Starting phenix.real_space_refine on Sun Apr 5 19:25:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jlp_22376/04_2026/7jlp_22376.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlp_22376/04_2026/7jlp_22376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jlp_22376/04_2026/7jlp_22376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlp_22376/04_2026/7jlp_22376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jlp_22376/04_2026/7jlp_22376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlp_22376/04_2026/7jlp_22376.map" } resolution = 3.4 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= 0.010 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 69 5.16 5 C 8643 2.51 5 N 2034 2.21 5 O 2133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12891 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "C" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "A" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Unusual residues: {'POV': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 9} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Unusual residues: {'POV': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 9} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Unusual residues: {'POV': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 9} Unresolved non-hydrogen planarities: 84 Time building chain proxies: 2.87, per 1000 atoms: 0.22 Number of scatterers: 12891 At special positions: 0 Unit cell: (128.142, 123.606, 90.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 12 15.00 O 2133 8.00 N 2034 7.00 C 8643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 122 " distance=2.03 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: 0.84 Conformation dependent library (CDL) restraints added in 574.6 milliseconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 9 sheets defined 72.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.502A pdb=" N HIS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 86 Processing helix chain 'A' and resid 111 through 116 removed outlier: 4.042A pdb=" N ALA A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 116' Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 132 through 166 removed outlier: 3.784A pdb=" N ILE A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.560A pdb=" N THR A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.526A pdb=" N ASN A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.785A pdb=" N ARG A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A 276 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 317 Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.618A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.678A pdb=" N CYS A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 3.739A pdb=" N ARG A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 370 through 398 removed outlier: 3.694A pdb=" N VAL A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 406 removed outlier: 5.969A pdb=" N GLU A 405 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 406 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 422 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.618A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.706A pdb=" N ARG A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 481 through 493 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 508 removed outlier: 3.640A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 removed outlier: 3.502A pdb=" N HIS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 86 Processing helix chain 'B' and resid 111 through 116 removed outlier: 4.041A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 116' Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 132 through 166 removed outlier: 3.784A pdb=" N ILE B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.560A pdb=" N THR B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 213 through 225 removed outlier: 3.527A pdb=" N ASN B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.784A pdb=" N ARG B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY B 276 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY B 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 317 Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.618A pdb=" N LEU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.677A pdb=" N CYS B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 3.739A pdb=" N ARG B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 398 removed outlier: 3.695A pdb=" N VAL B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 406 removed outlier: 5.969A pdb=" N GLU B 405 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS B 406 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 422 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.619A pdb=" N ARG B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.706A pdb=" N ARG B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 481 through 493 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 