Starting phenix.real_space_refine on Thu Mar 5 08:37:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s89_24891/03_2026/7s89_24891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s89_24891/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s89_24891/03_2026/7s89_24891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s89_24891/03_2026/7s89_24891.map" model { file = "/net/cci-nas-00/data/ceres_data/7s89_24891/03_2026/7s89_24891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s89_24891/03_2026/7s89_24891.cif" } 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-5986/lib/python3.9/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: 215 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: 185 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: 155 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: 7.12, per 1000 atoms: 0.35 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: 1.69 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.64 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: 3.59 Time building geometry restraints manager: 2.28 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: 12539 31.55 - 63.09: 629 63.09 - 94.64: 36 94.64 - 126.18: 4 126.18 - 157.73: 16 Dihedral angle restraints: 13224 sinusoidal: 6260 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 13221 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.390 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.020 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 16.969 157.730 8696 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 covalent geometry : bond 0.01211 (20768) covalent geometry : angle 1.28134 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.24640 ( 1096) hydrogen bonds : angle 7.29950 ( 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 : 0.837 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: 0.7323 time to fit residues: 446.4928 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 : 0.616 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3890 r_free = 0.3890 target = 0.168336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123278 restraints weight = 20427.616| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.52 r_work: 0.3118 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20768 Z= 0.151 Angle : 0.667 10.118 28012 Z= 0.333 Chirality : 0.041 0.202 3116 Planarity : 0.006 0.057 3416 Dihedral : 17.842 164.436 4125 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.96 % Allowed : 10.90 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2360 helix: -0.09 (0.12), residues: 1468 sheet: -0.79 (0.54), residues: 84 loop : -0.10 (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 555 PHE 0.013 0.002 PHE A 456 TRP 0.012 0.002 TRP D 593 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00340 (20768) covalent geometry : angle 0.66675 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.05216 ( 1096) hydrogen bonds : angle 4.22067 ( 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 515 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 454 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8283 (tt0) cc_final: 0.7923 (tt0) REVERT: A 218 LEU cc_start: 0.8060 (tt) cc_final: 0.7805 (tp) REVERT: A 309 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.8058 (p0) REVERT: A 358 ASN cc_start: 0.7315 (m110) cc_final: 0.7005 (m110) REVERT: A 381 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7338 (mtpp) REVERT: A 383 ASP cc_start: 0.8016 (m-30) cc_final: 0.7697 (m-30) REVERT: A 588 GLU cc_start: 0.8292 (pt0) cc_final: 0.7889 (pt0) REVERT: A 610 ARG cc_start: 0.6690 (mmp-170) cc_final: 0.6400 (tpm170) REVERT: B 96 MET cc_start: 0.6385 (mtp) cc_final: 0.6084 (mmm) REVERT: B 177 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6701 (mm-30) REVERT: B 213 CYS cc_start: 0.7943 (m) cc_final: 0.7738 (t) REVERT: B 218 LEU cc_start: 0.8094 (tt) cc_final: 0.7850 (tp) REVERT: B 260 MET cc_start: 0.7934 (tpt) cc_final: 0.7648 (tpt) REVERT: B 309 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8051 (p0) REVERT: B 324 TYR cc_start: 0.8234 (m-80) cc_final: 0.8005 (m-80) REVERT: B 358 ASN cc_start: 0.7208 (m110) cc_final: 0.6942 (m110) REVERT: B 381 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7330 (mtpp) REVERT: B 383 ASP cc_start: 0.7972 (m-30) cc_final: 0.7601 (m-30) REVERT: B 588 GLU cc_start: 0.8299 (pt0) cc_final: 0.7892 (pt0) REVERT: B 610 ARG cc_start: 0.6649 (mmp-170) cc_final: 0.6332 (tpt170) REVERT: C 96 MET cc_start: 0.6346 (mtp) cc_final: 0.6025 (mmm) REVERT: C 177 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6715 (mm-30) REVERT: C 213 CYS cc_start: 0.7932 (m) cc_final: 0.7731 (t) REVERT: C 218 LEU cc_start: 0.8093 (tt) cc_final: 0.7797 (tp) REVERT: C 309 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8044 (p0) REVERT: C 358 ASN cc_start: 0.7211 (m110) cc_final: 0.6934 (m110) REVERT: C 381 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7349 (mtpp) REVERT: C 383 ASP cc_start: 0.7988 (m-30) cc_final: 0.7613 (m-30) REVERT: C 588 GLU cc_start: 0.8325 (pt0) cc_final: 0.7925 (pt0) REVERT: C 610 ARG cc_start: 0.6708 (mmp-170) cc_final: 0.6353 (tpm170) REVERT: D 96 MET cc_start: 0.6370 (mtp) cc_final: 0.6050 (mmm) REVERT: D 218 LEU cc_start: 0.8101 (tt) cc_final: 0.7839 (tp) REVERT: D 260 MET cc_start: 0.7939 (tpt) cc_final: 0.7635 (tpt) REVERT: D 309 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.8024 (p0) REVERT: D 358 ASN cc_start: 0.7234 (m110) cc_final: 0.6961 (m110) REVERT: D 381 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7359 (mtpp) REVERT: D 383 ASP cc_start: 0.7965 (m-30) cc_final: 0.7590 (m-30) REVERT: D 588 GLU cc_start: 0.8303 (pt0) cc_final: 0.7918 (pt0) REVERT: D 610 ARG cc_start: 0.6706 (mmp-170) cc_final: 0.6389 (tpt170) outliers start: 61 outliers final: 23 residues processed: 484 average time/residue: 0.7171 time to fit residues: 386.6687 Evaluate side-chains 411 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 384 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 83 LEU 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 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 259 LEU Chi-restraints excluded: chain C residue 309 ASP 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: 0.9980 chunk 23 optimal weight: 6.9990 chunk 139 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 235 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN B 37 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 374 GLN ** D 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.167327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120461 restraints weight = 20538.795| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.49 r_work: 0.3117 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 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 = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20768 Z= 0.151 Angle : 0.634 12.165 28012 Z= 0.316 Chirality : 0.041 0.192 3116 Planarity : 0.005 0.054 3416 Dihedral : 16.734 166.634 4115 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.96 % Allowed : 13.03 % Favored : 84.01 % 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: 0.71 (0.18), residues: 2360 helix: 0.85 (0.13), residues: 1468 sheet: -0.79 (0.55), residues: 84 loop : 0.14 (0.25), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 606 TYR 0.019 0.002 TYR D 324 PHE 0.018 0.002 PHE A 537 TRP 0.010 0.001 TRP C 593 HIS 0.004 0.001 HIS D 238 Details of bonding type rmsd covalent geometry : bond 0.00354 (20768) covalent geometry : angle 0.63461 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.04731 ( 1096) hydrogen bonds : angle 4.06641 ( 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 439 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 378 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6744 (ttmm) REVERT: A 110 MET cc_start: 0.7314 (mtp) cc_final: 0.7060 (mtm) REVERT: A 118 GLN cc_start: 0.8198 (tt0) cc_final: 0.7920 (tt0) REVERT: A 175 SER cc_start: 0.7967 (t) cc_final: 0.7751 (t) REVERT: A 309 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7892 (t0) REVERT: A 358 ASN cc_start: 0.7318 (m110) cc_final: 0.7032 (m110) REVERT: A 383 ASP cc_start: 0.8065 (m-30) cc_final: 0.7746 (m-30) REVERT: A 610 ARG cc_start: 0.6622 (mmp-170) cc_final: 0.6215 (tpp-160) REVERT: B 88 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6742 (mt) REVERT: B 96 MET cc_start: 0.6337 (mtp) cc_final: 0.5995 (mmm) REVERT: B 99 MET cc_start: 0.5317 (mmm) cc_final: 0.5072 (mmp) REVERT: B 110 MET cc_start: 0.7256 (mtp) cc_final: 0.7011 (mtm) REVERT: B 260 MET cc_start: 0.7979 (tpt) cc_final: 0.7626 (tpt) REVERT: B 279 ASP cc_start: 0.8338 (t0) cc_final: 0.8099 (t0) REVERT: B 309 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7885 (t0) REVERT: B 324 TYR cc_start: 0.8305 (m-80) cc_final: 0.8082 (m-80) REVERT: B 358 ASN cc_start: 0.7221 (m110) cc_final: 0.6980 (m110) REVERT: B 383 ASP cc_start: 0.8081 (m-30) cc_final: 0.7763 (m-30) REVERT: C 88 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6804 (mt) REVERT: C 90 ASP cc_start: 0.6917 (t70) cc_final: 0.6448 (t70) REVERT: C 96 MET cc_start: 0.6386 (mtp) cc_final: 0.6081 (mmm) REVERT: C 110 MET cc_start: 0.7278 (mtp) cc_final: 0.6998 (mtm) REVERT: C 279 ASP cc_start: 0.8340 (t0) cc_final: 0.8101 (t0) REVERT: C 309 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7874 (t0) REVERT: C 358 ASN cc_start: 0.7222 (m110) cc_final: 0.6934 (m110) REVERT: C 383 ASP cc_start: 0.8053 (m-30) cc_final: 0.7743 (m-30) REVERT: C 610 ARG cc_start: 0.6562 (mmp-170) cc_final: 0.6187 (tpp-160) REVERT: D 42 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6805 (ttmm) REVERT: D 88 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6798 (mt) REVERT: D 90 ASP cc_start: 0.6914 (t70) cc_final: 0.6454 (t70) REVERT: D 96 MET cc_start: 0.6383 (mtp) cc_final: 0.6110 (mmm) REVERT: D 99 MET cc_start: 0.5386 (mmm) cc_final: 0.5131 (mmp) REVERT: D 110 MET cc_start: 0.7279 (mtp) cc_final: 0.7031 (mtm) REVERT: D 213 CYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7818 (t) REVERT: D 260 MET cc_start: 0.7945 (tpt) cc_final: 0.7630 (tpt) REVERT: D 309 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7845 (t0) REVERT: D 358 ASN cc_start: 0.7239 (m110) cc_final: 0.6970 (m110) REVERT: D 383 ASP cc_start: 0.8059 (m-30) cc_final: 0.7712 (m-30) REVERT: D 610 ARG cc_start: 0.6616 (mmp-170) cc_final: 0.6379 (tpm170) outliers start: 61 outliers final: 26 residues processed: 426 average time/residue: 0.7223 time to fit residues: 342.5702 Evaluate side-chains 385 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 349 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 B residue 83 LEU Chi-restraints excluded: chain B residue 88 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 331 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 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 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 88 LEU 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 309 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 210 optimal