Starting phenix.real_space_refine on Sat Jul 4 12:26:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s89_24891/07_2026/7s89_24891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s89_24891/07_2026/7s89_24891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s89_24891/07_2026/7s89_24891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s89_24891/07_2026/7s89_24891.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s89_24891/07_2026/7s89_24891.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s89_24891/07_2026/7s89_24891.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s89_24891/07_2026/7s89_24891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s89_24891/07_2026/7s89_24891.map" } resolution = 2.54 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 8 5.49 5 S 156 5.16 5 C 13436 2.51 5 N 3232 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20425 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "B" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "A" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 339 Unusual residues: {' CA': 1, 'PCW': 1, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 5, 'POV:plan-3': 5, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 318 Unusual residues: {'PCW': 1, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 4, 'POV:plan-3': 4, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 298 Unusual residues: {'PCW': 1, 'POV': 6, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'POV:plan-2': 3, 'POV:plan-1': 1, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Restraints were copied for chains: C Time building chain proxies: 7.41, per 1000 atoms: 0.36 Number of scatterers: 20425 At special positions: 0 Unit cell: (125.179, 125.179, 119.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 156 16.00 P 8 15.00 O 3592 8.00 N 3232 7.00 C 13436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 70 " - pdb=" SG CYS C 70 " distance=0.00 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 157 " distance=0.00 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 172 " distance=0.00 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 213 " distance=0.00 Simple disulfide: pdb=" SG CYS C 330 " - pdb=" SG CYS C 330 " distance=0.00 Simple disulfide: pdb=" SG CYS C 342 " - pdb=" SG CYS C 342 " distance=0.00 Simple disulfide: pdb=" SG CYS C 346 " - pdb=" SG CYS C 346 " distance=0.00 Simple disulfide: pdb=" SG CYS C 347 " - pdb=" SG CYS C 347 " distance=0.00 Simple disulfide: pdb=" SG CYS C 463 " - pdb=" SG CYS C 463 " distance=0.00 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 494 " distance=0.00 Simple disulfide: pdb=" SG CYS C 611 " - pdb=" SG CYS C 611 " distance=0.00 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 619 " distance=0.00 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: 1.77 Conformation dependent library (CDL) restraints added in 790.3 milliseconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 8 sheets defined 65.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.509A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.535A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.556A pdb=" N PHE A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.646A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.575A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.607A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 308 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.512A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.063A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 Processing helix chain 'A' and resid 424 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.533A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 4.859A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.854A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.618A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.508A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.535A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.556A pdb=" N PHE B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.646A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.575A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.607A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.512A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.062A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.533A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 4.858A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.853A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.618A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.509A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.535A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.556A pdb=" N PHE C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.646A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.576A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.607A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 308 Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.512A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.063A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 Processing helix chain 'C' and resid 424 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.533A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 4.859A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.854A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.619A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.509A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.536A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.555A pdb=" N PHE D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.646A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.575A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.607A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 308 Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.512A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.062A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 Processing helix chain 'D' and resid 424 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.532A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 4.858A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.853A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.619A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.635A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.635A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.634A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.634A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1096 hydrogen bonds defined for protein. 