80) cc_final: 0.9236 (pmt-80) REVERT: K 152 LEU cc_start: 0.9363 (mt) cc_final: 0.9056 (mt) REVERT: L 228 LEU cc_start: 0.9574 (tt) cc_final: 0.9308 (tp) REVERT: M 139 GLU cc_start: 0.9841 (tm-30) cc_final: 0.9557 (mt-10) REVERT: M 197 LEU cc_start: 0.9515 (tt) cc_final: 0.9163 (mt) REVERT: M 228 LEU cc_start: 0.9613 (mt) cc_final: 0.9386 (tp) REVERT: M 232 LEU cc_start: 0.9230 (mm) cc_final: 0.8878 (mm) REVERT: M 238 ARG cc_start: 0.9559 (mmp-170) cc_final: 0.9124 (tpt90) REVERT: M 241 PHE cc_start: 0.9586 (m-80) cc_final: 0.9362 (m-80) REVERT: N 1 MET cc_start: 0.8632 (pmm) cc_final: 0.7192 (pmm) REVERT: O 46 LEU cc_start: 0.9381 (tp) cc_final: 0.9101 (tp) outliers start: 2 outliers final: 0 residues processed: 799 average time/residue: 0.2253 time to fit residues: 270.2560 Evaluate side-chains 567 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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: 7.9990 chunk 62 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 268 optimal weight: 0.7980 chunk 275 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** 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 137 GLN E 92 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.032768 restraints weight = 228692.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.034302 restraints weight = 147806.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.035466 restraints weight = 106512.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.036371 restraints weight = 82202.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.037020 restraints weight = 66647.424| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29145 Z= 0.217 Angle : 0.827 12.552 39338 Z= 0.431 Chirality : 0.049 0.314 4354 Planarity : 0.006 0.149 5094 Dihedral : 6.631 81.905 4000 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.66 % 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: 0.40 (0.12), residues: 1790 sheet: -0.77 (0.25), residues: 420 loop : -0.28 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 102 TYR 0.042 0.002 TYR B 294 PHE 0.048 0.003 PHE B 223 TRP 0.056 0.003 TRP D 86 HIS 0.011 0.002 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00462 (29145) covalent geometry : angle 0.82690 (39338) hydrogen bonds : bond 0.05390 ( 1632) hydrogen bonds : angle 5.26081 ( 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 782 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 780 time to evaluate : 1.109 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: A 82 MET cc_start: 0.9705 (tpt) cc_final: 0.9468 (tpp) REVERT: A 119 MET cc_start: 0.9115 (ppp) cc_final: 0.8839 (ppp) REVERT: A 122 ILE cc_start: 0.9703 (mm) cc_final: 0.9433 (tt) REVERT: A 132 MET cc_start: 0.9060 (ptp) cc_final: 0.8511 (mpp) REVERT: A 325 MET cc_start: 0.4508 (tpt) cc_final: 0.4290 (tpt) REVERT: B 73 HIS cc_start: 0.9098 (m-70) cc_final: 0.8891 (m90) REVERT: B 104 LEU cc_start: 0.9801 (mm) cc_final: 0.9426 (pp) REVERT: B 176 MET cc_start: 0.9146 (mtm) cc_final: 0.8706 (mpp) REVERT: B 179 ASP cc_start: 0.9415 (m-30) cc_final: 0.8858 (m-30) REVERT: B 188 TYR cc_start: 0.9315 (t80) cc_final: 0.8874 (t80) REVERT: B 207 GLU cc_start: 0.9595 (mm-30) cc_final: 0.9387 (mp0) REVERT: B 269 MET cc_start: 0.6649 (ttm) cc_final: 0.6329 (ttm) REVERT: B 275 HIS cc_start: 0.9258 (p-80) cc_final: 0.9039 (p-80) REVERT: B 294 TYR cc_start: 0.9347 (m-80) cc_final: 0.9126 (m-80) REVERT: B 375 PHE cc_start: 0.9426 (t80) cc_final: 0.9225 (t80) REVERT: C 31 PHE cc_start: 0.9350 (p90) cc_final: 0.9025 (p90) REVERT: C 73 HIS cc_start: 0.8798 (m90) cc_final: 0.8169 (m90) REVERT: C 107 GLU cc_start: 0.8916 (tt0) cc_final: 0.8669 (pm20) REVERT: C 119 MET cc_start: 0.9794 (ptp) cc_final: 0.9577 (mmt) REVERT: C 122 ILE cc_start: 0.9746 (pt) cc_final: 0.9528 (pt) REVERT: C 132 MET cc_start: 0.9499 (tmm) cc_final: 0.9129 (tmm) REVERT: C 262 PHE cc_start: 0.9507 (m-10) cc_final: 0.8753 (m-10) REVERT: C 267 ILE cc_start: 0.9645 (pt) cc_final: 0.9427 (pt) REVERT: C 297 ASN cc_start: 0.9678 (t0) cc_final: 0.9266 (m110) REVERT: C 313 MET cc_start: 0.9500 (tpp) cc_final: 0.9068 (tpt) REVERT: C 316 GLU cc_start: 0.9722 (tp30) cc_final: 0.9366 (tm-30) REVERT: D 12 ASN cc_start: 0.9697 (m110) cc_final: 0.9307 (p0) REVERT: D 47 MET cc_start: 0.8347 (mmp) cc_final: 0.7932 (mmm) REVERT: D 165 ILE cc_start: 0.9722 (mm) cc_final: 0.9415 (tp) REVERT: D 176 MET cc_start: 0.9302 (mtm) cc_final: 0.8493 (mtp) REVERT: D 178 LEU cc_start: 0.9515 (tp) cc_final: 0.9227 (tp) REVERT: D 179 ASP cc_start: 0.8932 (m-30) cc_final: 0.8469 (m-30) REVERT: D 213 LYS cc_start: 0.9720 (pttm) cc_final: 0.9485 (pttp) REVERT: D 223 PHE cc_start: 0.9237 (t80) cc_final: 0.8861 (t80) REVERT: D 236 LEU cc_start: 0.8790 (mm) cc_final: 0.8514 (pp) REVERT: D 250 ILE cc_start: 0.9756 (mm) cc_final: 0.9521 (tp) REVERT: D 257 CYS cc_start: 0.9670 (t) cc_final: 0.9437 (t) REVERT: D 269 MET cc_start: 0.9150 (tpt) cc_final: 0.8836 (tpp) REVERT: D 274 ILE cc_start: 0.9717 (pt) cc_final: 0.9488 (pt) REVERT: D 284 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8289 (pttm) REVERT: D 297 ASN cc_start: 0.9644 (t0) cc_final: 0.9185 (m110) REVERT: D 355 MET cc_start: 0.9566 (mmp) cc_final: 0.9309 (mmm) REVERT: E 53 TYR cc_start: 0.8739 (m-10) cc_final: 0.8333 (m-80) REVERT: E 69 TYR cc_start: 0.8944 (m-10) cc_final: 0.8647 (m-10) REVERT: E 73 HIS cc_start: 0.9278 (m90) cc_final: 0.8829 (m-70) REVERT: E 86 TRP cc_start: 0.9743 (m-90) cc_final: 0.9342 (m-90) REVERT: E 122 ILE cc_start: 0.9668 (mt) cc_final: 0.9328 (mt) REVERT: E 151 ILE cc_start: 0.9518 (tt) cc_final: 0.9263 (tt) REVERT: E 165 ILE cc_start: 0.9806 (mm) cc_final: 0.9521 (tp) REVERT: E 169 TYR cc_start: 0.9744 (m-80) cc_final: 0.9241 (m-80) REVERT: E 178 LEU cc_start: 0.9235 (tp) cc_final: 0.8797 (tp) REVERT: E 179 ASP cc_start: 0.9306 (m-30) cc_final: 0.8565 (m-30) REVERT: E 190 MET cc_start: 0.9707 (ptp) cc_final: 0.9480 (ptp) REVERT: E 206 ARG cc_start: 0.9531 (mpp-170) cc_final: 0.9257 (ptp-170) REVERT: E 213 LYS cc_start: 0.9693 (ptpp) cc_final: 0.9383 (ptpp) REVERT: E 274 ILE cc_start: 0.9659 (pt) cc_final: 0.9459 (pt) REVERT: E 294 TYR cc_start: 0.9594 (m-80) cc_final: 0.9352 (m-80) REVERT: E 334 GLU cc_start: 0.9474 (pm20) cc_final: 0.8979 (tm-30) REVERT: E 352 PHE cc_start: 0.9722 (t80) cc_final: 0.9492 (t80) REVERT: E 375 PHE cc_start: 0.9023 (t80) cc_final: 0.8704 (t80) REVERT: F 73 HIS cc_start: 0.9130 (m-70) cc_final: 0.8798 (m170) REVERT: F 85 ILE cc_start: 0.9853 (mm) cc_final: 0.9582 (mm) REVERT: F 190 MET cc_start: 0.9617 (ptp) cc_final: 0.9412 (ptp) REVERT: F 213 LYS cc_start: 0.9808 (pttm) cc_final: 0.9367 (ptpp) REVERT: F 262 PHE cc_start: 0.9578 (m-10) cc_final: 0.9202 (m-80) REVERT: F 269 MET cc_start: 0.9124 (ttm) cc_final: 0.8883 (ttm) REVERT: F 305 MET cc_start: 0.9447 (tpp) cc_final: 0.9227 (tpp) REVERT: G 132 MET cc_start: 0.9189 (tmm) cc_final: 0.8718 (tmm) REVERT: G 180 LEU cc_start: 0.9548 (tp) cc_final: 0.9007 (tp) REVERT: G 269 MET cc_start: 0.8792 (ttt) cc_final: 0.8079 (ttt) REVERT: I 79 THR cc_start: 0.9837 (p) cc_final: 0.9283 (p) REVERT: I 80 ARG cc_start: 0.9596 (tpm170) cc_final: 0.9281 (mtm180) REVERT: I 91 PHE cc_start: 0.9634 (m-80) cc_final: 0.9324 (m-80) REVERT: I 139 LYS cc_start: 0.7957 (mppt) cc_final: 0.6429 (tptt) REVERT: J 224 LEU cc_start: 0.9300 (mm) cc_final: 0.9083 (mm) REVERT: J 229 LEU cc_start: 0.8554 (mp) cc_final: 0.8253 (mt) REVERT: J 231 GLU cc_start: 0.9533 (pp20) cc_final: 0.9167 (pp20) REVERT: L 141 MET cc_start: 0.8660 (mpp) cc_final: 0.8299 (mpp) REVERT: M 139 GLU cc_start: 0.9884 (tm-30) cc_final: 0.9566 (mt-10) REVERT: M 197 LEU cc_start: 0.9644 (tt) cc_final: 0.9341 (mt) REVERT: N 1 MET cc_start: 0.8294 (pmm) cc_final: 0.6986 (ppp) REVERT: O 46 LEU cc_start: 0.9556 (tp) cc_final: 0.9313 (tp) outliers start: 2 outliers final: 0 residues processed: 781 average time/residue: 0.2180 time to fit residues: 257.6170 Evaluate side-chains 562 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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: 4.9990 chunk 157 optimal weight: 7.9990 chunk 260 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 247 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** 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 353 GLN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 ASN ** 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 = 0.3088 r_free = 0.3088 target = 0.050568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.032053 restraints weight = 230078.