weight: 0.0980 chunk 160 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 374 GLN B 208 ASN B 374 GLN C 374 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** 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 = 0.3847 r_free = 0.3847 target = 0.164858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118720 restraints weight = 20459.940| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.46 r_work: 0.3044 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20768 Z= 0.210 Angle : 0.688 12.598 28012 Z= 0.341 Chirality : 0.045 0.199 3116 Planarity : 0.005 0.055 3416 Dihedral : 16.478 168.798 4115 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.68 % Allowed : 14.24 % Favored : 82.07 % 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: 0.87 (0.18), residues: 2360 helix: 0.99 (0.13), residues: 1468 sheet: -1.02 (0.55), residues: 88 loop : 0.20 (0.26), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 606 TYR 0.018 0.003 TYR D 555 PHE 0.018 0.002 PHE D 537 TRP 0.010 0.002 TRP D 593 HIS 0.004 0.001 HIS C 238 Details of bonding type rmsd covalent geometry : bond 0.00506 (20768) covalent geometry : angle 0.68821 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.05047 ( 1096) hydrogen bonds : angle 4.11521 ( 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 458 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 382 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6835 (ttmm) REVERT: A 175 SER cc_start: 0.8050 (t) cc_final: 0.7842 (t) REVERT: A 233 ASP cc_start: 0.7221 (p0) cc_final: 0.6824 (p0) REVERT: A 309 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7921 (t0) REVERT: A 322 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8276 (mtmt) REVERT: A 324 TYR cc_start: 0.8276 (m-80) cc_final: 0.8043 (m-80) REVERT: A 358 ASN cc_start: 0.7386 (m110) cc_final: 0.7155 (m110) REVERT: A 381 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7556 (mttp) REVERT: A 383 ASP cc_start: 0.8099 (m-30) cc_final: 0.7773 (m-30) REVERT: A 610 ARG cc_start: 0.6557 (mmp-170) cc_final: 0.6289 (tpp-160) REVERT: B 42 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6858 (ttmm) REVERT: B 88 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6884 (mt) REVERT: B 90 ASP cc_start: 0.6791 (t70) cc_final: 0.6289 (t70) REVERT: B 221 SER cc_start: 0.7625 (OUTLIER) cc_final: 0.7369 (m) REVERT: B 257 GLN cc_start: 0.8102 (mt0) cc_final: 0.7879 (tt0) REVERT: B 279 ASP cc_start: 0.8380 (t0) cc_final: 0.8136 (t0) REVERT: B 309 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7920 (t0) REVERT: B 324 TYR cc_start: 0.8381 (m-80) cc_final: 0.8155 (m-80) REVERT: B 358 ASN cc_start: 0.7302 (m110) cc_final: 0.7068 (m110) REVERT: B 381 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7572 (mttp) REVERT: B 383 ASP cc_start: 0.8103 (m-30) cc_final: 0.7774 (m-30) REVERT: C 42 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6880 (ttmm) REVERT: C 88 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6898 (mt) REVERT: C 90 ASP cc_start: 0.6886 (t70) cc_final: 0.6361 (t70) REVERT: C 221 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7373 (m) REVERT: C 233 ASP cc_start: 0.7202 (p0) cc_final: 0.6790 (p0) REVERT: C 257 GLN cc_start: 0.8094 (mt0) cc_final: 0.7874 (tt0) REVERT: C 279 ASP cc_start: 0.8402 (t0) cc_final: 0.8166 (t0) REVERT: C 309 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7922 (t0) REVERT: C 357 ASN cc_start: 0.7632 (p0) cc_final: 0.7432 (p0) REVERT: C 358 ASN cc_start: 0.7281 (m110) cc_final: 0.6972 (m110) REVERT: C 381 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7576 (mttp) REVERT: C 383 ASP cc_start: 0.8128 (m-30) cc_final: 0.7806 (m-30) REVERT: D 42 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6911 (ttmm) REVERT: D 85 ILE cc_start: 0.7439 (mm) cc_final: 0.7204 (mp) REVERT: D 88 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6932 (mt) REVERT: D 90 ASP cc_start: 0.6868 (t70) cc_final: 0.6344 (t70) REVERT: D 110 MET cc_start: 0.7322 (mtp) cc_final: 0.7071 (mtp) REVERT: D 118 GLN cc_start: 0.8214 (tt0) cc_final: 0.7909 (tt0) REVERT: D 221 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.7354 (m) REVERT: D 233 ASP cc_start: 0.7192 (p0) cc_final: 0.6776 (p0) REVERT: D 309 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7920 (t0) REVERT: D 358 ASN cc_start: 0.7279 (m110) cc_final: 0.7034 (m110) REVERT: D 381 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7581 (mttp) REVERT: D 383 ASP cc_start: 0.8114 (m-30) cc_final: 0.7794 (m-30) REVERT: D 610 ARG cc_start: 0.6553 (mmp-170) cc_final: 0.6299 (tpp-160) outliers start: 76 outliers final: 31 residues processed: 431 average time/residue: 0.7397 time to fit residues: 355.1901 Evaluate side-chains 409 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 363 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 309 ASP 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 83 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 210 THR 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 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 42 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 210 THR 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 309 ASP 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 88 LEU 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 274 THR 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 Chi-restraints excluded: chain D residue 631 LEU 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: 0.8980 chunk 171 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN B 374 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121792 restraints weight = 20330.453| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.52 r_work: 0.3126 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20768 Z= 0.121 Angle : 0.592 12.045 28012 Z= 0.292 Chirality : 0.039 0.196 3116 Planarity : 0.005 0.051 3416 Dihedral : 15.701 167.434 4115 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.00 % Allowed : 15.16 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2360 helix: 1.41 (0.14), residues: 1468 sheet: -0.72 (0.56), residues: 88 loop : 0.17 (0.25), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 606 TYR 0.017 0.002 TYR A 115 PHE 0.011 0.001 PHE B 537 TRP 0.010 0.001 TRP D 593 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00272 (20768) covalent geometry : angle 0.59256 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.04083 ( 1096) hydrogen bonds : angle 3.88862 ( 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 441 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 379 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6797 (ttmm) REVERT: A 108 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6392 (mm-30) REVERT: A 118 GLN cc_start: 0.8259 (tt0) cc_final: 0.7831 (tt0) REVERT: A 130 MET cc_start: 0.6469 (tpt) cc_final: 0.6045 (tpp) REVERT: A 175 SER cc_start: 0.7925 (t) cc_final: 0.7713 (t) REVERT: A 324 TYR cc_start: 0.8220 (m-80) cc_final: 0.7993 (m-80) REVERT: A 358 ASN cc_start: 0.7311 (m110) cc_final: 0.7053 (m110) REVERT: A 381 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7518 (mttp) REVERT: A 383 ASP cc_start: 0.8098 (m-30) cc_final: 0.7787 (m-30) REVERT: A 610 ARG cc_start: 0.6531 (mmp-170) cc_final: 0.6242 (tpp-160) REVERT: B 42 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6794 (ttmm) REVERT: B 90 ASP cc_start: 0.6780 (t70) cc_final: 0.6245 (t70) REVERT: B 96 MET cc_start: 0.6432 (mtp) cc_final: 0.6169 (mmm) REVERT: B 99 MET cc_start: 0.5670 (mmm) cc_final: 0.5367 (mmp) REVERT: B 110 MET cc_start: 0.7151 (mtp) cc_final: 0.6861 (mtp) REVERT: B 118 GLN cc_start: 0.8265 (tt0) cc_final: 0.7875 (tt0) REVERT: B 324 TYR cc_start: 0.8319 (m-80) cc_final: 0.8084 (m-80) REVERT: B 358 ASN cc_start: 0.7259 (m110) cc_final: 0.7023 (m110) REVERT: B 381 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7508 (mttp) REVERT: B 383 ASP cc_start: 0.8084 (m-30) cc_final: 0.7771 (m-30) REVERT: B 622 GLU cc_start: 0.6791 (pt0) cc_final: 0.6542 (pp20) REVERT: C 42 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6830 (ttmm) REVERT: C 90 ASP cc_start: 0.6790 (t70) cc_final: 0.6239 (t70) REVERT: C 110 MET cc_start: 0.7160 (mtp) cc_final: 0.6904 (mtp) REVERT: C 118 GLN cc_start: 0.8235 (tt0) cc_final: 0.7882 (tt0) REVERT: C 358 ASN cc_start: 0.7237 (m110) cc_final: 0.6987 (m110) REVERT: C 381 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7531 (mttp) REVERT: C 383 ASP cc_start: 0.8098 (m-30) cc_final: 0.7785 (m-30) REVERT: C 622 GLU cc_start: 0.6808 (pt0) cc_final: 0.6513 (pp20) REVERT: D 42 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6805 (ttmm) REVERT: D 90 ASP cc_start: 0.6766 (t70) cc_final: 0.6204 (t70) REVERT: D 96 MET cc_start: 0.6427 (mtp) cc_final: 0.6188 (mmm) REVERT: D 99 MET cc_start: 0.5491 (mmm) cc_final: 0.5172 (mmp) REVERT: D 118 GLN cc_start: 0.8187 (tt0) cc_final: 0.7928 (tt0) REVERT: D 358 ASN cc_start: 0.7249 (m110) cc_final: 0.7003 (m110) REVERT: D 381 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7518 (mttp) REVERT: D 383 ASP cc_start: 0.8092 (m-30) cc_final: 0.7780 (m-30) REVERT: D 622 GLU cc_start: 0.6800 (pt0) cc_final: 0.6534 (pp20) outliers start: 62 outliers final: 25 residues processed: 425 average time/residue: 0.7620 time to fit residues: 360.1398 Evaluate side-chains 393 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 364 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 297 ILE Chi-restraints excluded: chain A residue 311 THR 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 631 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 220 LEU 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 C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 220 LEU 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 299 THR 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: 4.9990 chunk 28 optimal weight: 0.2980 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.166427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120319 restraints weight = 20154.427| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.57 r_work: 0.3085 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 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 = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20768 Z= 0.172 Angle : 0.651 11.993 28012 Z= 0.321 Chirality : 0.042 0.193 3116 Planarity : 0.005 0.054 3416 Dihedral : 15.604 168.578 4115 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.81 % Allowed : 14.87 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2360 helix: 1.36 (0.13), residues: 1468 sheet: -0.79 (0.56), residues: 88 loop : 0.19 (0.26), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 606 TYR 0.016 0.002 TYR D 555 PHE 0.014 0.002 PHE B 537 TRP 0.015 0.001 TRP B 613 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00410 (20768) covalent geometry : angle 0.65134 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.04624 ( 1096) hydrogen bonds : angle 3.99609 ( 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 434 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 376 