Starting phenix.real_space_refine on Sun Jul 5 23:55:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mih_23851/07_2026/7mih_23851_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mih_23851/07_2026/7mih_23851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mih_23851/07_2026/7mih_23851_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mih_23851/07_2026/7mih_23851_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mih_23851/07_2026/7mih_23851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mih_23851/07_2026/7mih_23851.map" } resolution = 2.8 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= 0.202 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 P 12 5.49 5 Mg 4 5.21 5 S 92 5.16 5 C 9984 2.51 5 N 2684 2.21 5 O 2840 1.98 5 H 15640 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31256 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7731 Classifications: {'peptide': 483} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 459} Chain breaks: 6 Chain: "B" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7731 Classifications: {'peptide': 483} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 459} Chain breaks: 6 Chain: "C" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7731 Classifications: {'peptide': 483} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 459} Chain breaks: 6 Chain: "E" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7731 Classifications: {'peptide': 483} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 459} Chain breaks: 6 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Inner-chain residues flagged as termini: ['pdbres="GLN A 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Inner-chain residues flagged as termini: ['pdbres="GLN C 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU A 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU A 155 " occ=0.75 residue: pdb=" N CYS A 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS A 243 " occ=0.75 residue: pdb=" N GLU B 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU B 155 " occ=0.75 residue: pdb=" N CYS B 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS B 243 " occ=0.75 residue: pdb=" N GLU C 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU C 155 " occ=0.75 residue: pdb=" N CYS C 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS C 243 " occ=0.75 residue: pdb=" N GLU E 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU E 155 " occ=0.75 residue: pdb=" N CYS E 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS E 243 " occ=0.75 Time building chain proxies: 4.31, per 1000 atoms: 0.14 Number of scatterers: 31256 At special positions: 0 Unit cell: (124.95, 139.65, 87.15, 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) S 92 16.00 P 12 15.00 Mg 4 11.99 O 2840 8.00 N 2684 7.00 C 9984 6.00 H 15640 1.00 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: 2.26 Conformation dependent library (CDL) restraints added in 686.7 milliseconds 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 12 sheets defined 47.9% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 11 through 14 removed outlier: 4.037A pdb=" N ILE A 14 " --> pdb=" O ILE A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 112 through 130 removed outlier: 7.115A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.969A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 314 through 327 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.626A pdb=" N PHE A 529 " --> pdb=" O HIS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 547 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'B' and resid 11 through 14 removed outlier: 4.037A pdb=" N ILE B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 15 through 30 Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 90 through 104 Processing helix chain 'B' and resid 112 through 130 removed outlier: 7.115A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.969A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 194 through 207 Processing helix chain 'B' and resid 223 through 234 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 261 through 271 Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 314 through 327 Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 399 through 410 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.626A pdb=" N PHE B 529 " --> pdb=" O HIS B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 547 Processing helix chain 'B' and resid 550 through 555 Processing helix chain 'C' and resid 11 through 14 removed outlier: 4.037A pdb=" N ILE C 14 " --> pdb=" O ILE C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 11 through 14' Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 112 through 130 removed outlier: 7.115A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 169 removed outlier: 3.969A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 194 through 207 Processing helix chain 'C' and resid 223 through 234 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 314 through 327 Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 381 through 392 Processing helix chain 'C' and resid 399 through 410 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.626A pdb=" N PHE C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 547 Processing helix chain 'C' and resid 550 through 555 Processing helix chain 'E' and resid 11 through 14 removed outlier: 4.037A pdb=" N ILE E 14 " --> pdb=" O ILE E 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 11 through 14' Processing helix chain 'E' and resid 15 through 30 Processing helix chain 'E' and resid 69 through 79 Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 90 through 104 Processing helix chain 'E' and resid 112 through 130 removed outlier: 7.116A pdb=" N THR E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 156 through 169 removed outlier: 3.969A pdb=" N PHE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 223 through 234 Processing helix chain 'E' and resid 237 through 239 No H-bonds generated for 'chain 'E' and resid 237 through 239' Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 252 through 260 Processing helix chain 'E' and resid 261 through 271 Processing helix chain 'E' and resid 283 through 294 Processing helix chain 'E' and resid 314 through 327 