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.033548 restraints weight = 148534.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.034676 restraints weight = 107071.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035546 restraints weight = 82694.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.036202 restraints weight = 67105.535| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.8313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 29145 Z= 0.218 Angle : 0.831 12.561 39338 Z= 0.436 Chirality : 0.049 0.345 4354 Planarity : 0.006 0.141 5094 Dihedral : 6.659 80.399 4000 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 0.45 (0.12), residues: 1833 sheet: -0.85 (0.25), residues: 420 loop : -0.36 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 116 TYR 0.036 0.002 TYR B 294 PHE 0.051 0.003 PHE B 223 TRP 0.062 0.003 TRP D 86 HIS 0.013 0.002 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00470 (29145) covalent geometry : angle 0.83120 (39338) hydrogen bonds : bond 0.05378 ( 1632) hydrogen bonds : angle 5.41926 ( 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 771 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 771 time to evaluate : 1.177 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: A 82 MET cc_start: 0.9716 (tpt) cc_final: 0.9477 (tpp) REVERT: A 122 ILE cc_start: 0.9718 (mm) cc_final: 0.9470 (tt) REVERT: B 73 HIS cc_start: 0.9173 (m-70) cc_final: 0.8937 (m90) REVERT: B 104 LEU cc_start: 0.9804 (mm) cc_final: 0.9431 (pp) REVERT: B 120 THR cc_start: 0.9746 (t) cc_final: 0.9476 (p) REVERT: B 176 MET cc_start: 0.9099 (mtm) cc_final: 0.8735 (mpp) REVERT: B 179 ASP cc_start: 0.9378 (m-30) cc_final: 0.8806 (m-30) REVERT: B 188 TYR cc_start: 0.9430 (t80) cc_final: 0.8795 (t80) REVERT: B 207 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9371 (mp0) REVERT: B 269 MET cc_start: 0.6718 (ttm) cc_final: 0.6438 (ttm) REVERT: C 21 PHE cc_start: 0.9210 (m-80) cc_final: 0.8772 (m-80) REVERT: C 73 HIS cc_start: 0.8735 (m90) cc_final: 0.8054 (m90) REVERT: C 107 GLU cc_start: 0.8666 (tt0) cc_final: 0.8454 (pm20) REVERT: C 122 ILE cc_start: 0.9740 (pt) cc_final: 0.9525 (pt) REVERT: C 132 MET cc_start: 0.9482 (tmm) cc_final: 0.9136 (tmm) REVERT: C 262 PHE cc_start: 0.9531 (m-10) cc_final: 0.8784 (m-10) REVERT: C 297 ASN cc_start: 0.9687 (t0) cc_final: 0.9260 (m110) REVERT: C 313 MET cc_start: 0.9495 (tpp) cc_final: 0.9062 (tpt) REVERT: C 316 GLU cc_start: 0.9746 (tp30) cc_final: 0.9538 (tm-30) REVERT: C 317 ILE cc_start: 0.9838 (mm) cc_final: 0.9473 (pt) REVERT: D 12 ASN cc_start: 0.9688 (m110) cc_final: 0.9209 (p0) REVERT: D 47 MET cc_start: 0.8500 (mmp) cc_final: 0.8014 (mmp) REVERT: D 85 ILE cc_start: 0.9894 (mm) cc_final: 0.9615 (mt) REVERT: D 104 LEU cc_start: 0.9331 (mm) cc_final: 0.9041 (mm) REVERT: D 132 MET cc_start: 0.9462 (ppp) cc_final: 0.9217 (ppp) REVERT: D 165 ILE cc_start: 0.9732 (mm) cc_final: 0.9426 (tp) REVERT: D 176 MET cc_start: 0.9329 (mtm) cc_final: 0.8805 (mtp) REVERT: D 178 LEU cc_start: 0.9524 (tp) cc_final: 0.9222 (tp) REVERT: D 179 ASP cc_start: 0.9023 (m-30) cc_final: 0.8611 (m-30) REVERT: D 223 PHE cc_start: 0.9266 (t80) cc_final: 0.9024 (t80) REVERT: D 236 LEU cc_start: 0.8716 (mm) cc_final: 0.8205 (pp) REVERT: D 250 ILE cc_start: 0.9752 (mm) cc_final: 0.9463 (tp) REVERT: D 257 CYS cc_start: 0.9637 (t) cc_final: 0.9427 (t) REVERT: D 269 MET cc_start: 0.9218 (tpt) cc_final: 0.8928 (tpp) REVERT: D 274 ILE cc_start: 0.9592 (pt) cc_final: 0.9323 (pt) REVERT: D 297 ASN cc_start: 0.9598 (t0) cc_final: 0.9155 (m110) REVERT: D 355 MET cc_start: 0.9629 (mmp) cc_final: 0.9339 (mmm) REVERT: D 