497 through 508 removed outlier: 3.640A pdb=" N ILE B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 removed outlier: 3.502A pdb=" N HIS C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 86 Processing helix chain 'C' and resid 111 through 116 removed outlier: 4.041A pdb=" N ALA C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 116' Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 132 through 166 removed outlier: 3.784A pdb=" N ILE C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 159 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.560A pdb=" N THR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 213 through 225 removed outlier: 3.527A pdb=" N ASN C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.784A pdb=" N ARG C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY C 276 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 277 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 317 Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.618A pdb=" N LEU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 removed outlier: 3.677A pdb=" N CYS C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.739A pdb=" N ARG C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 Processing helix chain 'C' and resid 370 through 398 removed outlier: 3.695A pdb=" N VAL C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 406 removed outlier: 5.969A pdb=" N GLU C 405 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS C 406 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 422 Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.618A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 removed outlier: 3.706A pdb=" N ARG C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 481 Processing helix chain 'C' and resid 481 through 493 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 497 through 508 removed outlier: 3.641A pdb=" N ILE C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AA2, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 512 Processing sheet with id=AA4, first strand: chain 'B' and resid 231 through 234 Processing sheet with id=AA5, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 512 Processing sheet with id=AA7, first strand: chain 'C' and resid 231 through 234 Processing sheet with id=AA8, first strand: chain 'C' and resid 331 through 332 Processing sheet with id=AA9, first strand: chain 'C' and resid 509 through 512 693 hydrogen bonds defined for protein. 1980 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: 1.97 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3735 1.34 - 1.46: 2104 1.46 - 1.58: 7226 1.58 - 1.69: 12 1.69 - 1.81: 105 Bond restraints: 13182 Sorted by residual: bond pdb=" C29 POV B 615 " pdb="C210 POV B 615 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C29 POV C 602 " pdb="C210 POV C 602 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C29 POV C 612 " pdb="C210 POV C 612 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C29 POV B 610 " pdb="C210 POV B 610 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C29 POV A 615 " pdb="C210 POV A 615 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 ... (remaining 13177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 17315 3.60 - 7.20: 283 7.20 - 10.81: 33 10.81 - 14.41: 3 14.41 - 18.01: 36 Bond angle restraints: 17670 Sorted by residual: angle pdb=" C28 POV B 605 " pdb=" C29 POV B 605 " pdb="C210 POV B 605 " ideal model delta sigma weight residual 127.79 109.78 18.01 3.00e+00 1.11e-01 3.60e+01 angle pdb=" C28 POV C 607 " pdb=" C29 POV C 607 " pdb="C210 POV C 607 " ideal model delta sigma weight residual 127.79 109.81 17.98 3.00e+00 1.11e-01 3.59e+01 angle pdb=" C28 POV A 605 " pdb=" C29 POV A 605 " pdb="C210 POV A 605 " ideal model delta sigma weight residual 127.79 109.84 17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" C28 POV C 613 " pdb=" C29 POV C 613 " pdb="C210 POV C 613 " ideal model delta sigma weight residual 127.79 109.91 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C28 POV A 611 " pdb=" C29 POV A 611 " pdb="C210 POV A 611 " ideal model delta sigma weight residual 127.79 109.92 17.87 3.00e+00 1.11e-01 3.55e+01 ... (remaining 17665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.36: 6849 18.36 - 36.73: 726 36.73 - 55.09: 198 55.09 - 73.46: 48 73.46 - 91.82: 42 Dihedral angle restraints: 7863 sinusoidal: 3585 harmonic: 4278 Sorted by residual: dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 122 " pdb=" CB CYS A 122 " ideal model delta sinusoidal sigma weight residual -86.00 -121.29 35.29 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 122 " pdb=" CB CYS B 122 " ideal model delta sinusoidal sigma weight residual -86.00 -121.29 35.29 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 122 " pdb=" CB CYS C 122 " ideal model delta sinusoidal sigma weight residual -86.00 -121.28 35.28 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 7860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1050 