Processing helix chain 'E' and resid 357 through 363 Processing helix chain 'E' and resid 381 through 392 Processing helix chain 'E' and resid 399 through 410 Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 526 through 531 removed outlier: 3.626A pdb=" N PHE E 529 " --> pdb=" O HIS E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 547 Processing helix chain 'E' and resid 550 through 555 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 8.218A pdb=" N ILE A 88 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS A 38 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 2 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE A 145 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 4 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A 147 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 6 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 178 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 5 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL A 180 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A 7 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU A 182 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N LEU A 213 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN A 177 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL A 215 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS A 179 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG A 217 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 181 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 336 removed outlier: 6.516A pdb=" N LYS A 297 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN A 333 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS A 299 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET A 335 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 301 " --> pdb=" O MET A 335 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N GLY A 366 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER A 300 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 368 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA A 302 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 395 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL A 523 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY A 397 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET A 509 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN A 502 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 511 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 89 removed outlier: 8.218A pdb=" N ILE B 88 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS B 38 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS B 2 " --> pdb=" O CYS B 143 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE B 145 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE B 4 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B 147 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 6 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE B 178 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 5 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL B 180 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR B 7 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU B 182 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N LEU B 213 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN B 177 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL B 215 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS B 179 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG B 217 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER B 181 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA6, first strand: chain 'B' and resid 330 through 336 removed outlier: 6.515A pdb=" N LYS B 297 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN B 333 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS B 299 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET B 335 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 301 " --> pdb=" O MET B 335 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N GLY B 366 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER B 300 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU B 368 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA B 302 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE B 395 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL B 523 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY B 397 " --> pdb=" O VAL B 523 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET B 509 " --> pdb=" O GLN B 502 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 502 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 511 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 removed outlier: 8.219A pdb=" N ILE C 88 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS C 38 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS C 2 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE C 145 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE C 4 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU C 147 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 6 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N LEU C 213 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN C 177 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL C 215 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS C 179 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG C 217 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER C 181 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AA9, first strand: chain 'C' and resid 330 through 336 removed outlier: 6.515A pdb=" N LYS C 297 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN C 333 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS C 299 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET C 335 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 301 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N GLY C 366 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER C 300 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU C 368 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA C 302 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE C 395 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL C 523 