356 TRP cc_start: 0.7008 (m-90) cc_final: 0.6103 (t-100) REVERT: E 16 LEU cc_start: 0.9656 (mp) cc_final: 0.9404 (mp) REVERT: E 69 TYR cc_start: 0.8997 (m-10) cc_final: 0.8680 (m-10) REVERT: E 73 HIS cc_start: 0.9136 (m90) cc_final: 0.8924 (m-70) REVERT: E 86 TRP cc_start: 0.9704 (m-90) cc_final: 0.9339 (m-10) REVERT: E 107 GLU cc_start: 0.9243 (tt0) cc_final: 0.8913 (pm20) REVERT: E 122 ILE cc_start: 0.9669 (mt) cc_final: 0.9340 (mt) REVERT: E 151 ILE cc_start: 0.9464 (tt) cc_final: 0.9224 (tt) REVERT: E 165 ILE cc_start: 0.9795 (mm) cc_final: 0.9538 (tp) REVERT: E 169 TYR cc_start: 0.9725 (m-80) cc_final: 0.9215 (m-80) REVERT: E 178 LEU cc_start: 0.9196 (tp) cc_final: 0.8808 (tp) REVERT: E 179 ASP cc_start: 0.9265 (m-30) cc_final: 0.8746 (m-30) REVERT: E 190 MET cc_start: 0.9714 (ptp) cc_final: 0.9454 (ptp) REVERT: E 213 LYS cc_start: 0.9657 (ptpp) cc_final: 0.9281 (ptpp) REVERT: E 248 ILE cc_start: 0.9854 (pt) cc_final: 0.9603 (pt) REVERT: E 294 TYR cc_start: 0.9607 (m-80) cc_final: 0.9349 (m-80) REVERT: E 352 PHE cc_start: 0.9739 (t80) cc_final: 0.9510 (t80) REVERT: E 375 PHE cc_start: 0.8945 (t80) cc_final: 0.8486 (t80) REVERT: F 73 HIS cc_start: 0.9077 (m-70) cc_final: 0.8783 (m-70) REVERT: F 82 MET cc_start: 0.9659 (ppp) cc_final: 0.9441 (ppp) REVERT: F 86 TRP cc_start: 0.9786 (m-90) cc_final: 0.9578 (m-90) REVERT: F 122 ILE cc_start: 0.9650 (mm) cc_final: 0.9365 (mm) REVERT: F 123 MET cc_start: 0.9834 (mmp) cc_final: 0.9580 (mmm) REVERT: F 178 LEU cc_start: 0.9195 (tp) cc_final: 0.8902 (tp) REVERT: F 190 MET cc_start: 0.9625 (ptp) cc_final: 0.9422 (ptp) REVERT: F 213 LYS cc_start: 0.9781 (pttm) cc_final: 0.9395 (ptpp) REVERT: F 255 PHE cc_start: 0.9558 (p90) cc_final: 0.8241 (p90) REVERT: F 262 PHE cc_start: 0.9567 (m-10) cc_final: 0.9290 (m-80) REVERT: F 274 ILE cc_start: 0.9703 (pt) cc_final: 0.9352 (pt) REVERT: F 297 ASN cc_start: 0.9753 (t0) cc_final: 0.9469 (p0) REVERT: F 305 MET cc_start: 0.9380 (tpp) cc_final: 0.9165 (tpp) REVERT: G 269 MET cc_start: 0.8680 (ttt) cc_final: 0.8382 (ttm) REVERT: I 79 THR cc_start: 0.9780 (p) cc_final: 0.9540 (p) REVERT: I 80 ARG cc_start: 0.9675 (tpm170) cc_final: 0.9389 (mtm180) REVERT: I 91 PHE cc_start: 0.9763 (m-80) cc_final: 0.9517 (m-80) REVERT: I 139 LYS cc_start: 0.7882 (mppt) cc_final: 0.6385 (tptt) REVERT: I 163 ARG cc_start: 0.9150 (mtm-85) cc_final: 0.8787 (ptt90) REVERT: J 224 LEU cc_start: 0.9476 (mm) cc_final: 0.9094 (mm) REVERT: J 229 LEU cc_start: 0.8671 (mp) cc_final: 0.7765 (mp) REVERT: K 152 LEU cc_start: 0.8992 (mt) cc_final: 0.8781 (mt) REVERT: L 141 MET cc_start: 0.8586 (mpp) cc_final: 0.8231 (mpp) REVERT: M 172 ILE cc_start: 0.9295 (mm) cc_final: 0.8959 (tt) REVERT: M 197 LEU cc_start: 0.9635 (tt) cc_final: 0.9323 (mt) REVERT: M 238 ARG cc_start: 0.9642 (mmp-170) cc_final: 0.9191 (tpt90) REVERT: N 1 MET cc_start: 0.8473 (pmm) cc_final: 0.6853 (ppp) REVERT: O 1 MET cc_start: 0.9156 (pmm) cc_final: 0.8611 (pmm) REVERT: O 46 LEU cc_start: 0.9558 (tp) cc_final: 0.9307 (tp) outliers start: 0 outliers final: 0 residues processed: 771 average time/residue: 0.2204 time to fit residues: 256.4172 Evaluate side-chains 556 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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: 0.5980 chunk 278 optimal weight: 2.9990 chunk 337 optimal weight: 0.9980 chunk 150 optimal weight: 0.0870 chunk 240 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 208 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.043733 restraints weight = 224537.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.045352 restraints weight = 142699.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.046561 restraints weight = 101753.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.047484 restraints weight = 78093.