3144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3126 1.31 - 1.44: 5344 1.44 - 1.57: 12018 1.57 - 1.69: 16 1.69 - 1.82: 264 Bond restraints: 20768 Sorted by residual: bond pdb=" C29 POV D 710 " pdb="C210 POV D 710 " ideal model delta sigma weight residual 1.333 1.550 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C29 POV C 708 " pdb="C210 POV C 708 " ideal model delta sigma weight residual 1.333 1.550 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C29 POV A 807 " pdb="C210 POV A 807 " ideal model delta sigma weight residual 1.333 1.550 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C29 POV B 708 " pdb="C210 POV B 708 " ideal model delta sigma weight residual 1.333 1.549 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C21 POV D 704 " pdb=" O21 POV D 704 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 20763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 27411 3.46 - 6.92: 456 6.92 - 10.38: 85 10.38 - 13.84: 44 13.84 - 17.30: 4 Bond angle restraints: 28000 Sorted by residual: angle pdb=" C28 POV B 708 " pdb=" C29 POV B 708 " pdb="C210 POV B 708 " ideal model delta sigma weight residual 127.79 110.49 17.30 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C28 POV D 710 " pdb=" C29 POV D 710 " pdb="C210 POV D 710 " ideal model delta sigma weight residual 127.79 110.50 17.29 3.00e+00 1.11e-01 3.32e+01 angle pdb=" C28 POV A 807 " pdb=" C29 POV A 807 " pdb="C210 POV A 807 " ideal model delta sigma weight residual 127.79 110.56 17.23 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C28 POV C 708 " pdb=" C29 POV C 708 " pdb="C210 POV C 708 " ideal model delta sigma weight residual 127.79 110.58 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C12 POV D 708 " pdb=" N POV D 708 " pdb=" C14 POV D 708 " ideal model delta sigma weight residual 107.13 120.91 -13.78 3.00e+00 1.11e-01 2.11e+01 ... (remaining 27995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.55: 11880 31.55 - 63.09: 536 63.09 - 94.64: 36 94.64 - 126.18: 4 126.18 - 157.73: 16 Dihedral angle restraints: 12472 sinusoidal: 5508 harmonic: 6964 Sorted by residual: dihedral pdb=" CB CYS C 70 " pdb=" SG CYS C 70 " pdb=" SG CYS C 70 " pdb=" CB CYS C 70 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS C 157 " pdb=" SG CYS C 157 " pdb=" SG CYS C 157 " pdb=" CB CYS C 157 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS C 172 " pdb=" SG CYS C 172 " pdb=" SG CYS C 172 " pdb=" CB CYS C 172 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 ... (remaining 12469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2841 0.097 - 0.194: 231 0.194 - 0.291: 28 0.291 - 0.388: 12 0.388 - 0.485: 4 Chirality restraints: 3116 Sorted by residual: chirality pdb=" CG LEU C 458 " pdb=" CB LEU C 458 " pdb=" CD1 LEU C 458 " pdb=" CD2 LEU C 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" CG LEU B 458 " pdb=" CB LEU B 458 " pdb=" CD1 LEU B 458 " pdb=" CD2 LEU B 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.85e+00 ... (remaining 3113 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 230 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO D 231 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 231 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 231 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 230 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO B 231 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 231 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 231 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 230 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO C 231 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 231 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 231 " -0.043 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3422 2.76 - 3.29: 18865 3.29 - 3.83: 34590 3.83 - 4.36: 44769 4.36 - 4.90: 72306 Nonbonded interactions: 173952 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.223 3.040 nonbonded pdb=" OE2 GLU D 535 " pdb=" O HOH D 801 " model vdw 2.293 3.040 ... (remaining 173947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or (resid 810 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'B' and (resid 28 through 637 or (resid 710 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'C' and (resid 28 through 637 or (resid 710 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'D' and (resid 28 through 637 or (resid 710 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216)))) } 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=0.45 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.460 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 0.217 20768 Z= 0.524 Angle : 1.281 17.305 28012 Z= 0.617 Chirality : 0.065 0.485 3116 Planarity : 0.009 0.078 3416 Dihedral : 16.921 157.730 7944 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.74 % Allowed : 2.86 % Favored : 95.40 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.14), residues: 2360 helix: -2.75 (0.09), residues: 1464 sheet: -1.10 (0.53), residues: 84 loop : -1.06 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 470 TYR 0.019 0.004 TYR C 349 PHE 0.032 0.005 PHE A 169 TRP 0.021 0.003 TRP D 593 HIS 0.021 0.004 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.01211 / 0.52 (20768) covalent geometry : angle 1.28134 / 0.62 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.24640 / 16.43 ( 1096) hydrogen bonds : angle 7.29950 / 5.18 ( 3144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 522 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6745 (tm) REVERT: A 98 LEU cc_start: 0.5990 (mt) cc_final: 0.5504 (tt) REVERT: A 233 ASP cc_start: 0.7091 (p0) cc_final: 0.6868 (p0) REVERT: A 260 MET cc_start: 0.7738 (tpt) cc_final: 0.7259 (tpt) REVERT: A 358 ASN cc_start: 0.7182 (m110) cc_final: 0.6928 (m110) REVERT: A 383 ASP cc_start: 0.7557 (m-30) cc_final: 0.7202 (m-30) REVERT: A 458 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8597 (mt) REVERT: B 260 