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY C 397 " --> pdb=" O VAL C 523 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET C 509 " --> pdb=" O GLN C 502 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN C 502 " --> pdb=" O MET C 509 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE C 511 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 87 through 89 removed outlier: 8.218A pdb=" N ILE E 88 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS E 38 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS E 2 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE E 145 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE E 4 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU E 147 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL E 6 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR E 3 " --> pdb=" O CYS E 176 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE E 178 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU E 5 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL E 180 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR E 7 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU E 182 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N LEU E 213 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN E 177 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL E 215 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS E 179 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG E 217 " --> pdb=" O HIS E 179 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER E 181 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AB3, first strand: chain 'E' and resid 330 through 336 removed outlier: 6.516A pdb=" N LYS E 297 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN E 333 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS E 299 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET E 335 " --> pdb=" O CYS E 299 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 301 " --> pdb=" O MET E 335 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N GLY E 366 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER E 300 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU E 368 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA E 302 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE E 395 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL E 523 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY E 397 " --> pdb=" O VAL E 523 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET E 509 " --> pdb=" O GLN E 502 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN E 502 " --> pdb=" O MET E 509 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE E 511 " --> pdb=" O VAL E 500 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1896 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: 6.91 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 15600 1.09 - 1.29: 2540 1.29 - 1.49: 6384 1.49 - 1.69: 6900 1.69 - 1.88: 148 Bond restraints: 31572 Sorted by residual: bond pdb=" N ILE C 37 " pdb=" H ILE C 37 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N VAL B 369 " pdb=" H VAL B 369 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CD1 TYR B 554 " pdb=" HD1 TYR B 554 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NE2 GLN E 296 " pdb="HE22 GLN E 296 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLU C 322 " pdb=" H GLU C 322 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 31567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.49: 57043 8.49 - 16.97: 73 16.97 - 25.46: 4 25.46 - 33.95: 4 33.95 - 42.43: 12 Bond angle restraints: 57136 Sorted by residual: angle pdb=" CA MET C 448 " pdb=" N MET C 448 " pdb=" H MET C 448 " ideal model delta sigma weight residual 114.00 156.43 -42.43 3.00e+00 1.11e-01 2.00e+02 angle pdb=" CA MET B 448 " pdb=" N MET B 448 " pdb=" H MET B 448 " ideal model delta sigma weight residual 114.00 156.43 -42.43 3.00e+00 1.11e-01 2.00e+02 angle pdb=" CA MET A 448 " pdb=" N MET A 448 " pdb=" H MET A 448 " ideal model delta sigma weight residual 114.00 156.43 -42.43 3.00e+00 1.11e-01 2.00e+02 angle pdb=" CA MET E 448 " pdb=" N MET E 448 " pdb=" H MET E 448 " ideal model delta sigma weight residual 114.00 156.43 -42.43 3.00e+00 1.11e-01 2.00e+02 angle pdb=" C ARG B 217 " pdb=" CA ARG B 217 " pdb=" HA ARG B 217 " ideal model delta sigma weight residual 109.00 72.91 36.09 3.00e+00 1.11e-01 1.45e+02 ... (remaining 57131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 13240 17.50 - 35.00: 904 35.00 - 52.51: 316 52.51 - 70.01: 360 70.01 - 87.51: 48 Dihedral angle restraints: 14868 sinusoidal: 8348 harmonic: 6520 Sorted by residual: dihedral pdb=" CA VAL B 133 " pdb=" C VAL B 133 " pdb=" N ASP B 134 " pdb=" CA ASP B 134 " ideal model delta harmonic sigma weight residual 180.00 147.27 32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA VAL C 133 " pdb=" C VAL C 133 " pdb=" N ASP C 134 " pdb=" CA ASP C 134 " ideal model delta harmonic sigma weight residual 180.00 147.27 32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA VAL A 133 " pdb=" C VAL A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta harmonic sigma weight residual 180.00 147.27 32.73 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 14865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1341 0.098 - 0.196: 782 0.196 - 0.294: 196 0.294 - 0.392: 53 0.392 - 0.490: 28 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CB THR C 118 " pdb=" CA THR C 118 " pdb=" OG1 THR C 118 " pdb=" CG2 THR C 118 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CB THR A 118 " pdb=" CA THR A 118 " pdb=" OG1 THR A 118 " pdb=" CG2 THR A 118 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CB THR B 118 " pdb=" CA THR B 118 " pdb=" OG1 THR B 118 " pdb=" CG2 THR B 118 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 2397 not shown) Planarity restraints: 4540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 74 " 0.319 2.00e-02 2.50e+03 1.43e-01 6.17e+02 pdb=" CG TYR C 74 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR C 74 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR C 74 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR C 74 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR C 74 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR C 74 " 0.058 