0.028 - 0.055: 554 0.055 - 0.083: 199 0.083 - 0.111: 69 0.111 - 0.138: 6 Chirality restraints: 1878 Sorted by residual: chirality pdb=" CA ILE A 425 " pdb=" N ILE A 425 " pdb=" C ILE A 425 " pdb=" CB ILE A 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE C 425 " pdb=" N ILE C 425 " pdb=" C ILE C 425 " pdb=" CB ILE C 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE B 425 " pdb=" N ILE B 425 " pdb=" C ILE B 425 " pdb=" CB ILE B 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1875 not shown) Planarity restraints: 2154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 605 " -0.158 2.00e-02 2.50e+03 3.01e-01 9.07e+02 pdb=" C29 POV B 605 " 0.392 2.00e-02 2.50e+03 pdb="C210 POV B 605 " -0.397 2.00e-02 2.50e+03 pdb="C211 POV B 605 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 607 " -0.158 2.00e-02 2.50e+03 3.01e-01 9.07e+02 pdb=" C29 POV C 607 " 0.392 2.00e-02 2.50e+03 pdb="C210 POV C 607 " -0.397 2.00e-02 2.50e+03 pdb="C211 POV C 607 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 605 " -0.158 2.00e-02 2.50e+03 3.01e-01 9.06e+02 pdb=" C29 POV A 605 " 0.392 2.00e-02 2.50e+03 pdb="C210 POV A 605 " -0.397 2.00e-02 2.50e+03 pdb="C211 POV A 605 " 0.162 2.00e-02 2.50e+03 ... (remaining 2151 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2760 2.78 - 3.31: 11275 3.31 - 3.84: 19746 3.84 - 4.37: 23908 4.37 - 4.90: 42034 Nonbonded interactions: 99723 Sorted by model distance: nonbonded pdb=" NH2 ARG C 337 " pdb=" OE1 GLN C 351 " model vdw 2.252 3.120 nonbonded pdb=" NH2 ARG B 337 " pdb=" OE1 GLN B 351 " model vdw 2.252 3.120 nonbonded pdb=" NH2 ARG A 337 " pdb=" OE1 GLN A 351 " model vdw 2.252 3.120 nonbonded pdb=" O HIS A 406 " pdb=" OG1 THR A 410 " model vdw 2.273 3.040 nonbonded pdb=" O HIS C 406 " pdb=" OG1 THR C 410 " model vdw 2.273 3.040 ... (remaining 99718 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 36 through 532 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C310 or name C311 or name C312 or name C313 or name C314)) \ or (resid 605 and (name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28)) or resid 611 or (resid 613 and (name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215)) or resid 615)) selection = (chain 'B' and (resid 36 through 532 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C310 or name C311 or name C312 or name C313 or name C314)) \ or (resid 605 and (name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28)) or resid 611 or (resid 613 and (name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215)) or resid 615)) selection = (chain 'C' and (resid 36 through 532 or (resid 603 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or n \ ame O14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid 60 \ 4 or (resid 605 and (name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28)) or (resid 611 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O21 or name O22 or name C210 or name C211 or name C212 or name C213 or n \ ame C214 or name C215)) or resid 613 or (resid 615 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O21 or name O22 or name C210 or name C211 or 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=1.00 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: 0.590 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.009 0.189 13185 Z= 0.450 Angle : 1.270 18.010 17676 Z= 0.493 Chirality : 0.038 0.138 1878 Planarity : 0.018 0.301 2154 Dihedral : 17.666 91.820 5082 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.70 % Allowed : 2.09 % Favored : 97.22 % 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: -2.07 (0.21), residues: 1443 helix: -0.55 (0.16), residues: 957 sheet: -1.93 (0.89), residues: 30 loop : -3.02 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 458 TYR 0.005 0.001 TYR C 177 PHE 0.014 0.001 PHE A 163 TRP 0.007 0.001 TRP A 180 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00905 (13182) covalent geometry : angle 1.27066 (17670) SS BOND : bond 0.00133 ( 3) SS BOND : angle 0.57835 ( 6) hydrogen bonds : bond 0.14722 ( 693) hydrogen bonds : angle 5.84978 ( 1980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.417 Fit side-chains REVERT: B 62 MET cc_start: 0.7912 (ttp) cc_final: 0.7626 (ttp) REVERT: B 91 ILE cc_start: 0.8718 (pt) cc_final: 0.8517 (pt) REVERT: B 191 GLN cc_start: 0.8041 (pp30) cc_final: 0.7740 (pp30) REVERT: B 306 ILE cc_start: 0.8944 (mt) cc_final: 0.8709 (mt) REVERT: B 524 MET cc_start: 0.4129 (ptp) cc_final: 0.3515 (ptp) REVERT: C 91 ILE cc_start: 0.8666 (pt) cc_final: 0.8438 (pt) REVERT: C 121 VAL cc_start: 0.7418 (p) cc_final: 0.7156 (t) outliers start: 9 outliers final: 7 residues processed: 168 average time/residue: 0.1186 time to fit residues: 27.8372 Evaluate side-chains 130 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 406 HIS A 428 GLN B 184 GLN B 250 ASN B 406 HIS B 507 ASN C 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.112758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.091739 