MET cc_start: 0.7725 (tpt) cc_final: 0.7213 (tpt) REVERT: B 263 ARG cc_start: 0.7750 (mtt-85) cc_final: 0.7446 (mtp85) REVERT: B 358 ASN cc_start: 0.7133 (m110) cc_final: 0.6857 (m110) REVERT: B 383 ASP cc_start: 0.7533 (m-30) cc_final: 0.7176 (m-30) REVERT: B 434 PHE cc_start: 0.7601 (t80) cc_final: 0.7285 (t80) REVERT: B 458 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8620 (mt) REVERT: C 260 MET cc_start: 0.7719 (tpt) cc_final: 0.7203 (tpt) REVERT: C 358 ASN cc_start: 0.7168 (m110) cc_final: 0.6925 (m110) REVERT: C 383 ASP cc_start: 0.7585 (m-30) cc_final: 0.7245 (m-30) REVERT: C 434 PHE cc_start: 0.7625 (t80) cc_final: 0.7308 (t80) REVERT: C 458 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8640 (mt) REVERT: D 83 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6605 (tm) REVERT: D 85 ILE cc_start: 0.7656 (mm) cc_final: 0.7311 (mp) REVERT: D 93 GLU cc_start: 0.7432 (mp0) cc_final: 0.7217 (mp0) REVERT: D 257 GLN cc_start: 0.7447 (mt0) cc_final: 0.7228 (mt0) REVERT: D 260 MET cc_start: 0.7644 (tpt) cc_final: 0.7109 (tpt) REVERT: D 263 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.7419 (mtp85) REVERT: D 358 ASN cc_start: 0.7151 (m110) cc_final: 0.6826 (m110) REVERT: D 383 ASP cc_start: 0.7621 (m-30) cc_final: 0.7156 (m-30) REVERT: D 434 PHE cc_start: 0.7585 (t80) cc_final: 0.7207 (t80) REVERT: D 458 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8568 (mt) outliers start: 36 outliers final: 5 residues processed: 550 average time/residue: 0.6875 time to fit residues: 422.1877 Evaluate side-chains 424 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 413 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 62 ASN A 174 ASN A 217 ASN A 365 ASN A 369 GLN A 374 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN B 37 ASN B 174 ASN B 217 ASN B 365 ASN B 369 GLN B 374 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN C 174 ASN C 217 ASN C 365 ASN C 369 GLN C 374 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 174 ASN D 217 ASN D 365 ASN D 369 GLN D 374 GLN ** D 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121509 restraints weight = 20427.346| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.39 r_work: 0.3108 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20768 Z= 0.153 Angle : 0.670 9.800 28012 Z= 0.335 Chirality : 0.041 0.203 3116 Planarity : 0.006 0.058 3416 Dihedral : 18.638 164.835 3373 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.91 % Allowed : 10.85 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 2360 helix: -0.13 (0.12), residues: 1468 sheet: -0.80 (0.54), residues: 84 loop : -0.12 (0.24), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 606 TYR 0.016 0.002 TYR A 524 PHE 0.014 0.002 PHE A 456 TRP 0.013 0.002 TRP D 593 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (20768) covalent geometry : angle 0.66972 / 0.33 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.05433 / 3.60 ( 1096) hydrogen bonds : angle 4.24088 / 2.98 ( 3144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 453 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8300 (tt0) cc_final: 0.7947 (tt0) REVERT: A 218 LEU cc_start: 0.8116 (tt) cc_final: 0.7916 (tp) REVERT: A 309 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8053 (p0) REVERT: A 358 ASN cc_start: 0.7325 (m110) cc_final: 0.7058 (m110) REVERT: A 383 ASP cc_start: 0.7999 (m-30) cc_final: 0.7595 (m-30) REVERT: A 588 GLU cc_start: 0.8313 (pt0) cc_final: 0.7905 (pt0) REVERT: A 610 ARG cc_start: 0.6700 (mmp-170) cc_final: 0.6394 (tpm170) REVERT: B 88 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7126 (mt) REVERT: B 96 MET cc_start: 0.6409 (mtp) cc_final: 0.6079 (mmm) REVERT: B 177 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6669 (mm-30) REVERT: B 218 LEU cc_start: 0.8132 (tt) cc_final: 0.7899 (tp) REVERT: B 260 MET cc_start: 0.7945 (tpt) cc_final: 0.7667 (tpt) REVERT: B 309 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 328 TYR cc_start: 0.8518 (m-10) cc_final: 0.8307 (m-80) REVERT: B 358 ASN cc_start: 0.7221 (m110) cc_final: 0.6954 (m110) REVERT: B 383 ASP cc_start: 0.8023 (m-30) cc_final: 0.7632 (m-30) REVERT: B 588 GLU cc_start: 0.8339 (pt0) cc_final: 0.7951 (pt0) REVERT: B 610 ARG cc_start: 0.6679 (mmp-170) cc_final: 0.6353 (tpt170) REVERT: C 88 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7080 (mt) REVERT: C 177 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6685 (mm-30) REVERT: C 218 LEU cc_start: 0.8117 (tt) cc_final: 0.7864 (tp) REVERT: C 309 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8056 (p0) REVERT: C 358 ASN cc_start: 0.7222 (m110) cc_final: 0.6944 (m110) REVERT: C 381 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7360 (mtpp) REVERT: C 383 ASP cc_start: 0.8006 (m-30) cc_final: 0.7641 (m-30) REVERT: C 588 GLU cc_start: 0.8348 (pt0) cc_final: 0.7952 (pt0) REVERT: C 610 ARG cc_start: 0.6715 (mmp-170) cc_final: 0.6344 (tpm170) REVERT: D 96 MET cc_start: 0.6376 (mtp) cc_final: 0.6054 (mmm) REVERT: D 213 CYS cc_start: 0.7952 (m) cc_final: 0.7747 (t) REVERT: D 218 LEU cc_start: 0.8154 (tt) cc_final: 0.7903 (tp) REVERT: D 257 GLN cc_start: 0.7882 (mt0) cc_final: 0.7670 (mt0) REVERT: D 260 MET cc_start: 0.7930 (tpt) cc_final: 0.7658 (tpt) REVERT: D 309 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8060 (p0) REVERT: D 358 ASN cc_start: 0.7242 (m110) cc_final: 0.6966 (m110) REVERT: D 383 ASP cc_start: 0.7976 (m-30) cc_final: 0.7540 (m-30) REVERT: D 588 GLU cc_start: 0.8348 (pt0) cc_final: 0.7976 (pt0) REVERT: D 610 ARG cc_start: 0.6717 (mmp-170) cc_final: 0.6387 (tpt170) outliers start: 60 outliers final: 25 residues processed: 482 average time/residue: 0.6598 time to fit residues: 355.8344 Evaluate side-chains 419 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 388 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 128 optimal weight: 0.3980 chunk 199 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN B 208 ASN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.168401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123046 restraints weight = 20467.601| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.49 r_work: 0.3113 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20768 Z= 0.137 Angle : 0.614 11.877 28012 Z= 0.306 Chirality : 0.040 0.194 