2.00e-02 2.50e+03 pdb=" OH TYR C 74 " 0.255 2.00e-02 2.50e+03 pdb=" HD1 TYR C 74 " -0.144 2.00e-02 2.50e+03 pdb=" HD2 TYR C 74 " -0.169 2.00e-02 2.50e+03 pdb=" HE1 TYR C 74 " -0.103 2.00e-02 2.50e+03 pdb=" HE2 TYR C 74 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 74 " -0.318 2.00e-02 2.50e+03 1.43e-01 6.17e+02 pdb=" CG TYR A 74 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 74 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR A 74 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR A 74 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR A 74 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 74 " -0.059 2.00e-02 2.50e+03 pdb=" OH TYR A 74 " -0.255 2.00e-02 2.50e+03 pdb=" HD1 TYR A 74 " 0.144 2.00e-02 2.50e+03 pdb=" HD2 TYR A 74 " 0.169 2.00e-02 2.50e+03 pdb=" HE1 TYR A 74 " 0.104 2.00e-02 2.50e+03 pdb=" HE2 TYR A 74 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 74 " 0.318 2.00e-02 2.50e+03 1.43e-01 6.16e+02 pdb=" CG TYR E 74 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR E 74 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR E 74 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR E 74 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR E 74 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR E 74 " 0.059 2.00e-02 2.50e+03 pdb=" OH TYR E 74 " 0.255 2.00e-02 2.50e+03 pdb=" HD1 TYR E 74 " -0.144 2.00e-02 2.50e+03 pdb=" HD2 TYR E 74 " -0.169 2.00e-02 2.50e+03 pdb=" HE1 TYR E 74 " -0.104 2.00e-02 2.50e+03 pdb=" HE2 TYR E 74 " -0.073 2.00e-02 2.50e+03 ... (remaining 4537 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 346 1.86 - 2.55: 26654 2.55 - 3.23: 100272 3.23 - 3.92: 135889 3.92 - 4.60: 206002 Nonbonded interactions: 469163 Sorted by model distance: nonbonded pdb=" HD1 PHE E 373 " pdb=" H1 GLN E 604 " model vdw 1.177 2.100 nonbonded pdb=" HD1 PHE C 373 " pdb=" H1 GLN C 603 " model vdw 1.177 2.100 nonbonded pdb=" HD1 PHE A 373 " pdb=" H1 GLN A 603 " model vdw 1.177 2.100 nonbonded pdb=" HD1 PHE B 373 " pdb=" H1 GLN B 604 " model vdw 1.177 2.100 nonbonded pdb="HE22 GLN A 95 " pdb=" OE1 GLN C 95 " model vdw 1.373 2.450 ... (remaining 469158 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 556) selection = (chain 'B' and resid 1 through 556) selection = (chain 'C' and resid 1 through 556) selection = (chain 'E' and resid 1 through 556) } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.200 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 24.880 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 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 : 0.012 0.123 15932 Z= 0.715 Angle : 2.038 9.322 21548 Z= 1.365 Chirality : 0.132 0.490 2400 Planarity : 0.014 0.137 2728 Dihedral : 14.158 87.512 6148 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.84 % Allowed : 5.81 % Favored : 92.36 % Cbeta Deviations : 1.56 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.16 (0.17), residues: 1876 helix: -1.61 (0.14), residues: 832 sheet: -1.26 (0.24), residues: 388 loop : -0.91 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 205 TYR 0.236 0.025 TYR C 74 PHE 0.066 0.018 PHE B 163 TRP 0.100 0.036 TRP B 387 HIS 0.024 0.006 HIS C 323 Details of bonding type rmsd/Z covalent geometry : bond 0.01234 / 0.71 (15932) covalent geometry : angle 2.03808 / 1.37 (21548) hydrogen bonds : bond 0.18428 / 11.77 ( 656) hydrogen bonds : angle 7.95951 / 5.63 ( 1896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 481 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 450 time to evaluate : 0.758 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: A 75 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 169 LYS cc_start: 0.6881 (mtpt) cc_final: 0.6534 (mttt) REVERT: A 205 ARG cc_start: 0.7532 (ttm170) cc_final: 0.7218 (mtm110) REVERT: A 288 MET cc_start: 0.7656 (mtm) cc_final: 0.7335 (mtt) REVERT: A 450 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8430 (tp) REVERT: B 75 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7559 (mt-10) REVERT: B 169 LYS cc_start: 0.6852 (mtpt) cc_final: 0.6536 (mttt) REVERT: B 205 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7235 (mtm110) REVERT: B 288 MET cc_start: 0.7658 (mtm) cc_final: 0.7337 (mtt) REVERT: C 75 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 169 LYS cc_start: 0.6821 (mtpt) cc_final: 0.6495 (mttt) REVERT: C 205 ARG cc_start: 0.7533 (ttm170) cc_final: 0.7257 (mtm110) REVERT: C 283 PHE cc_start: 0.5638 (t80) cc_final: 0.5435 (t80) REVERT: C 288 MET cc_start: 0.7622 (mtm) cc_final: 0.7309 (mtt) REVERT: E 75 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7577 (mt-10) REVERT: E 169 LYS cc_start: 0.6812 (mtpt) cc_final: 0.6498 (mttt) REVERT: E 205 ARG cc_start: 0.7535 (ttm170) cc_final: 0.7241 (mtm110) REVERT: E 288 MET cc_start: 0.7660 (mtm) cc_final: 0.7325 (mtt) outliers start: 31 outliers final: 12 residues processed: 469 average time/residue: 0.9930 time to fit residues: 527.8390 Evaluate side-chains 311 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 298 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 524 GLN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 483 GLU Chi-restraints excluded: chain E residue 524 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 165 GLN A 271 HIS A 383 GLN A 491 GLN A 502 GLN A 556 GLN B 128 GLN B 165 GLN B 383 GLN B 491 GLN B 502 GLN B 556 GLN C 128 GLN C 165 GLN C 271 HIS C 383 GLN C 491 GLN C 502 GLN C 556 GLN E 128 GLN E 165 GLN E 383 GLN E 491 GLN E 502 GLN E 556 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.165873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.140746 restraints weight = 49105.945| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.63 r_work: 0.3368 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15932 Z= 0.161 Angle : 0.646 5.321 21548 Z= 0.344 Chirality : 0.049 0.373 2400 Planarity : 0.005 0.049 2728 Dihedral : 7.852 57.458 2382 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.99 % Favored : 96.80 % Rotamer: Outliers : 2.67 % Allowed : 15.05 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1876 helix: -0.12 (0.17), residues: 832 sheet: -1.64 (0.24), residues: 380 loop : -0.50 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 532 TYR 0.019 0.002 TYR B 42 PHE 0.016 0.002 PHE B 318 TRP 0.014 0.002 TRP C 387 