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.048232 restraints weight = 62726.245| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.8341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29145 Z= 0.165 Angle : 0.824 12.072 39338 Z= 0.433 Chirality : 0.050 0.349 4354 Planarity : 0.005 0.123 5094 Dihedral : 6.572 81.598 4000 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.03 % Allowed : 0.88 % Favored : 99.09 % 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: 0.03 (0.14), residues: 3569 helix: 0.49 (0.12), residues: 1831 sheet: -0.67 (0.25), residues: 420 loop : -0.21 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 116 TYR 0.047 0.002 TYR B 294 PHE 0.053 0.003 PHE B 223 TRP 0.070 0.003 TRP D 86 HIS 0.010 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00353 (29145) covalent geometry : angle 0.82398 (39338) hydrogen bonds : bond 0.05327 ( 1632) hydrogen bonds : angle 5.38080 ( 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 812 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 811 time to evaluate : 1.173 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: A 119 MET cc_start: 0.9072 (ppp) cc_final: 0.8780 (ppp) REVERT: A 122 ILE cc_start: 0.9660 (mm) cc_final: 0.9398 (tt) REVERT: A 132 MET cc_start: 0.8968 (mtm) cc_final: 0.8368 (mpp) REVERT: A 269 MET cc_start: 0.6898 (ttt) cc_final: 0.6287 (ttt) REVERT: B 73 HIS cc_start: 0.9009 (m-70) cc_final: 0.8796 (m90) REVERT: B 104 LEU cc_start: 0.9797 (mm) cc_final: 0.9425 (pp) REVERT: B 176 MET cc_start: 0.9180 (mtm) cc_final: 0.8760 (mpp) REVERT: B 179 ASP cc_start: 0.9358 (m-30) cc_final: 0.8875 (m-30) REVERT: B 188 TYR cc_start: 0.9248 (t80) cc_final: 0.8739 (t80) REVERT: B 207 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9352 (mp0) REVERT: B 269 MET cc_start: 0.7192 (ttm) cc_final: 0.6938 (ttm) REVERT: C 21 PHE cc_start: 0.9044 (m-80) cc_final: 0.8592 (m-80) REVERT: C 73 HIS cc_start: 0.8723 (m90) cc_final: 0.8089 (m90) REVERT: C 107 GLU cc_start: 0.8979 (tt0) cc_final: 0.8143 (pm20) REVERT: C 115 ASN cc_start: 0.9592 (m-40) cc_final: 0.9367 (t0) REVERT: C 132 MET cc_start: 0.9455 (tmm) cc_final: 0.8908 (tmm) REVERT: C 262 PHE cc_start: 0.9514 (m-10) cc_final: 0.9109 (m-10) REVERT: C 269 MET cc_start: 0.9354 (mpp) cc_final: 0.9084 (mpp) REVERT: C 297 ASN cc_start: 0.9685 (t0) cc_final: 0.9266 (m110) REVERT: C 313 MET cc_start: 0.9536 (tpp) cc_final: 0.8851 (tpp) REVERT: C 316 GLU cc_start: 0.9670 (tp30) cc_final: 0.9381 (tm-30) REVERT: C 317 ILE cc_start: 0.9862 (mm) cc_final: 0.9344 (pt) REVERT: D 12 ASN cc_start: 0.9781 (m110) cc_final: 0.9261 (p0) REVERT: D 47 MET cc_start: 0.8325 (mmp) cc_final: 0.7890 (mmp) REVERT: D 85 ILE cc_start: 0.9914 (mm) cc_final: 0.9707 (mt) REVERT: D 115 ASN cc_start: 0.9570 (m110) cc_final: 0.9309 (m110) REVERT: D 132 MET cc_start: 0.9541 (ppp) cc_final: 0.9336 (ppp) REVERT: D 165 ILE cc_start: 0.9733 (mm) cc_final: 0.9433 (tp) REVERT: D 176 MET cc_start: 0.9279 (mtm) cc_final: 0.8448 (mtp) REVERT: D 178 LEU cc_start: 0.9289 (tp) cc_final: 0.8906 (tp) REVERT: D 179 ASP cc_start: 0.9012 (m-30) cc_final: 0.8605 (m-30) REVERT: D 183 ARG cc_start: 0.9492 (ttm170) cc_final: 0.9076 (mtm-85) REVERT: D 223 PHE cc_start: 0.9220 (t80) cc_final: 0.8995 (t80) REVERT: D 236 LEU cc_start: 0.8325 (mm) cc_final: 0.7869 (pp) REVERT: D 250 ILE cc_start: 0.9751 (mm) cc_final: 0.9460 (tp) REVERT: D 257 CYS cc_start: 0.9575 (t) cc_final: 0.9292 (t) REVERT: D 269 MET cc_start: 0.9127 (tpt) cc_final: 0.8873 (tpp) REVERT: D 274 ILE cc_start: 0.9574 (pt) cc_final: 0.9303 (pt) REVERT: D 284 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8201 (pttp) REVERT: D 297 ASN cc_start: 0.9599 (t0) cc_final: 0.9211 (m110) REVERT: D 355 MET cc_start: 0.9511 (mmp) cc_final: 0.9243 (mmm) REVERT: D 356 TRP cc_start: 0.6456 (m-90) cc_final: 0.5769 (t-100) REVERT: E 69 TYR cc_start: 0.8970 (m-10) cc_final: 0.8627 (m-10) REVERT: E 73 HIS cc_start: 0.9032 (m90) cc_final: 0.8496 (m-70) REVERT: E 86 TRP cc_start: 0.9689 (m-90) cc_final: 0.9305 (m-90) REVERT: E 122 ILE cc_start: 0.9626 (mt) cc_final: 0.9310 (pt) REVERT: E 151 ILE cc_start: 0.9463 (tt) cc_final: 0.9169 (tt) REVERT: E 165 ILE cc_start: 0.9761 (mm) cc_final: 0.9432 (tp) REVERT: E 169 TYR cc_start: 0.9782 (m-80) cc_final: 0.9211 (m-80) REVERT: E 179 ASP