3116 Planarity : 0.005 0.053 3416 Dihedral : 17.192 166.098 3363 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.96 % Allowed : 12.74 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2360 helix: 0.88 (0.13), residues: 1468 sheet: -0.71 (0.56), residues: 84 loop : 0.13 (0.25), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 606 TYR 0.019 0.002 TYR B 324 PHE 0.017 0.002 PHE A 537 TRP 0.010 0.001 TRP C 593 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (20768) covalent geometry : angle 0.61421 / 0.31 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.04537 / 3.03 ( 1096) hydrogen bonds : angle 4.01140 / 2.81 ( 3144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 386 time to evaluate : 0.800 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 42 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6708 (ttmm) REVERT: A 108 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6354 (mm-30) REVERT: A 110 MET cc_start: 0.7271 (mtp) cc_final: 0.7012 (mtm) REVERT: A 118 GLN cc_start: 0.8227 (tt0) cc_final: 0.7937 (tt0) REVERT: A 175 SER cc_start: 0.7884 (t) cc_final: 0.7632 (t) REVERT: A 309 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7892 (t0) REVERT: A 324 TYR cc_start: 0.8183 (m-80) cc_final: 0.7955 (m-80) REVERT: A 328 TYR cc_start: 0.8451 (m-10) cc_final: 0.8246 (m-80) REVERT: A 358 ASN cc_start: 0.7288 (m110) cc_final: 0.6999 (m110) REVERT: A 381 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7343 (mtpp) REVERT: A 383 ASP cc_start: 0.8142 (m-30) cc_final: 0.7823 (m-30) REVERT: B 96 MET cc_start: 0.6372 (mtp) cc_final: 0.6003 (mmm) REVERT: B 99 MET cc_start: 0.5338 (mmm) cc_final: 0.5080 (mmp) REVERT: B 257 GLN cc_start: 0.7966 (mt0) cc_final: 0.7764 (tt0) REVERT: B 260 MET cc_start: 0.7957 (tpt) cc_final: 0.7620 (tpt) REVERT: B 309 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7835 (t0) REVERT: B 358 ASN cc_start: 0.7171 (m110) cc_final: 0.6926 (m110) REVERT: B 381 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7467 (mttp) REVERT: B 383 ASP cc_start: 0.8102 (m-30) cc_final: 0.7790 (m-30) REVERT: C 90 ASP cc_start: 0.6929 (t70) cc_final: 0.6467 (t70) REVERT: C 96 MET cc_start: 0.6417 (mtp) cc_final: 0.6094 (mmm) REVERT: C 99 MET cc_start: 0.5448 (mmm) cc_final: 0.5189 (mmp) REVERT: C 110 MET cc_start: 0.7268 (mtp) cc_final: 0.6999 (mtm) REVERT: C 279 ASP cc_start: 0.8344 (t0) cc_final: 0.8015 (t0) REVERT: C 309 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7829 (t0) REVERT: C 358 ASN cc_start: 0.7245 (m110) cc_final: 0.6978 (m110) REVERT: C 383 ASP cc_start: 0.8046 (m-30) cc_final: 0.7697 (m-30) REVERT: D 42 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6766 (ttmm) REVERT: D 88 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6778 (mt) REVERT: D 90 ASP cc_start: 0.6911 (t70) cc_final: 0.6451 (t70) REVERT: D 96 MET cc_start: 0.6388 (mtp) cc_final: 0.6102 (mmm) REVERT: D 110 MET cc_start: 0.7280 (mtp) cc_final: 0.7037 (mtm) REVERT: D 118 GLN cc_start: 0.8257 (tt0) cc_final: 0.8037 (tt0) REVERT: D 218 LEU cc_start: 0.8107 (tt) cc_final: 0.7897 (tp) REVERT: D 260 MET cc_start: 0.7966 (tpt) cc_final: 0.7630 (tpt) REVERT: D 309 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7840 (t0) REVERT: D 358 ASN cc_start: 0.7201 (m110) cc_final: 0.6928 (m110) REVERT: D 381 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7496 (mttp) REVERT: D 383 ASP cc_start: 0.8066 (m-30) cc_final: 0.7721 (m-30) outliers start: 61 outliers final: 22 residues processed: 433 average time/residue: 0.6612 time to fit residues: 320.1699 Evaluate side-chains 388 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 359 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 121 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 374 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 374 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** D 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123321 restraints weight = 20464.361| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.44 r_work: 0.3131 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20768 Z= 0.130 Angle : 0.597 11.933 28012 Z= 0.294 Chirality : 0.039 0.192 3116 Planarity : 0.005 0.050 3416 Dihedral : 16.476 167.374 3363 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.96 % Allowed : 13.91 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.18), residues: 2360 helix: 1.32 (0.14), residues: 1472 sheet: -0.55 (0.57), residues: 84 loop : 0.17 (0.25), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 606 TYR 0.016 0.002 TYR B 115 PHE 0.015 0.001 PHE A 537 TRP 0.009 0.001 TRP A 593 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (20768) covalent geometry : angle 0.59693 / 0.29 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.04248 / 2.84 ( 1096) hydrogen bonds : angle 3.87662 / 2.72 ( 3144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 378 time to evaluate : 0.691 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 42 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6747 (ttmm) REVERT: A 108 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6359 (mm-30) REVERT: A 118 GLN cc_start: 0.8174 (tt0) cc_final: 0.7886 (tt0) REVERT: A 175 SER cc_start: 0.7877 (t) cc_final: 0.7657 (t) REVERT: A 279 ASP cc_start: 0.8330 (t0) cc_final: 0.8042 (t0) REVERT: A 322 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8288 (mtmt) REVERT: A 324 TYR cc_start: 0.8146 (m-80) cc_final: 0.7925 (m-80) REVERT: A 358 ASN cc_start: 0.7290 (m110) cc_final: 0.7019 (m110) REVERT: A 383 ASP cc_start: 0.8093 (m-30) cc_final: 0.7782 (m-30) REVERT: A 612 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6948 (mm) REVERT: B 42 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6796 (ttmm) REVERT: B 80 GLU cc_start: 0.6984 (pm20) cc_final: 0.6711 (pm20) REVERT: B 96 MET cc_start: 0.6385 (mtp) cc_final: 0.6130 (mmm) REVERT: B 118 GLN cc_start: 0.8247 (tt0) cc_final: 0.8006 (tt0) REVERT: B 260 MET cc_start: 0.7971 (tpt) cc_final: 0.7630 (tpt) REVERT: B 279 ASP cc_start: 0.8362 (t0) cc_final: 0.8098 (t0) REVERT: B 322 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8309 (mtmt) REVERT: B 358 ASN cc_start: 0.7199 (m110) cc_final: 0.6960 (m110) REVERT: B 381 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7498 (mttp) REVERT: B 383 