HIS 0.007 0.002 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15932) covalent geometry : angle 0.64620 / 0.34 (21548) hydrogen bonds : bond 0.04439 / 2.91 ( 656) hydrogen bonds : angle 5.49357 / 3.92 ( 1896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 326 time to evaluate : 0.834 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: A 46 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7660 (p0) REVERT: A 169 LYS cc_start: 0.6951 (mtpt) cc_final: 0.6508 (mttt) REVERT: A 191 GLU cc_start: 0.7699 (tt0) cc_final: 0.7227 (tp30) REVERT: A 202 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7673 (ttp-110) REVERT: A 217 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8313 (mmm160) REVERT: A 258 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6746 (mm-30) REVERT: A 288 MET cc_start: 0.8051 (mtm) cc_final: 0.7785 (mtt) REVERT: A 300 SER cc_start: 0.7490 (p) cc_final: 0.7241 (p) REVERT: A 512 ILE cc_start: 0.8328 (pt) cc_final: 0.7991 (pp) REVERT: B 169 LYS cc_start: 0.6974 (mtpt) cc_final: 0.6521 (mttt) REVERT: B 191 GLU cc_start: 0.7660 (tt0) cc_final: 0.7180 (tp30) REVERT: B 205 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7605 (mtm110) REVERT: B 217 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8289 (mmm160) REVERT: B 288 MET cc_start: 0.8056 (mtm) cc_final: 0.7846 (mtt) REVERT: B 300 SER cc_start: 0.7470 (p) cc_final: 0.7218 (p) REVERT: C 169 LYS cc_start: 0.6931 (mtpt) cc_final: 0.6505 (mttt) REVERT: C 191 GLU cc_start: 0.7633 (tt0) cc_final: 0.7209 (tp30) REVERT: C 205 ARG cc_start: 0.8146 (ttm170) cc_final: 0.7598 (mtm110) REVERT: C 217 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8281 (mmm160) REVERT: C 300 SER cc_start: 0.7512 (p) cc_final: 0.7282 (p) REVERT: C 454 ARG cc_start: 0.7683 (ttm170) cc_final: 0.7319 (ttm170) REVERT: C 512 ILE cc_start: 0.8250 (pt) cc_final: 0.7909 (pp) REVERT: E 169 LYS cc_start: 0.6950 (mtpt) cc_final: 0.6487 (mttt) REVERT: E 191 GLU cc_start: 0.7662 (tt0) cc_final: 0.7181 (tp30) REVERT: E 205 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7601 (mtm110) REVERT: E 217 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8281 (mmm160) REVERT: E 288 MET cc_start: 0.8064 (mtm) cc_final: 0.7819 (mtt) REVERT: E 300 SER cc_start: 0.7479 (p) cc_final: 0.7245 (p) REVERT: E 454 ARG cc_start: 0.7639 (ttm170) cc_final: 0.7379 (ttm170) REVERT: E 512 ILE cc_start: 0.8313 (pt) cc_final: 0.7979 (pp) outliers start: 45 outliers final: 14 residues processed: 347 average time/residue: 1.2522 time to fit residues: 483.5443 Evaluate side-chains 304 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 285 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 258 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.160204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.134332 restraints weight = 49639.404| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.64 r_work: 0.3323 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15932 Z= 0.137 Angle : 0.573 5.555 21548 Z= 0.300 Chirality : 0.048 0.379 2400 Planarity : 0.005 0.038 2728 Dihedral : 6.864 45.492 2352 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.99 % Favored : 96.80 % Rotamer: Outliers : 2.96 % Allowed : 17.24 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.55 (0.20), residues: 1876 helix: 0.41 (0.18), residues: 832 sheet: -1.53 (0.25), residues: 380 loop : -0.36 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 33 TYR 0.016 0.001 TYR C 42 PHE 0.011 0.001 PHE A 163 TRP 0.011 0.002 TRP C 387 HIS 0.005 0.002 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (15932) covalent geometry : angle 0.57263 / 0.30 (21548) hydrogen bonds : bond 0.03656 / 2.39 ( 656) hydrogen bonds : angle 5.18747 / 3.73 ( 1896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 297 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7662 (mtm-85) REVERT: A 103 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7578 (mtm110) REVERT: A 123 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: A 169 LYS cc_start: 0.7089 (mtpt) cc_final: 0.6649 (mttt) REVERT: A 185 GLN cc_start: 0.8294 (tt0) cc_final: 0.8063 (tt0) REVERT: A 191 GLU cc_start: 0.7676 (tt0) cc_final: 0.7260 (tp30) REVERT: A 202 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7720 (ttp-110) REVERT: A 258 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6641 (mm-30) REVERT: A 300 SER cc_start: 0.7473 (p) cc_final: 0.7249 (p) REVERT: A 389 ARG cc_start: 0.6639 (ttp-110) cc_final: 0.6404 (ttp-110) REVERT: A 512 ILE cc_start: 0.8364 (pt) cc_final: 0.8001 (pp) REVERT: B 33 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7718 (mtm-85) REVERT: B 169 LYS cc_start: 0.7155 (mtpt) cc_final: 0.6708 (mttt) REVERT: B 191 GLU cc_start: 0.7648 (tt0) cc_final: 0.7300 (tp30) REVERT: B 300 SER cc_start: 0.7406 (p) cc_final: 0.7180 (p) REVERT: B 389 ARG cc_start: 0.6640 (ttp-110) cc_final: 0.6393 (ttp-110) REVERT: B 512 ILE cc_start: 0.8372 (pt) cc_final: 0.7995 (pp) REVERT: C 33 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7694 (mtm-85) REVERT: C 169 LYS cc_start: 0.7069 (mtpt) cc_final: 0.6634 (mttt) REVERT: C 185 GLN cc_start: 0.8219 (tt0) cc_final: 0.7995 (tt0) REVERT: C 389 ARG cc_start: 0.6618 (ttp-110) cc_final: 0.6385 (ttp-110) REVERT: C 512 ILE cc_start: 0.8355 (pt) cc_final: 0.7988 (pp) REVERT: E 33 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7693 (mtm-85) REVERT: E 169 LYS cc_start: 0.7098 (mtpt) cc_final: 0.6684 (mttt) REVERT: E 191 GLU cc_start: 0.7673 (tt0) cc_final: 0.7295 (tp30) REVERT: E 512 ILE cc_start: 0.8294 (pt) cc_final: 0.8028 (pp) outliers start: 50 outliers final: 22 residues processed: 321 average time/residue: 1.0643 time to fit residues: 383.4222 Evaluate side-chains 294 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 17 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 HIS A 185 GLN A 198 GLN A 240 GLN B 198 GLN B 235 HIS B 240 GLN C 55 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN C 235 HIS C 240 GLN E 55 HIS E 198 GLN E 240 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.155711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.129406 restraints weight = 49358.540| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.65 r_work: 0.3261 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15932 Z= 