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6771 (ttmm) REVERT: A 90 ASP cc_start: 0.6695 (t70) cc_final: 0.6196 (t70) REVERT: A 108 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6413 (mm-30) REVERT: A 130 MET cc_start: 0.6425 (tpt) cc_final: 0.6217 (tpt) REVERT: A 175 SER cc_start: 0.7790 (t) cc_final: 0.7589 (t) REVERT: A 233 ASP cc_start: 0.7106 (p0) cc_final: 0.6689 (p0) REVERT: A 279 ASP cc_start: 0.8329 (t0) cc_final: 0.8092 (t0) REVERT: A 324 TYR cc_start: 0.8254 (m-80) cc_final: 0.7996 (m-80) REVERT: A 358 ASN cc_start: 0.7369 (m110) cc_final: 0.7164 (m110) REVERT: A 381 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7524 (mttp) REVERT: A 383 ASP cc_start: 0.8115 (m-30) cc_final: 0.7804 (m-30) REVERT: A 606 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7526 (ttm-80) REVERT: A 622 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6628 (pp20) REVERT: B 42 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6790 (ttmm) REVERT: B 90 ASP cc_start: 0.6774 (t70) cc_final: 0.6255 (t70) REVERT: B 108 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6478 (mm-30) REVERT: B 279 ASP cc_start: 0.8319 (t0) cc_final: 0.8081 (t0) REVERT: B 358 ASN cc_start: 0.7280 (m110) cc_final: 0.6999 (m110) REVERT: B 381 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7524 (mttp) REVERT: B 383 ASP cc_start: 0.8116 (m-30) cc_final: 0.7813 (m-30) REVERT: B 606 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7406 (ttm-80) REVERT: B 622 GLU cc_start: 0.6791 (pt0) cc_final: 0.6530 (pp20) REVERT: C 42 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6815 (ttmm) REVERT: C 90 ASP cc_start: 0.6829 (t70) cc_final: 0.6253 (t70) REVERT: C 108 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6466 (mm-30) REVERT: C 110 MET cc_start: 0.7216 (mtp) cc_final: 0.6980 (mtm) REVERT: C 358 ASN cc_start: 0.7270 (m110) cc_final: 0.6976 (m110) REVERT: C 381 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7525 (mttp) REVERT: C 383 ASP cc_start: 0.8087 (m-30) cc_final: 0.7783 (m-30) REVERT: D 42 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6788 (ttmm) REVERT: D 90 ASP cc_start: 0.6898 (t70) cc_final: 0.6316 (t70) REVERT: D 96 MET cc_start: 0.6407 (mtp) cc_final: 0.6200 (mmm) REVERT: D 99 MET cc_start: 0.5463 (mmm) cc_final: 0.5191 (mmp) REVERT: D 108 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6462 (mm-30) REVERT: D 110 MET cc_start: 0.7151 (mtp) cc_final: 0.6772 (mtp) REVERT: D 118 GLN cc_start: 0.8165 (tt0) cc_final: 0.7755 (tt0) REVERT: D 130 MET cc_start: 0.6468 (tpt) cc_final: 0.6249 (tpp) REVERT: D 221 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7362 (m) REVERT: D 358 ASN cc_start: 0.7278 (m110) cc_final: 0.6985 (m110) REVERT: D 381 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7531 (mttp) REVERT: D 383 ASP cc_start: 0.8094 (m-30) cc_final: 0.7791 (m-30) REVERT: D 606 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7495 (ttm-80) REVERT: D 622 GLU cc_start: 0.6793 (pt0) cc_final: 0.6539 (pp20) outliers start: 58 outliers final: 29 residues processed: 419 average time/residue: 0.7441 time to fit residues: 346.6597 Evaluate side-chains 404 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 369 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 361 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 220 LEU 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 631 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 114 LEU 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 311 THR 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 299 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 91 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 181 optimal weight: 0.0270 chunk 119 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 233 optimal weight: 0.0000 chunk 137 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 374 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 374 GLN C 118 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123893 restraints weight = 20304.592| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.44 r_work: 0.3134 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20768 Z= 0.115 Angle : 0.592 11.172 28012 Z= 0.289 Chirality : 0.038 0.184 3116 Planarity : 0.005 0.052 3416 Dihedral : 14.794 167.924 4115 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.18 % Allowed : 16.04 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.18), residues: 2360 helix: 1.64 (0.14), residues: 1468 sheet: -0.48 (0.59), residues: 88 loop : 0.08 (0.25), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 606 TYR 0.016 0.001 TYR C 324 PHE 0.010 0.001 PHE A 537 TRP 0.011 0.001 TRP B 613 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00258 (20768) covalent geometry : angle 0.59185 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.03827 ( 1096) hydrogen bonds : angle 3.79452 ( 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 418 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 373 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6813 (ttmm) REVERT: A 90 ASP cc_start: 0.6666 (t70) cc_final: 0.6156 (t70) REVERT: A 108 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6291 (mm-30) REVERT: A 118 GLN cc_start: 0.8347 (tt0) cc_final: 0.7985 (tt0) REVERT: A 177 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7331 (mm-30) REVERT: A 279 ASP cc_start: 0.8360 (t0) cc_final: 0.8108 (t0) REVERT: A 324 TYR cc_start: 0.8217 (m-80) cc_final: 0.7994 (m-80) REVERT: A 358 ASN cc_start: 0.7339 (m110) cc_final: 0.7098 (m110) REVERT: A 381 