ASP cc_start: 0.8084 (m-30) cc_final: 0.7779 (m-30) REVERT: B 612 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6895 (mm) REVERT: C 42 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6827 (ttmm) REVERT: C 90 ASP cc_start: 0.6804 (t70) cc_final: 0.6302 (t70) REVERT: C 96 MET cc_start: 0.6456 (mtp) cc_final: 0.6179 (mmm) REVERT: C 118 GLN cc_start: 0.8164 (tt0) cc_final: 0.7930 (tt0) REVERT: C 358 ASN cc_start: 0.7185 (m110) cc_final: 0.6899 (m110) REVERT: C 381 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7457 (mtpp) REVERT: C 383 ASP cc_start: 0.8103 (m-30) cc_final: 0.7800 (m-30) REVERT: D 42 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6779 (ttmm) REVERT: D 85 ILE cc_start: 0.7477 (mm) cc_final: 0.7276 (mp) REVERT: D 90 ASP cc_start: 0.6810 (t70) cc_final: 0.6283 (t70) REVERT: D 96 MET cc_start: 0.6450 (mtp) cc_final: 0.6228 (mmm) REVERT: D 99 MET cc_start: 0.5464 (mmm) cc_final: 0.5166 (mmp) REVERT: D 118 GLN cc_start: 0.8170 (tt0) cc_final: 0.7924 (tt0) REVERT: D 260 MET cc_start: 0.7986 (tpt) cc_final: 0.7642 (tpt) REVERT: D 279 ASP cc_start: 0.8350 (t0) cc_final: 0.8120 (t0) REVERT: D 358 ASN cc_start: 0.7182 (m110) cc_final: 0.6931 (m110) REVERT: D 381 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7530 (mttp) REVERT: D 383 ASP cc_start: 0.8061 (m-30) cc_final: 0.7764 (m-30) outliers start: 61 outliers final: 25 residues processed: 427 average time/residue: 0.6663 time to fit residues: 316.9175 Evaluate side-chains 401 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 368 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 75 optimal weight: 0.0050 chunk 113 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 374 GLN C 257 GLN C 374 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121114 restraints weight = 20359.455| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.46 r_work: 0.3112 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20768 Z= 0.127 Angle : 0.595 11.516 28012 Z= 0.294 Chirality : 0.039 0.187 3116 Planarity : 0.005 0.050 3416 Dihedral : 15.941 167.027 3363 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.62 % Allowed : 15.26 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.18), residues: 2360 helix: 1.47 (0.14), residues: 1472 sheet: -0.49 (0.58), residues: 84 loop : 0.14 (0.25), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 606 TYR 0.017 0.002 TYR A 115 PHE 0.013 0.001 PHE B 537 TRP 0.009 0.001 TRP A 593 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (20768) covalent geometry : angle 0.59561 / 0.29 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.04111 / 2.75 ( 1096) hydrogen bonds : angle 3.84625 / 2.70 ( 3144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 376 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6755 (ttmm) REVERT: A 108 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6354 (mm-30) REVERT: A 118 GLN cc_start: 0.8243 (tt0) cc_final: 0.7772 (tt0) REVERT: A 130 MET cc_start: 0.6468 (tpt) cc_final: 0.6145 (tpp) REVERT: A 175 SER cc_start: 0.7880 (t) cc_final: 0.7675 (t) REVERT: A 324 TYR cc_start: 0.8241 (m-80) cc_final: 0.8020 (m-80) REVERT: A 358 ASN cc_start: 0.7295 (m110) cc_final: 0.7045 (m110) REVERT: A 381 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7432 (mtpp) REVERT: A 383 ASP cc_start: 0.8110 (m-30) cc_final: 0.7797 (m-30) REVERT: A 622 GLU cc_start: 0.6789 (pt0) cc_final: 0.6496 (pp20) REVERT: B 42 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6778 (ttmm) REVERT: B 90 ASP cc_start: 0.6731 (t70) cc_final: 0.6259 (t70) REVERT: B 99 MET cc_start: 0.5813 (mmp) cc_final: 0.5561 (mmm) REVERT: B 218 LEU cc_start: 0.8326 (tm) cc_final: 0.8117 (tp) REVERT: B 279 ASP cc_start: 0.8370 (t0) cc_final: 0.8152 (t0) REVERT: B 358 ASN cc_start: 0.7201 (m110) cc_final: 0.6925 (m110) REVERT: B 381 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7487 (mttp) REVERT: B 383 ASP cc_start: 0.8105 (m-30) cc_final: 0.7804 (m-30) REVERT: B 605 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 610 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6398 (tpm170) REVERT: B 622 GLU cc_start: 0.6774 (pt0) cc_final: 0.6492 (pp20) REVERT: C 42 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6771 (ttmm) REVERT: C 90 ASP cc_start: 0.6814 (t70) cc_final: 0.6256 (t70) REVERT: C 99 MET cc_start: 0.5857 (mmp) cc_final: 0.5637 (mmm) REVERT: C 110 MET cc_start: 0.7222 (mtp) cc_final: 0.6880 (mtp) REVERT: C 118 GLN cc_start: 0.8149 (tt0) cc_final: 0.7757 (tt0) REVERT: C 358 ASN cc_start: 0.7188 (m110) cc_final: 0.6880 (m110) REVERT: C 381 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7520 (mttp) REVERT: C 383 ASP cc_start: 0.8123 (m-30) cc_final: 0.7823 (m-30) REVERT: C 622 GLU cc_start: 0.6855 (pt0) cc_final: 0.6553 (pp20) REVERT: D 42 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6754 (ttmm) REVERT: D 90 ASP cc_start: 0.6880 (t70) cc_final: 0.6323 (t70) REVERT: D 96 MET cc_start: 0.6478 (mtp) cc_final: 0.6212 (mmm) REVERT: D 99 MET cc_start: 0.5482 (mmm) cc_final: 0.5229 (mmp) REVERT: D 110 MET cc_start: 0.7170 (mtp) cc_final: 0.6855 (mtp) REVERT: D 118 GLN cc_start: 0.8120 (tt0) cc_final: 0.7718 (tt0) REVERT: D 279 ASP cc_start: 0.8357 (t0) cc_final: 0.8137 (t0) REVERT: D 358 ASN cc_start: 0.7196 (m110) cc_final: 0.6886 (m110) REVERT: D 381 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7508 (mttp) REVERT: D 383 ASP cc_start: 0.8092 (m-30) cc_final: 0.7792 (m-30) REVERT: D 622 GLU cc_start: 0.6786 (pt0) cc_final: 0.6475 (pp20) outliers start: 54 outliers final: 25 residues processed: 419 average time/residue: 0.6256 time to fit residues: 293.7543 Evaluate side-chains 396 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 366 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 610 ARG Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 170 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN A 374 GLN B 257 GLN B 374 GLN C 257 GLN C 374 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118120 restraints weight = 20209.820| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.48 r_work: 0.3041 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 20768 Z= 0.237 Angle : 0.700 7.818 28012 Z= 0.349 Chirality : 0.046 0.227 3116 Planarity : 0.006 0.055 3416 Dihedral : 16.463 168.645 3363 