0.226 Angle : 0.620 5.693 21548 Z= 0.327 Chirality : 0.050 0.371 2400 Planarity : 0.005 0.037 2728 Dihedral : 7.482 51.129 2352 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.41 % Favored : 96.38 % Rotamer: Outliers : 3.97 % Allowed : 15.94 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.53 (0.20), residues: 1876 helix: 0.28 (0.18), residues: 828 sheet: -1.26 (0.26), residues: 380 loop : -0.33 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 102 TYR 0.017 0.002 TYR C 265 PHE 0.013 0.002 PHE C 159 TRP 0.010 0.002 TRP C 387 HIS 0.009 0.002 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (15932) covalent geometry : angle 0.61991 / 0.33 (21548) hydrogen bonds : bond 0.03900 / 2.55 ( 656) hydrogen bonds : angle 5.22503 / 3.74 ( 1896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 369 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 302 time to evaluate : 0.607 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: A 46 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7955 (p0) REVERT: A 57 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7059 (pp20) REVERT: A 123 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: A 169 LYS cc_start: 0.7152 (mtpt) cc_final: 0.6689 (mttt) REVERT: A 191 GLU cc_start: 0.7759 (tt0) cc_final: 0.7317 (tp30) REVERT: A 258 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6560 (mm-30) REVERT: A 512 ILE cc_start: 0.8399 (pt) cc_final: 0.8094 (pp) REVERT: B 123 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: B 169 LYS cc_start: 0.7189 (mtpt) cc_final: 0.6720 (mttt) REVERT: B 286 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.7039 (mtt-85) REVERT: B 512 ILE cc_start: 0.8376 (pt) cc_final: 0.8063 (pp) REVERT: C 57 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7191 (pp20) REVERT: C 103 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7620 (mtm110) REVERT: C 123 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: C 169 LYS cc_start: 0.7050 (mtpt) cc_final: 0.6580 (mttt) REVERT: C 512 ILE cc_start: 0.8340 (pt) cc_final: 0.8013 (pp) REVERT: E 123 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: E 169 LYS cc_start: 0.7126 (mtpt) cc_final: 0.6679 (mttt) REVERT: E 258 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6145 (mt-10) REVERT: E 512 ILE cc_start: 0.8354 (pt) cc_final: 0.8038 (pp) outliers start: 67 outliers final: 30 residues processed: 332 average time/residue: 0.9990 time to fit residues: 374.7648 Evaluate side-chains 327 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 288 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 286 ARG Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 HIS B 55 HIS C 55 HIS E 55 HIS E 237 ASN E 240 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.157720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.131551 restraints weight = 49762.376| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.65 r_work: 0.3282 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15932 Z= 0.141 Angle : 0.548 5.411 21548 Z= 0.286 Chirality : 0.047 0.363 2400 Planarity : 0.004 0.035 2728 Dihedral : 6.819 45.895 2352 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.99 % Favored : 96.80 % Rotamer: Outliers : 3.26 % Allowed : 17.12 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.28 (0.20), residues: 1876 helix: 0.52 (0.18), residues: 828 sheet: -1.28 (0.26), residues: 376 loop : -0.16 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 33 TYR 0.014 0.001 TYR E 42 PHE 0.009 0.001 PHE A 163 TRP 0.011 0.002 TRP C 387 HIS 0.008 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (15932) covalent geometry : angle 0.54780 / 0.29 (21548) hydrogen bonds : bond 0.03425 / 2.25 ( 656) hydrogen bonds : angle 4.96538 / 3.57 ( 1896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7051 (pp20) REVERT: A 123 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: A 169 LYS cc_start: 0.7082 (mtpt) cc_final: 0.6626 (mttt) REVERT: A 191 GLU cc_start: 0.7853 (tt0) cc_final: 0.7362 (tm-30) REVERT: A 258 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6568 (mm-30) REVERT: A 465 ARG cc_start: 0.7515 (ttt180) cc_final: 0.6991 (ttm170) REVERT: A 512 ILE cc_start: 0.8227 (pt) cc_final: 0.7959 (pp) REVERT: B 103 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7631 (mtm110) REVERT: B 169 LYS cc_start: 0.7109 (mtpt) cc_final: 0.6642 (mttt) REVERT: B 191 GLU cc_start: 0.7816 (tt0) cc_final: 0.7343 (tm-30) REVERT: B 465 ARG cc_start: 0.7540 (ttt180) cc_final: 0.7016 (ttm170) REVERT: B 512 ILE cc_start: 0.8223 (pt) cc_final: 0.7942 (pp) REVERT: C 46 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7985 (p0) REVERT: C 57 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: C 103 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7631 (mtm110) REVERT: C 169 LYS cc_start: 0.7001 (mtpt) cc_final: 0.6466 (mttt) REVERT: C 465 ARG cc_start: 0.7545 (ttt180) cc_final: 0.7007 (ttm170) REVERT: C 512 ILE cc_start: 0.8274 (pt) cc_final: 0.7961 (pp) REVERT: E 169 LYS cc_start: 0.6992 (mtpt) cc_final: 0.6533 (mttt) REVERT: E 465 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7030 (ttm170) REVERT: E 512 ILE cc_start: 0.8286 (pt) cc_final: 0.8014 (pp) outliers start: 55 outliers final: 35 residues processed: 315 average time/residue: 1.0411 time to fit residues: 372.0576 Evaluate side-chains 306 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 HIS B 55 HIS C 55 HIS E 55 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.155798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129560 restraints weight = 49613.138| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.64 r_work: 0.3243 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15932 Z= 0.220 Angle : 0.595 5.695 21548 Z= 0.313 Chirality : 0.049 0.361 2400 Planarity : 0.005 0.034 2728 Dihedral : 7.335 50.963 2352 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.46 % Favored : 96.32 % Rotamer: Outliers : 3.26 % Allowed : 17.59 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.42 (0.20), residues: 1876 helix: 0.35 (0.18), residues: 832 sheet: -1.22 (0.26), residues: 376 loop : -0.25 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 33 TYR 0.017 0.002 TYR B 265 PHE 0.011 0.001 PHE C 163 TRP 0.010 0.002 TRP C 387 HIS 0.008 0.002 