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7467 (mttp) REVERT: A 383 ASP cc_start: 0.8095 (m-30) cc_final: 0.7840 (m-30) REVERT: A 589 ARG cc_start: 0.7785 (ptm-80) cc_final: 0.7472 (ptm-80) REVERT: A 622 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6712 (pp20) REVERT: B 42 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6789 (ttmm) REVERT: B 90 ASP cc_start: 0.6818 (t70) cc_final: 0.6312 (t70) REVERT: B 99 MET cc_start: 0.5623 (mmm) cc_final: 0.5372 (mmp) REVERT: B 108 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6458 (mm-30) REVERT: B 118 GLN cc_start: 0.8313 (tt0) cc_final: 0.7860 (tt0) REVERT: B 279 ASP cc_start: 0.8366 (t0) cc_final: 0.8077 (t0) REVERT: B 358 ASN cc_start: 0.7187 (m110) cc_final: 0.6963 (m110) REVERT: B 381 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7476 (mttp) REVERT: B 383 ASP cc_start: 0.8102 (m-30) cc_final: 0.7804 (m-30) REVERT: B 622 GLU cc_start: 0.6787 (pt0) cc_final: 0.6556 (pp20) REVERT: C 42 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6814 (ttmm) REVERT: C 90 ASP cc_start: 0.6918 (t70) cc_final: 0.6341 (t70) REVERT: C 358 ASN cc_start: 0.7180 (m110) cc_final: 0.6903 (m110) REVERT: C 381 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7483 (mttp) REVERT: C 383 ASP cc_start: 0.8112 (m-30) cc_final: 0.7818 (m-30) REVERT: C 589 ARG cc_start: 0.7800 (ptm-80) cc_final: 0.7489 (ptm-80) REVERT: C 610 ARG cc_start: 0.6494 (tpt170) cc_final: 0.6138 (tpp-160) REVERT: C 622 GLU cc_start: 0.6846 (pt0) cc_final: 0.6593 (pp20) REVERT: D 42 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6790 (ttmm) REVERT: D 80 GLU cc_start: 0.7250 (pm20) cc_final: 0.6856 (pm20) REVERT: D 90 ASP cc_start: 0.6857 (t70) cc_final: 0.6286 (t70) REVERT: D 99 MET cc_start: 0.5475 (mmm) cc_final: 0.5162 (mmp) REVERT: D 110 MET cc_start: 0.7255 (mtp) cc_final: 0.7045 (mtp) REVERT: D 118 GLN cc_start: 0.8103 (tt0) cc_final: 0.7738 (tt0) REVERT: D 279 ASP cc_start: 0.8358 (t0) cc_final: 0.7954 (t0) REVERT: D 358 ASN cc_start: 0.7182 (m110) cc_final: 0.6913 (m110) REVERT: D 381 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7510 (mttp) REVERT: D 383 ASP cc_start: 0.8103 (m-30) cc_final: 0.7808 (m-30) REVERT: D 622 GLU cc_start: 0.6809 (pt0) cc_final: 0.6558 (pp20) outliers start: 45 outliers final: 18 residues processed: 404 average time/residue: 0.7598 time to fit residues: 341.1385 Evaluate side-chains 390 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 367 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 THR 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 622 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 221 SER 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 221 SER 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 297 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 150 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 214 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN 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 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 = 0.3898 r_free = 0.3898 target = 0.169326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122034 restraints weight = 20363.687| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.52 r_work: 0.3141 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20768 Z= 0.121 Angle : 0.604 11.220 28012 Z= 0.295 Chirality : 0.039 0.210 3116 Planarity : 0.005 0.053 3416 Dihedral : 14.434 167.511 4113 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.89 % Allowed : 16.28 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.18), residues: 2360 helix: 1.79 (0.14), residues: 1448 sheet: -0.44 (0.59), residues: 88 loop : 0.15 (0.25), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 606 TYR 0.018 0.002 TYR C 324 PHE 0.014 0.001 PHE D 472 TRP 0.014 0.001 TRP A 583 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00273 (20768) covalent geometry : angle 0.60414 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.03916 ( 1096) hydrogen bonds : angle 3.73615 ( 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: 39 poor density : 369 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6796 (ttmm) REVERT: A 90 ASP cc_start: 0.6738 (t70) cc_final: 0.6191 (t70) REVERT: A 108 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6390 (mm-30) REVERT: A 118 GLN cc_start: 0.8330 (tt0) cc_final: 0.8002 (tt0) REVERT: A 279 ASP cc_start: 0.8342 (t0) cc_final: 0.8095 (t0) REVERT: A 324 TYR cc_start: 0.8194 (m-80) cc_final: 0.7975 (m-80) REVERT: A 358 ASN cc_start: 0.7288 (m110) cc_final: 0.7050 (m110) REVERT: A 381 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7457 (mttp) REVERT: A 383 ASP cc_start: 0.8082 (m-30) cc_final: 0.7786 (m-30) REVERT: A 589 ARG cc_start: 0.7815 (ptm-80) cc_final: 0.7528 (ptm-80) REVERT: B 42 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6777 (ttmm) REVERT: B 90 ASP cc_start: 0.6857 (t70) cc_final: 0.6566 (t70) REVERT: B 260 MET cc_start: 0.8008 (tpt) cc_final: 0.7761 (tpt) REVERT: B 358 ASN cc_start: 0.7162 (m110) cc_final: 0.6910 (m110) REVERT: B 381 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7461 (mttp) REVERT: B 383 ASP cc_start: 0.8087 (m-30) cc_final: 0.7789 (m-30) REVERT: B 491 MET cc_start: 0.8375 (mtp) cc_final: 0.8082 (mtm) REVERT: C 42 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6783 (ttmm) REVERT: C 90 ASP cc_start: 0.6805 (t70) cc_final: 0.6462 (t70) REVERT: C 99 MET cc_start: 0.5972 (mmm) cc_final: 0.5699 (mmm) REVERT: C 108 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6387 (mm-30) REVERT: C 358 ASN cc_start: 0.7144 (m110) cc_final: 0.6919 (m110) REVERT: C 381 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7462 (mttp) REVERT: C 383 ASP cc_start: 0.8092 (m-30) cc_final: 0.7801 (m-30) REVERT: C 589 ARG cc_start: 0.7822 (ptm-80) cc_final: 0.7537 (ptm-80) REVERT: C 610 ARG cc_start: 0.6477 (tpt170) cc_final: 0.6258 (tpm170) REVERT: D 42 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6762 (ttmm) REVERT: D 80 GLU cc_start: 0.7306 (pm20) cc_final: 0.6885 (pm20) REVERT: D 90 ASP cc_start: 0.6819 (t70) cc_final: 0.6480 (t70) REVERT: D 99 MET cc_start: 0.5516 (mmm) cc_final: 0.5190 (mmp) REVERT: D 108 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6487 (mm-30) REVERT: D 260 MET cc_start: 0.8001 (tpt) cc_final: 0.7763 (tpt) REVERT: D 358 ASN cc_start: 0.7144 (m110) cc_final: 0.6919 (m110) REVERT: D 381 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7457 (mttp) REVERT: D 383 ASP cc_start: 0.8104 (m-30) cc_final: 0.7808 (m-30) REVERT: D 622 GLU cc_start: 0.6786 (pt0) cc_final: 0.6579 (pp20) outliers start: 39 outliers final: 19 residues processed: 396 average time/residue: 0.7842 time to fit residues: 344.6829 Evaluate side-chains 377 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 354 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 ILE 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 83 LEU 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 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 221 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 THR 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: 1.9990 chunk 216 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 173 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 257 GLN 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 257 GLN D 374 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.169532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121643 restraints weight = 20270.643| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.48 r_work: 0.3128 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20768 Z= 0.122 Angle : 0.606 11.132 28012 Z= 0.295 Chirality : 0.039 0.198 3116 Planarity : 0.005 0.055 3416 Dihedral : 14.103 167.172 4113 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.60 % Allowed : 16.81 % Favored : 81.59 % 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: 1.69 (0.18), residues: 2360 helix: 1.82 (0.14), residues: 1448 sheet: -0.37 (0.59), residues: 88 loop : 0.13 (0.25), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 615 TYR 0.021 0.002 TYR D 324 PHE 0.011 0.001 PHE A 537 TRP 0.014 0.001 TRP D 583 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00279 (20768) covalent geometry : angle 0.60587 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.03900 ( 1096) hydrogen bonds : angle 3.71863 ( 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: 33 poor density : 362 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6795 (ttmm) REVERT: A 80 GLU cc_start: 0.6653 (pt0) cc_final: 0.6195 (pm20) REVERT: A 90 ASP cc_start: 0.6766 (t70) cc_final: 0.6253 (t70) REVERT: A 108 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6484 (mm-30) REVERT: A 208 ASN cc_start: 0.7739 (t0) cc_final: 0.7500 (t0) REVERT: A 279 ASP cc_start: 0.8366 (t0) cc_final: 0.8161 (t0) REVERT: A 324 TYR cc_start: 0.8200 (m-80) cc_final: 0.7991 (m-80) REVERT: A 358 ASN cc_start: 0.7316 (m110) cc_final: 0.7087 (m110) REVERT: A 381 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7457 (mttp) REVERT: A 383 ASP cc_start: 0.8085 (m-30) cc_final: 0.7789 (m-30) REVERT: B 42 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6792 (ttmm) REVERT: B 80 GLU cc_start: 0.7206 (pm20) cc_final: 0.6833 (pm20) REVERT: B 90 ASP cc_start: 0.7017 (t70) cc_final: 0.6675 (t70) REVERT: B 260 MET cc_start: 0.8021 (tpt) cc_final: 0.7773 (tpt) REVERT: B 358 ASN cc_start: 0.7161 (m110) cc_final: 0.6941 (m110) REVERT: B 381 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7464 (mttp) REVERT: B 383 ASP cc_start: 0.8087 (m-30) cc_final: 0.7789 (m-30) REVERT: B 491 MET cc_start: 0.8414 (mtp) cc_final: 0.8115 (mtm) REVERT: C 42 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6817 (ttmm) REVERT: C 90 ASP cc_start: 0.6842 (t70) cc_final: 0.6478 (t70) REVERT: C 99 MET cc_start: 0.5990 (mmm) cc_final: 0.5779 (mmm) REVERT: C 358 ASN cc_start: 0.7146 (m110) cc_final: 0.6875 (m110) REVERT: C 381 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7478 (mttp) REVERT: C 383 ASP cc_start: 0.8108 (m-30) cc_final: 0.7818 (m-30) REVERT: C 610 ARG cc_start: 0.6409 (tpt170) cc_final: 0.6149 (tpp-160) REVERT: D 42 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6768 (ttmm) REVERT: D 80 GLU cc_start: 0.6976 (pm20) cc_final: 0.6587 (pm20) REVERT: D 90 ASP cc_start: 0.6879 (t70) cc_final: 0.6567 (t0) REVERT: D 108 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6502 (mm-30) REVERT: D 260 MET cc_start: 0.8056 (tpt) cc_final: 0.7814 (tpt) REVERT: D 358 ASN cc_start: 0.7128 (m110) cc_final: 0.6857 (m110) REVERT: D 381 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7474 (mttp) REVERT: D 383 ASP cc_start: 0.8111 (m-30) cc_final: 0.7814 (m-30) outliers start: 33 outliers final: 23 residues processed: 385 average time/residue: 0.7204 time to fit residues: 308.9945 Evaluate side-chains 374 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 347 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 299 THR 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 83 LEU Chi-restraints excluded: chain B residue 221 