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.96 % Allowed : 14.20 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2360 helix: 1.13 (0.13), residues: 1472 sheet: -0.88 (0.56), residues: 88 loop : 0.20 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 606 TYR 0.018 0.003 TYR B 555 PHE 0.018 0.002 PHE D 537 TRP 0.008 0.002 TRP C 593 HIS 0.005 0.002 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (20768) covalent geometry : angle 0.70055 / 0.35 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.05098 / 3.41 ( 1096) hydrogen bonds : angle 4.11711 / 2.90 ( 3144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 378 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6826 (ttmm) REVERT: A 90 ASP cc_start: 0.6733 (t70) cc_final: 0.6222 (t70) REVERT: A 108 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6478 (mm-30) REVERT: A 175 SER cc_start: 0.7929 (t) cc_final: 0.7703 (t) REVERT: A 324 TYR cc_start: 0.8325 (m-80) cc_final: 0.8025 (m-80) REVERT: A 358 ASN cc_start: 0.7402 (m110) cc_final: 0.7198 (m110) REVERT: A 381 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7588 (mttp) REVERT: A 383 ASP cc_start: 0.8143 (m-30) cc_final: 0.7819 (m-30) REVERT: B 42 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6843 (ttmm) REVERT: B 90 ASP cc_start: 0.6878 (t70) cc_final: 0.6396 (t70) REVERT: B 130 MET cc_start: 0.6575 (tpt) cc_final: 0.6360 (tpp) REVERT: B 279 ASP cc_start: 0.8353 (t0) cc_final: 0.8095 (t0) REVERT: B 357 ASN cc_start: 0.7607 (p0) cc_final: 0.7400 (p0) REVERT: B 358 ASN cc_start: 0.7317 (m110) cc_final: 0.7024 (m110) REVERT: B 381 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7552 (mttp) REVERT: B 383 ASP cc_start: 0.8154 (m-30) cc_final: 0.7837 (m-30) REVERT: C 42 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6861 (ttmm) REVERT: C 80 GLU cc_start: 0.7140 (pm20) cc_final: 0.6881 (pm20) REVERT: C 90 ASP cc_start: 0.6969 (t70) cc_final: 0.6669 (t70) REVERT: C 108 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6512 (mm-30) REVERT: C 130 MET cc_start: 0.6538 (tpt) cc_final: 0.6320 (tpp) REVERT: C 233 ASP cc_start: 0.7234 (p0) cc_final: 0.6809 (p0) REVERT: C 358 ASN cc_start: 0.7218 (m110) cc_final: 0.7015 (m110) REVERT: C 381 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7571 (mttp) REVERT: C 383 ASP cc_start: 0.8156 (m-30) cc_final: 0.7840 (m-30) REVERT: D 42 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6851 (ttmm) REVERT: D 90 ASP cc_start: 0.6935 (t70) cc_final: 0.6641 (t70) REVERT: D 99 MET cc_start: 0.5424 (mmm) cc_final: 0.5172 (mmp) REVERT: D 279 ASP cc_start: 0.8346 (t0) cc_final: 0.8103 (t0) REVERT: D 358 ASN cc_start: 0.7226 (m110) cc_final: 0.7024 (m110) REVERT: D 381 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7576 (mttp) REVERT: D 383 ASP cc_start: 0.8117 (m-30) cc_final: 0.7800 (m-30) REVERT: D 606 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7525 (ttm-80) REVERT: D 610 ARG cc_start: 0.6591 (tpm170) cc_final: 0.6338 (tpp-160) outliers start: 61 outliers final: 28 residues processed: 423 average time/residue: 0.6407 time to fit residues: 303.6915 Evaluate side-chains 391 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 359 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 91 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 233 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 116 optimal weight: 0.0000 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN B 257 GLN B 374 GLN C 118 GLN C 257 GLN C 374 GLN D 257 GLN D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.164778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116491 restraints weight = 20311.920| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.49 r_work: 0.3050 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20768 Z= 0.218 Angle : 0.697 8.296 28012 Z= 0.344 Chirality : 0.045 0.203 3116 Planarity : 0.005 0.055 3416 Dihedral : 16.287 168.949 3363 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.71 % Allowed : 15.55 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2360 helix: 1.11 (0.13), residues: 1472 sheet: -0.98 (0.55), residues: 88 loop : 0.13 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 606 TYR 0.020 0.003 TYR B 324 PHE 0.015 0.002 PHE B 537 TRP 0.019 0.002 TRP B 613 HIS 0.004 0.001 HIS D 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (20768) covalent geometry : angle 0.69706 / 0.34 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.04951 / 3.32 ( 1096) hydrogen bonds : angle 4.10977 / 2.89 ( 3144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 381 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6842 (ttmm) REVERT: A 80 GLU cc_start: 0.6728 (pt0) cc_final: 0.6219 (pm20) REVERT: A 90 ASP cc_start: 0.6717 (t70) cc_final: 0.6220 (t70) REVERT: A 108 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6409 (mm-30) REVERT: A 110 MET cc_start: 0.7124 (mtp) cc_final: 0.6917 (mtp) REVERT: A 175 SER cc_start: 0.7884 (t) cc_final: 0.7668 (t) REVERT: A 324 TYR cc_start: 0.8270 (m-80) cc_final: 0.7995 (m-80) REVERT: A 381 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7566 (mttp) REVERT: A 383 ASP cc_start: 0.8082 (m-30) cc_final: 0.7838 (m-30) REVERT: A 610 ARG cc_start: 0.6623 (tpm170) cc_final: 0.6320 (tpp-160) REVERT: A 622 GLU cc_start: 0.6808 (pt0) cc_final: 0.6555 (pp20) REVERT: B 42 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6883 (ttmm) REVERT: B 80 GLU cc_start: 0.7021 (pm20) cc_final: 0.6794 (pm20) REVERT: B 90 ASP cc_start: 0.6910 (t70) cc_final: 0.6656 (t70) REVERT: B 110 MET cc_start: 0.7037 (mtp) cc_final: 0.6794 (mtp) REVERT: B 357 ASN cc_start: 0.7570 (p0) cc_final: 0.7366 (p0) REVERT: B 358 ASN cc_start: 0.7308 (m110) cc_final: 0.7056 (m110) REVERT: B 381 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7533 (mttp) REVERT: B 383 ASP cc_start: 0.8103 (m-30) cc_final: 0.7855 (m-30) REVERT: B 622 GLU cc_start: 0.6852 (pt0) cc_final: 0.6618 (pp20) REVERT: C 42 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6886 (ttmm) REVERT: C 90 ASP cc_start: 0.6937 (t70) cc_final: 0.6576 (t70) REVERT: C 233 ASP cc_start: 0.7275 (p0) cc_final: 0.6857 (p0) REVERT: C 322 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8276 (mtmt) REVERT: C 381 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7585 (mttp) REVERT: C 