cc_start: 0.9154 (m-30) cc_final: 0.8427 (m-30) REVERT: E 190 MET cc_start: 0.9667 (ptp) cc_final: 0.9312 (ptp) REVERT: E 213 LYS cc_start: 0.9661 (ptpp) cc_final: 0.9254 (ptpp) REVERT: E 294 TYR cc_start: 0.9489 (m-80) cc_final: 0.9221 (m-80) REVERT: E 334 GLU cc_start: 0.9447 (pm20) cc_final: 0.8922 (tm-30) REVERT: E 352 PHE cc_start: 0.9695 (t80) cc_final: 0.9456 (t80) REVERT: E 375 PHE cc_start: 0.8837 (t80) cc_final: 0.8526 (t80) REVERT: F 11 ASP cc_start: 0.9408 (t70) cc_final: 0.8815 (t0) REVERT: F 18 LYS cc_start: 0.9469 (mppt) cc_final: 0.9204 (mppt) REVERT: F 73 HIS cc_start: 0.9027 (m-70) cc_final: 0.8687 (m-70) REVERT: F 82 MET cc_start: 0.9684 (ppp) cc_final: 0.9301 (ppp) REVERT: F 122 ILE cc_start: 0.9576 (mm) cc_final: 0.9312 (mm) REVERT: F 123 MET cc_start: 0.9841 (mmp) cc_final: 0.9625 (mmm) REVERT: F 178 LEU cc_start: 0.9055 (tp) cc_final: 0.8790 (tp) REVERT: F 190 MET cc_start: 0.9642 (ptp) cc_final: 0.9368 (ptp) REVERT: F 213 LYS cc_start: 0.9836 (pttm) cc_final: 0.9572 (ptpp) REVERT: F 255 PHE cc_start: 0.9542 (p90) cc_final: 0.8191 (p90) REVERT: F 262 PHE cc_start: 0.9463 (m-10) cc_final: 0.9137 (m-80) REVERT: F 269 MET cc_start: 0.8937 (ttt) cc_final: 0.8518 (tmm) REVERT: F 297 ASN cc_start: 0.9724 (t0) cc_final: 0.9440 (p0) REVERT: G 269 MET cc_start: 0.8772 (ttt) cc_final: 0.8424 (ttm) REVERT: H 103 MET cc_start: 0.7293 (mpp) cc_final: 0.6998 (mpp) REVERT: H 156 PHE cc_start: 0.7877 (p90) cc_final: 0.7601 (p90) REVERT: I 62 MET cc_start: 0.9431 (tpp) cc_final: 0.9218 (tpt) REVERT: I 79 THR cc_start: 0.9879 (p) cc_final: 0.9439 (p) REVERT: I 80 ARG cc_start: 0.9696 (tpm170) cc_final: 0.9412 (mtm180) REVERT: I 91 PHE cc_start: 0.9746 (m-80) cc_final: 0.9511 (m-80) REVERT: I 139 LYS cc_start: 0.7922 (mppt) cc_final: 0.6499 (tptt) REVERT: I 163 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8703 (ptt90) REVERT: J 224 LEU cc_start: 0.9211 (mm) cc_final: 0.8965 (mm) REVERT: J 229 LEU cc_start: 0.8255 (mp) cc_final: 0.7703 (mp) REVERT: M 139 GLU cc_start: 0.9901 (tm-30) cc_final: 0.9686 (mt-10) REVERT: M 172 ILE cc_start: 0.9177 (mm) cc_final: 0.8831 (tt) REVERT: M 197 LEU cc_start: 0.9545 (tt) cc_final: 0.9233 (mt) REVERT: N 1 MET cc_start: 0.8697 (pmm) cc_final: 0.7466 (ppp) REVERT: O 46 LEU cc_start: 0.9538 (tp) cc_final: 0.9291 (tp) outliers start: 1 outliers final: 0 residues processed: 812 average time/residue: 0.2220 time to fit residues: 271.6502 Evaluate side-chains 604 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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: 6.9990 chunk 308 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.0070 chunk 339 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 184 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 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 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 GLN ** 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 202 ASN ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033340 restraints weight = 227310.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.034900 restraints weight = 145867.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036076 restraints weight = 104562.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.036948 restraints weight = 80369.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.037666 restraints weight = 64965.224| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.8554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 29145 Z= 0.184 Angle : 0.832 13.107 39338 Z= 0.440 Chirality : 0.051 0.411 4354 Planarity : 0.006 0.081 5094 Dihedral : 6.607 88.078 4000 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.07 (0.14), residues: 3569 helix: 0.33 (0.12), residues: 1822 sheet: -0.67 (0.25), residues: 420 loop : -0.14 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 116 TYR 0.044 0.002 TYR B 294 PHE 0.051 0.003 PHE B 223 TRP 0.063 0.003 TRP D 86 HIS 0.007 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00402 (29145) covalent geometry : angle 0.83231 (39338) hydrogen bonds : bond 0.05344 ( 1632) hydrogen bonds : angle 5.47852 ( 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 781 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 781 time to evaluate : 1.174 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 82 MET cc_start: 0.9714 (tpt) cc_final: 0.9504 (tpp) REVERT: A 119 MET cc_start: 0.9094 (ppp) cc_final: 0.8791 (ppp) REVERT: A 132 MET cc_start: 0.9039 (mtm) cc_final: 0.8483 (mpp) REVERT: B 73 HIS cc_start: 0.9092 (m-70) cc_final: 0.8862 (m90) REVERT: B 179 ASP cc_start: 0.9391 (m-30) cc_final: 0.8877 (m-30) REVERT: B 188 TYR cc_start: 0.9395 (t80) cc_final: 0.8943 (t80) REVERT: B 207 GLU cc_start: 0.9566 (mm-30) cc_final: 0.9364 (mp0) REVERT: B 269 MET cc_start: 0.6850 (ttm) cc_final: 0.6591 (ttm) REVERT: B 275 HIS cc_start: 0.9449 (p-80) cc_final: 0.9102 (p-80) REVERT: B 294 TYR cc_start: 0.9252 (m-80) cc_final: 0.9050 (m-80) REVERT: C 21 PHE cc_start: 0.9071 (m-80) cc_final: 0.8562 (m-80) REVERT: C 73 HIS cc_start: 0.8781 (m90) cc_final: 0.8185 (m90) REVERT: C 107 GLU cc_start: 0.8586 (tt0) cc_final: 0.8289 (pm20) REVERT: C 115 ASN cc_start: 0.9676 (m-40) cc_final: 0.8972 (t0) REVERT: C 119 MET cc_start: 0.9798 (ptp) cc_final: 0.9458 (mmp) REVERT: C 122 ILE cc_start: 0.9715 (pt) cc_final: 0.9451 (pt) REVERT: C 132 MET cc_start: 0.9382 (tmm) cc_final: 0.8952 (tmm) REVERT: C 262 PHE cc_start: 0.9538 (m-10) cc_final: 0.8860 (m-10) REVERT: C 269 MET cc_start: 0.9337 (mpp) cc_final: 0.9061 (mpp) REVERT: C 297 ASN cc_start: 0.9673 (t0) cc_final: 0.9288 (m110) REVERT: C 313 MET cc_start: 0.9481 (tpp) cc_final: 0.9044 (tpt) REVERT: C 316 GLU cc_start: 0.9723 (tp30) cc_final: 0.9432 (tm-30) REVERT: C 352 PHE cc_start: 0.9808 (t80) cc_final: 0.9605 (t80) REVERT: C 356 TRP cc_start: 0.8181 (m100) cc_final: 0.7326 (m100) REVERT: D 12 ASN cc_start: 0.9757 (m110) cc_final: 0.9266 (p0) REVERT: D 16 LEU cc_start: 0.9703 (mt) cc_final: 0.9397 (mt) REVERT: D 85 ILE cc_start: 0.9911 (mm) cc_final: 0.9704 (mt) REVERT: D 165 ILE cc_start: 0.9743 (mm) cc_final: 0.9418 (tp) REVERT: D 176 MET cc_start: 0.9321 (mtm) cc_final: 0.8482 (mtp) REVERT: D 178 LEU cc_start: 0.9381 (tp) cc_final: 0.9058 (tp) REVERT: D 179 ASP cc_start: 0.9043 (m-30) cc_final: 0.8649 (m-30) REVERT: D 183 ARG cc_start: 0.9513 (ttm170) cc_final: 0.9079 (mtm-85) REVERT: D 191 LYS cc_start: 0.9750 (pttp) cc_final: 0.9526 (pttp) REVERT: D 223 PHE cc_start: 0.9313 (t80) cc_final: 0.9105 (t80) REVERT: D 225 ASN cc_start: 0.9549 (m-40) cc_final: 0.9303 (m-40) REVERT: D 250 ILE cc_start: 0.9719 (mm) cc_final: 0.9464 (tp) REVERT: D 269 MET cc_start: 0.9088 (tpt) cc_final: 0.8868 (tpp) REVERT: D 274 ILE cc_start: 0.9607 (pt) cc_final: 0.9357 (pt) REVERT: D 284 LYS cc_start: 0.8624 (ptpp) cc_final: 0.8240 (pttp) REVERT: D 297 ASN cc_start: 0.9582 (t0) cc_final: 0.9242 (m110) REVERT: D 355 MET cc_start: 0.9533 (mmp) cc_final: 0.9228 (mmm) REVERT: D 356 TRP cc_start: 0.6610 (m-90) cc_final: 0.5907 (t-100) REVERT: E 69 TYR cc_start: 0.9028 (m-10) cc_final: 0.8703 (m-10) REVERT: E 73 HIS cc_start: 0.9055 (m90) cc_final: 0.8521 (m-70) REVERT: E 86 TRP cc_start: 0.9688 (m-90) cc_final: 0.9268 (m-90) REVERT: E 122 ILE cc_start: 0.9675 (mt) cc_final: 0.9364 (pt) REVERT: E 151 ILE cc_start: 0.9438 (tt) cc_final: 0.9179 (tt) REVERT: E 165 ILE cc_start: 0.9783 (mm) cc_final: 0.9483 (tp) REVERT: E 169 TYR cc_start: 0.9759 (m-80) cc_final: 0.9302 (m-80) REVERT: E 178 LEU cc_start: 0.9120 (tp) cc_final: 0.8587 (tp) REVERT: E 179 ASP cc_start: 0.9204 (m-30) cc_final: 0.8411 (m-30) REVERT: E 190 MET cc_start: 0.9708 (ptp) cc_final: 0.9377 (ptp) REVERT: E 248 ILE cc_start: 0.9857 (pt) cc_final: 0.9569 (pt) REVERT: E 294 TYR cc_start: 0.9519 (m-80) cc_final: 0.9269 (m-80) REVERT: E 352 PHE cc_start: 0.9710 (t80) cc_final: 0.9484 (t80) REVERT: E 375 PHE cc_start: 0.8880 (t80) cc_final: 0.8557 (t80) REVERT: F 11 ASP cc_start: 0.9398 (t70) cc_final: 0.9066 (t0) REVERT: F 69 TYR cc_start: 0.9356 (m-10) cc_final: 0.9131 (m-80) REVERT: F 73 HIS cc_start: 0.9041 (m-70) cc_final: 