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (15932) covalent geometry : angle 0.59458 / 0.31 (21548) hydrogen bonds : bond 0.03727 / 2.45 ( 656) hydrogen bonds : angle 5.04280 / 3.62 ( 1896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 288 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: A 191 GLU cc_start: 0.7871 (tt0) cc_final: 0.7302 (tm-30) REVERT: A 258 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6578 (mm-30) REVERT: A 512 ILE cc_start: 0.8319 (pt) cc_final: 0.8038 (pp) REVERT: A 521 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8286 (m) REVERT: B 169 LYS cc_start: 0.7119 (mtpt) cc_final: 0.6660 (mttt) REVERT: B 191 GLU cc_start: 0.7857 (tt0) cc_final: 0.7276 (tm-30) REVERT: B 512 ILE cc_start: 0.8253 (pt) cc_final: 0.7959 (pp) REVERT: B 521 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8269 (m) REVERT: C 103 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7819 (mtm110) REVERT: C 169 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6641 (mttt) REVERT: C 512 ILE cc_start: 0.8260 (pt) cc_final: 0.7940 (pp) REVERT: C 521 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8223 (m) REVERT: E 169 LYS cc_start: 0.7082 (mtpt) cc_final: 0.6648 (mttt) REVERT: E 191 GLU cc_start: 0.7859 (tt0) cc_final: 0.7284 (tm-30) REVERT: E 512 ILE cc_start: 0.8304 (pt) cc_final: 0.8023 (pp) REVERT: E 521 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8246 (m) outliers start: 55 outliers final: 37 residues processed: 310 average time/residue: 0.9826 time to fit residues: 346.4241 Evaluate side-chains 324 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 HIS B 165 GLN C 55 HIS E 55 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.157612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131495 restraints weight = 49508.401| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.64 r_work: 0.3271 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15932 Z= 0.154 Angle : 0.548 5.830 21548 Z= 0.286 Chirality : 0.047 0.356 2400 Planarity : 0.004 0.034 2728 Dihedral : 6.883 46.518 2352 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 2.99 % Favored : 96.59 % Rotamer: Outliers : 3.02 % Allowed : 17.89 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.20), residues: 1876 helix: 0.73 (0.18), residues: 808 sheet: -1.23 (0.26), residues: 376 loop : 0.02 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 33 TYR 0.014 0.001 TYR B 42 PHE 0.011 0.001 PHE A 163 TRP 0.009 0.002 TRP E 387 HIS 0.008 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (15932) covalent geometry : angle 0.54753 / 0.29 (21548) hydrogen bonds : bond 0.03396 / 2.24 ( 656) hydrogen bonds : angle 4.88796 / 3.51 ( 1896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 328 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: A 169 LYS cc_start: 0.7078 (mtpt) cc_final: 0.6638 (mttt) REVERT: A 191 GLU cc_start: 0.7901 (tt0) cc_final: 0.7696 (tt0) REVERT: A 258 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6447 (mm-30) REVERT: A 318 PHE cc_start: 0.8772 (t80) cc_final: 0.8406 (t80) REVERT: A 512 ILE cc_start: 0.8244 (pt) cc_final: 0.8006 (pp) REVERT: A 521 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8271 (m) REVERT: B 103 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7597 (mtm110) REVERT: B 169 LYS cc_start: 0.7082 (mtpt) cc_final: 0.6637 (mttt) REVERT: B 191 GLU cc_start: 0.7885 (tt0) cc_final: 0.7667 (tt0) REVERT: B 512 ILE cc_start: 0.8244 (pt) cc_final: 0.8009 (pp) REVERT: C 103 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7652 (mtm110) REVERT: C 169 LYS cc_start: 0.7043 (mtpt) cc_final: 0.6608 (mttt) REVERT: C 512 ILE cc_start: 0.8256 (pt) cc_final: 0.7969 (pp) REVERT: E 103 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7704 (mtm110) REVERT: E 510 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6519 (mt-10) REVERT: E 512 ILE cc_start: 0.8264 (pt) cc_final: 0.8033 (pp) outliers start: 51 outliers final: 38 residues processed: 304 average time/residue: 0.9376 time to fit residues: 326.0678 Evaluate side-chains 314 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 45 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 167 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.0060 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.6456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.158846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.132720 restraints weight = 49570.036| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.65 r_work: 0.3287 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15932 Z= 0.130 Angle : 0.530 5.384 21548 Z= 0.276 Chirality : 0.046 0.353 2400 Planarity : 0.004 0.034 2728 Dihedral : 6.704 46.844 2352 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.46 % Favored : 96.11 % Rotamer: Outliers : 2.73 % Allowed : 18.31 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.13 (0.20), residues: 1876 helix: 0.89 (0.18), residues: 812 sheet: -1.22 (0.26), residues: 376 loop : 0.14 (0.27), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.014 0.001 TYR B 42 PHE 0.009 0.001 PHE A 163 TRP 0.009 0.001 TRP C 387 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (15932) covalent geometry : angle 0.53010 / 0.28 (21548) hydrogen bonds : bond 0.03223 / 2.13 ( 656) hydrogen bonds : angle 4.78846 / 3.44 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 323 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: A 169 LYS cc_start: 0.6984 (mtpt) cc_final: 0.6573 (mttt) REVERT: A 191 GLU cc_start: 0.7887 (tt0) cc_final: 0.7317 (tm-30) REVERT: A 258 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6452 (mm-30) REVERT: B 103 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7555 (mtm110) REVERT: B 169 LYS cc_start: 0.7008 (mtpt) cc_final: 0.6594 (mttt) REVERT: B 191 GLU cc_start: 0.7856 (tt0) cc_final: 0.7626 (tt0) REVERT: B 510 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6421 (mt-10) REVERT: C 103 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7605 (mtm110) REVERT: C 169 LYS cc_start: 0.7018 (mtpt) cc_final: 0.6628 (mttt) REVERT: C 191 GLU cc_start: 0.7850 (tt0) cc_final: 0.7594 (tt0) REVERT: C 512 ILE cc_start: 0.8197 (pt) cc_final: 0.7921 (pp) REVERT: E 103 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7645 (mtm110) REVERT: E 169 LYS cc_start: 0.6909 (mtpt) cc_final: 