383 ASP cc_start: 0.8098 (m-30) cc_final: 0.7834 (m-30) REVERT: C 622 GLU cc_start: 0.6852 (pt0) cc_final: 0.6601 (pp20) REVERT: D 42 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6903 (ttmm) REVERT: D 90 ASP cc_start: 0.6890 (t70) cc_final: 0.6544 (t70) REVERT: D 130 MET cc_start: 0.6365 (tpt) cc_final: 0.6132 (tpp) REVERT: D 381 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7540 (mttp) REVERT: D 383 ASP cc_start: 0.8102 (m-30) cc_final: 0.7854 (m-30) REVERT: D 610 ARG cc_start: 0.6595 (tpm170) cc_final: 0.6318 (tpp-160) REVERT: D 622 GLU cc_start: 0.6799 (pt0) cc_final: 0.6551 (pp20) outliers start: 56 outliers final: 38 residues processed: 409 average time/residue: 0.6793 time to fit residues: 310.8507 Evaluate side-chains 409 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 366 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 150 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN A 374 GLN B 257 GLN B 374 GLN C 257 GLN C 374 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.167857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122561 restraints weight = 20345.454| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.40 r_work: 0.3118 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20768 Z= 0.128 Angle : 0.609 9.072 28012 Z= 0.300 Chirality : 0.039 0.192 3116 Planarity : 0.005 0.054 3416 Dihedral : 15.400 168.442 3363 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.18 % Allowed : 16.18 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.18), residues: 2360 helix: 1.51 (0.14), residues: 1472 sheet: -0.64 (0.57), residues: 88 loop : 0.11 (0.26), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 606 TYR 0.022 0.002 TYR B 324 PHE 0.011 0.001 PHE A 537 TRP 0.012 0.001 TRP C 593 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (20768) covalent geometry : angle 0.60898 / 0.30 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.04088 / 2.73 ( 1096) hydrogen bonds : angle 3.87990 / 2.73 ( 3144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 363 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6835 (ttmm) REVERT: A 80 GLU cc_start: 0.6747 (pt0) cc_final: 0.6287 (pm20) REVERT: A 90 ASP cc_start: 0.6703 (t70) cc_final: 0.6199 (t70) REVERT: A 108 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6359 (mm-30) REVERT: A 324 TYR cc_start: 0.8226 (m-80) cc_final: 0.8005 (m-80) REVERT: A 381 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7595 (mttp) REVERT: A 383 ASP cc_start: 0.8091 (m-30) cc_final: 0.7859 (m-30) REVERT: B 42 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6881 (ttmm) REVERT: B 80 GLU cc_start: 0.7045 (pm20) cc_final: 0.6731 (pm20) REVERT: B 90 ASP cc_start: 0.6885 (t70) cc_final: 0.6636 (t70) REVERT: B 99 MET cc_start: 0.5565 (mmm) cc_final: 0.4957 (mmp) REVERT: B 110 MET cc_start: 0.7100 (mtp) cc_final: 0.6877 (mtm) REVERT: B 358 ASN cc_start: 0.7296 (m110) cc_final: 0.7065 (m110) REVERT: B 381 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7491 (mttp) REVERT: B 383 ASP cc_start: 0.8092 (m-30) cc_final: 0.7846 (m-30) REVERT: C 42 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6890 (ttmm) REVERT: C 80 GLU cc_start: 0.7184 (pm20) cc_final: 0.6827 (pm20) REVERT: C 90 ASP cc_start: 0.6922 (t70) cc_final: 0.6579 (t70) REVERT: C 99 MET cc_start: 0.5619 (mmm) cc_final: 0.4979 (mmp) REVERT: C 381 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7548 (mttp) REVERT: C 383 ASP cc_start: 0.8100 (m-30) cc_final: 0.7862 (m-30) REVERT: D 42 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6876 (ttmm) REVERT: D 80 GLU cc_start: 0.7206 (pm20) cc_final: 0.6748 (pm20) REVERT: D 90 ASP cc_start: 0.6877 (t70) cc_final: 0.6536 (t70) REVERT: D 99 MET cc_start: 0.5611 (mmm) cc_final: 0.5245 (mmp) REVERT: D 260 MET cc_start: 0.8049 (tpt) cc_final: 0.7846 (tpt) REVERT: D 279 ASP cc_start: 0.8298 (t0) cc_final: 0.7991 (t0) REVERT: D 322 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8270 (mtmt) REVERT: D 381 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7484 (mttp) REVERT: D 383 ASP cc_start: 0.8082 (m-30) cc_final: 0.7832 (m-30) outliers start: 45 outliers final: 20 residues processed: 393 average time/residue: 0.6757 time to fit residues: 298.0454 Evaluate side-chains 376 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 351 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 234 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN A 374 GLN B 257 GLN B 374 GLN C 257 GLN C 374 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.166638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119168 restraints weight = 20221.285| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.58 r_work: 0.3078 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20768 Z= 0.161 Angle : 0.648 8.070 28012 Z= 0.319 Chirality : 0.042 0.235 3116 Planarity : 0.005 0.056 3416 Dihedral : 15.288 168.686 3361 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.94 % Allowed : 16.38 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.18), residues: 2360 helix: 1.55 (0.14), residues: 1448 sheet: -0.63 (0.56), residues: 88 loop : 0.23 (0.25), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 594 TYR 0.024 0.002 TYR D 324 PHE 0.013 0.002 PHE D 537 TRP 0.016 0.002 TRP A 613 HIS 0.004 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (20768) covalent geometry : angle 0.64852 / 0.32 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.04437 / 2.98 ( 1096) hydrogen bonds : angle 3.93308 / 2.77 ( 3144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 355 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6850 (ttmm) REVERT: A 80 GLU cc_start: 0.6737 (pt0) cc_final: 0.6261 (pm20) REVERT: A 90 ASP cc_start: 0.6819 (t70) cc_final: 0.6544 (t70) REVERT: A 108 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6349 (mm-30) REVERT: A 324 TYR cc_start: 0.8271 (m-80) cc_final: 0.8005 (m-80) REVERT: A 381 LYS cc_start: 0.7973 (mtpp) cc_final: 0.7542 (mttp) REVERT: A 383 ASP cc_start: 0.8082 (m-30) cc_final: 0.7820 (m-30) REVERT: B 42 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6871 (ttmm) REVERT: B 80 GLU cc_start: 0.7047 (pm20) cc_final: 0.6731 (pm20) REVERT: B 90 ASP cc_start: 0.6949 (t70) cc_final: 0.6674 (t0) REVERT: B 381 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7447 (mttp) REVERT: B 383 ASP cc_start: 0.8087 (m-30) cc_final: 0.7831 (m-30) REVERT: B 612 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7040 (mm) REVERT: C 42 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6858 (ttmm) REVERT: C 80 GLU cc_start: 0.7220 (pm20) cc_final: 0.6812 (pm20) REVERT: C 90 ASP cc_start: 0.6909 (t70) cc_final: 0.6610 (t0) REVERT: C 381 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7540 (mttp) REVERT: C 383 ASP cc_start: 0.8090 (m-30) cc_final: 0.7827 (m-30) REVERT: D 42 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6861 (ttmm) REVERT: D 80 GLU cc_start: 0.7187 (pm20) cc_final: 0.6626 (pm20) REVERT: D 90 ASP cc_start: 0.6904 (t70) cc_final: 0.6554 (t70) REVERT: D 260 MET cc_start: 0.8039 (tpt) cc_final: 0.7813 (tpt) REVERT: D 279 ASP cc_start: 0.8333 (t0) cc_final: 0.8079 (t0) REVERT: D 322 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8261 (mtmt) REVERT: D 381 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7469 (mttp) REVERT: D 383 ASP cc_start: 0.8079 (m-30) cc_final: 0.7810 (m-30) outliers start: 40 outliers final: 25 residues processed: 382 average time/residue: 0.6855 time to fit residues: 293.2820 Evaluate side-chains 381 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 350 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 178 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 162 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 17 optimal weight: 0.0010 chunk 104 optimal weight: 0.8980 chunk 233 optimal weight: 0.0670 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN A 374 GLN B 257 GLN B 374 GLN C 257 GLN C 374 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.171018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125608 restraints weight = 20531.256| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.48 r_work: 0.3174 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20768 Z= 0.113 Angle : 0.595 9.978 28012 Z= 0.290 Chirality : 0.038 0.190 3116 Planarity : 0.005 0.057 3416 Dihedral : 14.370 166.910 3361 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.36 % Allowed : 17.39 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.18), residues: 2360 helix: 1.80 (0.14), residues: 1448 sheet: -0.43 (0.59), residues: 88 loop : 0.13 (0.25), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 615 TYR 0.020 0.001 TYR B 324 PHE 0.009 0.001 PHE A 537 TRP 0.017 0.002 TRP D 583 HIS 0.003 0.001 HIS D 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (20768) covalent geometry : angle 0.59493 / 0.29 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.03646 / 2.45 ( 1096) hydrogen bonds : angle 3.72098 / 2.62 ( 3144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 367 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6779 (ttmm) REVERT: A 80 GLU cc_start: 0.6640 (pt0) cc_final: 0.6330 (pm20) REVERT: A 90 ASP cc_start: 0.6788 (t70) cc_final: 0.6495 (t70) REVERT: A 177 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 381 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7455 (mttp) REVERT: A 383 ASP cc_start: 0.8125 (m-30) cc_final: 0.7916 (m-30) REVERT: A 589 ARG cc_start: 0.7825 (ptm-80) cc_final: 0.7568 (ptm160) REVERT: B 42 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6790 (ttmm) REVERT: B 90 ASP cc_start: 0.6920 (t70) cc_final: 0.6699 (t0) REVERT: B 381 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7440 (mtpp) REVERT: B 383 ASP cc_start: 0.8088 (m-30) cc_final: 0.7858 (m-30) REVERT: C 42 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6786 (ttmm) REVERT: C 80 GLU cc_start: 0.7413 (pm20) cc_final: 0.7145 (pm20) REVERT: C 90 ASP cc_start: 0.6913 (t70) cc_final: 0.6621 (t0) REVERT: C 108 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6392 (mm-30) REVERT: C 150 THR cc_start: 0.8636 (m) cc_final: 0.8422 (m) REVERT: C 381 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7425 (mttp) REVERT: C 383 ASP cc_start: 0.8104 (m-30) cc_final: 0.7869 (m-30) REVERT: D 42 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6759 (ttmm) REVERT: D 80 GLU cc_start: 0.7140 (pm20) cc_final: 0.6594 (pm20) REVERT: D 90 ASP cc_start: 0.6884 (t70) cc_final: 0.6585 (t0) REVERT: D 108 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6345 (mm-30) REVERT: D 130 MET cc_start: 0.6381 (tpt) cc_final: 0.6172 (tpp) REVERT: D 208 ASN cc_start: 0.7728 (t0) cc_final: 0.7495 (t0) REVERT: D 218 LEU cc_start: 0.8259 (tm) cc_final: 0.8013 (tp) REVERT: D 260 MET cc_start: 0.8012 (tpt) cc_final: 0.7738 (tpt) REVERT: D 279 ASP cc_start: 0.8289 (t0) cc_final: 0.7962 (t0) REVERT: D 381 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7396 (mtpp) REVERT: D 383 ASP cc_start: 0.8079 (m-30) cc_final: 0.7843 (m-30) outliers start: 28 outliers final: 12 residues processed: 389 average time/residue: 0.6494 time to fit residues: 283.0646 Evaluate side-chains 372 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 356 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 0.9990 chunk 81 optimal weight: 0.0050 chunk 176 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN B 257 GLN C 257 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.169420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124732 restraints weight = 20339.896| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.48 r_work: 0.3115 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20768 Z= 0.125 Angle : 0.620 10.007 28012 Z= 0.301 Chirality : 0.039 0.193 3116 Planarity : 0.005 0.057 3416 Dihedral : 14.187 166.762 3361 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.78 % Allowed : 17.59 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.18), residues: 2360 helix: 1.83 (0.14), residues: 1448 sheet: -0.38 (0.58), residues: 88 loop : 0.18 (0.25), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 628 TYR 0.021 0.002 TYR B 324 PHE 0.012 0.001 PHE A 537 TRP 0.020 0.002 TRP C 583 HIS 0.003 0.001 HIS D 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (20768) covalent geometry : angle 0.61986 / 0.30 (28000) SS BOND : angle 0.00000 / 0.00 ( 12) hydrogen bonds : bond 0.03909 / 2.62 ( 1096) hydrogen bonds : angle 3.75926 / 2.64 ( 3144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9461.46 seconds wall clock time: 161 minutes 12.81 seconds (9672.81 seconds total)