SER 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 221 SER Chi-restraints excluded: chain C residue 259 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 297 ILE 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 178 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 233 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 257 GLN A 374 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 374 GLN C 257 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 = 0.3909 r_free = 0.3909 target = 0.170340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134460 restraints weight = 20422.202| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.37 r_work: 0.3054 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20768 Z= 0.119 Angle : 0.601 10.769 28012 Z= 0.293 Chirality : 0.039 0.196 3116 Planarity : 0.005 0.056 3416 Dihedral : 13.763 166.503 4113 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.55 % Allowed : 16.91 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.18), residues: 2360 helix: 1.86 (0.14), residues: 1448 sheet: -0.26 (0.59), residues: 88 loop : 0.11 (0.25), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 615 TYR 0.020 0.002 TYR D 324 PHE 0.017 0.001 PHE A 456 TRP 0.020 0.001 TRP A 583 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00269 (20768) covalent geometry : angle 0.60095 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.03810 ( 1096) hydrogen bonds : angle 3.71357 ( 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 389 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 357 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6855 (ttmm) REVERT: A 80 GLU cc_start: 0.6660 (pt0) cc_final: 0.6328 (pm20) REVERT: A 90 ASP cc_start: 0.6819 (t70) cc_final: 0.6550 (t70) REVERT: A 108 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6455 (mm-30) REVERT: A 150 THR cc_start: 0.8595 (m) cc_final: 0.8372 (m) REVERT: A 208 ASN cc_start: 0.7766 (t0) cc_final: 0.7528 (t0) REVERT: A 358 ASN cc_start: 0.7387 (m110) cc_final: 0.7133 (m110) REVERT: A 381 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7525 (mttp) REVERT: A 383 ASP cc_start: 0.8085 (m-30) cc_final: 0.7822 (m-30) REVERT: B 42 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6841 (ttmm) REVERT: B 90 ASP cc_start: 0.7074 (t70) cc_final: 0.6789 (t0) REVERT: B 108 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6406 (mm-30) REVERT: B 208 ASN cc_start: 0.7748 (t0) cc_final: 0.7508 (t0) REVERT: B 260 MET cc_start: 0.8082 (tpt) cc_final: 0.7831 (tpt) REVERT: B 358 ASN cc_start: 0.7214 (m110) cc_final: 0.6958 (m110) REVERT: B 381 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7526 (mttp) REVERT: B 383 ASP cc_start: 0.8076 (m-30) cc_final: 0.7811 (m-30) REVERT: B 491 MET cc_start: 0.8318 (mtp) cc_final: 0.8037 (mtm) REVERT: C 42 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6837 (ttmm) REVERT: C 90 ASP cc_start: 0.6865 (t70) cc_final: 0.6543 (t0) REVERT: C 99 MET cc_start: 0.5975 (mmm) cc_final: 0.5731 (mmm) REVERT: C 108 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6415 (mm-30) REVERT: C 358 ASN cc_start: 0.7179 (m110) cc_final: 0.6956 (m110) REVERT: C 381 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7539 (mttp) REVERT: C 383 ASP cc_start: 0.8114 (m-30) cc_final: 0.7851 (m-30) REVERT: D 42 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6830 (ttmm) REVERT: D 90 ASP cc_start: 0.6866 (t70) cc_final: 0.6550 (t0) REVERT: D 208 ASN cc_start: 0.7775 (t0) cc_final: 0.7542 (t0) REVERT: D 260 MET cc_start: 0.8021 (tpt) cc_final: 0.7760 (tpt) REVERT: D 358 ASN cc_start: 0.7157 (m110) cc_final: 0.6937 (m110) REVERT: D 381 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7535 (mttp) REVERT: D 383 ASP cc_start: 0.8096 (m-30) cc_final: 0.7832 (m-30) outliers start: 32 outliers final: 21 residues processed: 380 average time/residue: 0.7296 time to fit residues: 309.3383 Evaluate side-chains 373 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 299 THR 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 83 LEU Chi-restraints excluded: chain B residue 221 SER 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 297 ILE 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: 2.9990 chunk 81 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN C 118 GLN C 257 GLN C 374 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 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 = 0.3883 r_free = 0.3883 target = 0.167994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120638 restraints weight = 20303.394| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.55 r_work: 0.3104 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20768 Z= 0.147 Angle : 0.643 11.231 28012 Z= 0.313 Chirality : 0.041 0.200 3116 Planarity : 0.005 0.056 3416 Dihedral : 13.828 166.963 4113 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.50 % Allowed : 17.30 % Favored : 81.20 % 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: 1.76 (0.14), residues: 1448 sheet: -0.31 (0.58), residues: 88 loop : 0.21 (0.26), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 615 TYR 0.022 0.002 TYR D 324 PHE 0.013 0.002 PHE A 493 TRP 0.019 0.002 TRP A 583 HIS 0.004 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00346 (20768) covalent geometry : angle 0.64319 (28000) SS BOND : angle 0.00000 ( 12) hydrogen bonds : bond 0.04252 ( 1096) hydrogen bonds : angle 3.82579 ( 3144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10199.93 seconds wall clock time: 173 minutes 36.58 seconds (10416.58 seconds total)