0.6493 (mttt) REVERT: E 191 GLU cc_start: 0.7849 (tt0) cc_final: 0.7600 (tt0) REVERT: E 510 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6464 (mt-10) outliers start: 46 outliers final: 38 residues processed: 301 average time/residue: 0.9082 time to fit residues: 312.6404 Evaluate side-chains 307 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 148 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.155451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129156 restraints weight = 49491.473| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.64 r_work: 0.3255 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15932 Z= 0.214 Angle : 0.592 6.061 21548 Z= 0.310 Chirality : 0.048 0.355 2400 Planarity : 0.005 0.034 2728 Dihedral : 7.228 50.508 2352 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.36 % Favored : 96.22 % Rotamer: Outliers : 3.14 % Allowed : 17.95 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.28 (0.20), residues: 1876 helix: 0.55 (0.18), residues: 832 sheet: -1.29 (0.26), residues: 376 loop : -0.19 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 102 TYR 0.017 0.002 TYR E 265 PHE 0.011 0.002 PHE B 473 TRP 0.008 0.002 TRP C 387 HIS 0.008 0.002 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (15932) covalent geometry : angle 0.59237 / 0.31 (21548) hydrogen bonds : bond 0.03593 / 2.36 ( 656) hydrogen bonds : angle 4.92278 / 3.53 ( 1896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: A 169 LYS cc_start: 0.7131 (mtpt) cc_final: 0.6734 (mttt) REVERT: A 258 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6464 (mm-30) REVERT: A 554 TYR cc_start: 0.8050 (t80) cc_final: 0.7765 (t80) REVERT: B 103 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7773 (mtm110) REVERT: B 169 LYS cc_start: 0.7164 (mtpt) cc_final: 0.6769 (mttt) REVERT: B 492 PHE cc_start: 0.6719 (m-80) cc_final: 0.6493 (m-80) REVERT: B 510 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: C 103 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7834 (mtm110) REVERT: C 169 LYS cc_start: 0.7074 (mtpt) cc_final: 0.6678 (mttt) REVERT: C 191 GLU cc_start: 0.7857 (tt0) cc_final: 0.7603 (tt0) REVERT: C 391 LYS cc_start: 0.7506 (mtpp) cc_final: 0.6971 (mtmm) REVERT: C 512 ILE cc_start: 0.8327 (pt) cc_final: 0.8048 (pp) REVERT: E 169 LYS cc_start: 0.7077 (mtpt) cc_final: 0.6700 (mttt) REVERT: E 191 GLU cc_start: 0.7879 (tt0) cc_final: 0.7628 (tt0) REVERT: E 510 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6507 (mt-10) outliers start: 53 outliers final: 39 residues processed: 307 average time/residue: 0.9455 time to fit residues: 331.0104 Evaluate side-chains 316 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 178 optimal weight: 0.0470 chunk 155 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.158326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.132389 restraints weight = 49441.013| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.64 r_work: 0.3286 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15932 Z= 0.126 Angle : 0.541 5.761 21548 Z= 0.281 Chirality : 0.046 0.349 2400 Planarity : 0.004 0.035 2728 Dihedral : 6.683 46.063 2352 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.30 % Favored : 96.22 % Rotamer: Outliers : 2.55 % Allowed : 18.96 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.09 (0.20), residues: 1876 helix: 0.89 (0.18), residues: 816 sheet: -1.34 (0.26), residues: 376 loop : 0.12 (0.27), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 33 TYR 0.014 0.001 TYR A 42 PHE 0.019 0.001 PHE B 473 TRP 0.009 0.001 TRP C 387 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15932) covalent geometry : angle 0.54103 / 0.28 (21548) hydrogen bonds : bond 0.03210 / 2.11 ( 656) hydrogen bonds : angle 4.76807 / 3.42 ( 1896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: A 169 LYS cc_start: 0.7041 (mtpt) cc_final: 0.6654 (mttt) REVERT: A 258 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6521 (mm-30) REVERT: A 318 PHE cc_start: 0.8789 (t80) cc_final: 0.8419 (t80) REVERT: B 103 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7573 (mtm110) REVERT: B 169 LYS cc_start: 0.7057 (mtpt) cc_final: 0.6650 (mttt) REVERT: B 492 PHE cc_start: 0.6621 (m-80) cc_final: 0.6401 (m-80) REVERT: B 510 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6375 (mt-10) REVERT: C 103 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7609 (mtm110) REVERT: C 169 LYS cc_start: 0.6995 (mtpt) cc_final: 0.6596 (mttt) REVERT: C 191 GLU cc_start: 0.7863 (tt0) cc_final: 0.7610 (tt0) REVERT: C 391 LYS cc_start: 0.7450 (mtpp) cc_final: 0.6952 (mtmm) REVERT: E 169 LYS cc_start: 0.6975 (mtpt) cc_final: 0.6579 (mttt) REVERT: E 191 GLU cc_start: 0.7878 (tt0) cc_final: 0.7638 (tt0) REVERT: E 465 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7091 (ttm170) REVERT: E 510 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6391 (mt-10) outliers start: 43 outliers final: 35 residues processed: 288 average time/residue: 0.9488 time to fit residues: 312.5661 Evaluate side-chains 298 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 157 optimal weight: 0.0050 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.159917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.134167 restraints weight = 49498.211| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.64 r_work: 0.3319 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15932 Z= 0.105 Angle : 0.526 6.334 21548 Z= 0.273 Chirality : 0.046 0.349 2400 Planarity : 0.005 0.103 2728 Dihedral : 6.360 44.687 2352 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.57 % Favored : 96.00 % Rotamer: Outliers : 2.25 % Allowed : 19.55 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.29 (0.20), residues: 1876 helix: 1.12 (0.18), residues: 816 sheet: -1.37 (0.26), residues: 368 loop : 0.21 (0.27), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 465 TYR 0.015 0.001 TYR A 42 PHE 0.014 0.001 PHE C 499 TRP 0.009 0.001 TRP E 387 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (15932) covalent geometry : angle 0.52641 / 0.27 (21548) hydrogen bonds : bond 0.03036 / 1.99 ( 656) hydrogen bonds : angle 4.66488 / 3.36 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10462.88 seconds wall clock time: 177 minutes 21.22 seconds (10641.22 seconds total)