0.8694 (m-70) REVERT: F 82 MET cc_start: 0.9674 (ppp) cc_final: 0.9337 (ppp) REVERT: F 86 TRP cc_start: 0.9774 (m-90) cc_final: 0.9562 (m-90) REVERT: F 123 MET cc_start: 0.9817 (mmp) cc_final: 0.9495 (mmm) REVERT: F 189 LEU cc_start: 0.9783 (tp) cc_final: 0.9574 (tp) REVERT: F 190 MET cc_start: 0.9638 (ptp) cc_final: 0.9379 (ptp) REVERT: F 213 LYS cc_start: 0.9817 (pttm) cc_final: 0.9563 (ptpp) REVERT: F 255 PHE cc_start: 0.9552 (p90) cc_final: 0.8957 (p90) REVERT: F 262 PHE cc_start: 0.9414 (m-10) cc_final: 0.9099 (m-80) REVERT: F 269 MET cc_start: 0.8910 (ttt) cc_final: 0.8472 (tmm) REVERT: F 274 ILE cc_start: 0.9670 (pt) cc_final: 0.9371 (pt) REVERT: F 297 ASN cc_start: 0.9735 (t0) cc_final: 0.9453 (p0) REVERT: F 305 MET cc_start: 0.9471 (tpp) cc_final: 0.9148 (mmt) REVERT: F 306 TYR cc_start: 0.8111 (m-10) cc_final: 0.7895 (m-10) REVERT: F 352 PHE cc_start: 0.9711 (t80) cc_final: 0.9505 (t80) REVERT: G 119 MET cc_start: 0.9553 (ppp) cc_final: 0.9318 (ppp) REVERT: H 103 MET cc_start: 0.7452 (mpp) cc_final: 0.7162 (mpp) REVERT: H 156 PHE cc_start: 0.7956 (p90) cc_final: 0.7662 (p90) REVERT: H 157 MET cc_start: 0.8220 (mmp) cc_final: 0.8017 (mmp) REVERT: I 80 ARG cc_start: 0.9691 (tpm170) cc_final: 0.9449 (mtm180) REVERT: I 91 PHE cc_start: 0.9764 (m-80) cc_final: 0.9533 (m-80) REVERT: I 139 LYS cc_start: 0.7883 (mppt) cc_final: 0.6355 (tptt) REVERT: I 163 ARG cc_start: 0.9130 (mtm-85) cc_final: 0.8766 (ptt90) REVERT: J 224 LEU cc_start: 0.9289 (mm) cc_final: 0.8945 (mm) REVERT: J 229 LEU cc_start: 0.8569 (mp) cc_final: 0.7815 (mp) REVERT: K 152 LEU cc_start: 0.8954 (mt) cc_final: 0.8729 (mt) REVERT: M 139 GLU cc_start: 0.9911 (tm-30) cc_final: 0.9669 (mt-10) REVERT: M 197 LEU cc_start: 0.9592 (tt) cc_final: 0.9280 (mt) REVERT: M 238 ARG cc_start: 0.9622 (mmp-170) cc_final: 0.9211 (tpt90) REVERT: M 241 PHE cc_start: 0.9625 (m-80) cc_final: 0.9362 (m-80) REVERT: N 1 MET cc_start: 0.8584 (pmm) cc_final: 0.7503 (ppp) REVERT: O 46 LEU cc_start: 0.9549 (tp) cc_final: 0.9302 (tp) outliers start: 0 outliers final: 0 residues processed: 781 average time/residue: 0.2153 time to fit residues: 253.9286 Evaluate side-chains 587 residues out of total 3076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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: 0.3980 chunk 35 optimal weight: 10.0000 chunk 304 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 325 optimal weight: 0.2980 chunk 184 optimal weight: 0.5980 chunk 316 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN F 173 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.053213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.034350 restraints weight = 221469.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.035931 restraints weight = 142914.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.037118 restraints weight = 102917.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.038039 restraints weight = 79435.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.038744 restraints weight = 64303.735| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.8617 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= 0.162 Angle : 0.819 15.966 39338 Z= 0.430 Chirality : 0.050 0.341 4354 Planarity : 0.005 0.135 5094 Dihedral : 6.511 87.672 4000 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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 : 0.03 % 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: -0.00 (0.14), residues: 3569 helix: 0.37 (0.12), residues: 1862 sheet: -0.53 (0.26), residues: 420 loop : -0.12 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 116 TYR 0.044 0.002 TYR B 294 PHE 0.050 0.003 PHE B 223 TRP 0.062 0.003 TRP D 86 HIS 0.014 0.001 HIS K 91 Details of bonding type rmsd covalent geometry : bond 0.00351 (29145) covalent geometry : angle 0.81871 (39338) hydrogen bonds : bond 0.05290 ( 1632) hydrogen bonds : angle 5.40795 ( 4581) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6986.62 seconds wall clock time: 121 minutes 15.59 seconds (7275.59 seconds total)