restraints weight = 15992.476| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.32 r_work: 0.2660 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13185 Z= 0.102 Angle : 0.443 5.963 17676 Z= 0.230 Chirality : 0.037 0.133 1878 Planarity : 0.004 0.040 2154 Dihedral : 15.754 86.820 2287 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.70 % Allowed : 6.57 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1443 helix: 1.03 (0.17), residues: 942 sheet: -1.74 (0.92), residues: 30 loop : -2.56 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 231 TYR 0.013 0.001 TYR A 152 PHE 0.010 0.001 PHE C 469 TRP 0.008 0.001 TRP A 292 HIS 0.004 0.000 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00216 (13182) covalent geometry : angle 0.44270 (17670) SS BOND : bond 0.00114 ( 3) SS BOND : angle 0.33220 ( 6) hydrogen bonds : bond 0.04064 ( 693) hydrogen bonds : angle 3.94197 ( 1980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.434 Fit side-chains REVERT: A 159 GLU cc_start: 0.8310 (tt0) cc_final: 0.8084 (tt0) REVERT: A 233 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7555 (tpp80) REVERT: A 245 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.7860 (mtm110) REVERT: A 524 MET cc_start: 0.5025 (ptp) cc_final: 0.3438 (ptm) REVERT: B 62 MET cc_start: 0.8369 (ttp) cc_final: 0.8050 (ttp) REVERT: B 91 ILE cc_start: 0.8791 (pt) cc_final: 0.8577 (pt) REVERT: B 191 GLN cc_start: 0.8293 (pp30) cc_final: 0.8006 (pt0) REVERT: B 306 ILE cc_start: 0.9017 (mt) cc_final: 0.8735 (mt) REVERT: B 375 LEU cc_start: 0.8870 (mt) cc_final: 0.8617 (mt) REVERT: B 477 LEU cc_start: 0.8922 (tp) cc_final: 0.8367 (mp) REVERT: B 479 GLU cc_start: 0.8619 (tp30) cc_final: 0.8351 (mm-30) REVERT: B 524 MET cc_start: 0.4596 (ptp) cc_final: 0.3792 (ptp) outliers start: 9 outliers final: 9 residues processed: 136 average time/residue: 0.1179 time to fit residues: 22.6971 Evaluate side-chains 123 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 23 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 0.0010 chunk 110 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN A 379 ASN B 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.110147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.088978 restraints weight = 16244.850| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.31 r_work: 0.2620 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13185 Z= 0.149 Angle : 0.467 5.321 17676 Z= 0.239 Chirality : 0.038 0.132 1878 Planarity : 0.003 0.029 2154 Dihedral : 15.266 89.320 2277 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.08 % Allowed : 8.04 % Favored : 90.87 % 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: 0.35 (0.23), residues: 1443 helix: 1.49 (0.17), residues: 948 sheet: -2.87 (0.63), residues: 60 loop : -2.21 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.013 0.001 TYR A 152 PHE 0.013 0.001 PHE C 469 TRP 0.011 0.001 TRP C 180 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00356 (13182) covalent geometry : angle 0.46669 (17670) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.32666 ( 6) hydrogen bonds : bond 0.04480 ( 693) hydrogen bonds : angle 3.84879 ( 1980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.425 Fit side-chains REVERT: A 159 GLU cc_start: 0.8356 (tt0) cc_final: 0.7993 (tt0) REVERT: A 233 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7616 (tpp80) REVERT: A 245 ARG cc_start: 0.8466 (mtt-85) cc_final: 0.7938 (mtm110) REVERT: A 524 MET cc_start: 0.5064 (ptp) cc_final: 0.3482 (ptm) REVERT: B 62 MET cc_start: 0.8533 (ttp) cc_final: 0.8170 (ttp) REVERT: B 191 GLN cc_start: 0.8257 (pp30) cc_final: 0.7971 (pt0) REVERT: B 306 ILE cc_start: 0.9053 (mt) cc_final: 0.8762 (mt) REVERT: B 375 LEU cc_start: 0.8888 (mt) cc_final: 0.8635 (mt) REVERT: B 524 MET cc_start: 0.4585 (ptp) cc_final: 0.3713 (ptp) REVERT: C 263 PHE cc_start: 0.9206 (m-80) cc_final: 0.8996 (m-80) REVERT: C 460 GLN cc_start: 0.8564 (tt0) cc_final: 0.8087 (pt0) outliers start: 14 outliers final: 13 residues processed: 132 average time/residue: 0.1133 time to fit residues: 21.9230 Evaluate side-chains 125 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 131 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN B 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.110613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.089478 restraints weight = 16096.537| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.32 r_work: 0.2626 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13185 Z= 0.139 Angle : 0.455 5.662 17676 Z= 0.233 Chirality : 0.038 0.135 1878 Planarity : 0.003 0.030 2154 Dihedral : 14.824 89.304 2277 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.01 % Allowed : 9.44 % Favored : 89.56 % 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: 0.86 (0.23), residues: 1443 helix: 1.76 (0.18), residues: 951 sheet: -1.37 (0.90), residues: 30 loop : -1.92 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 125 TYR 0.013 0.001 TYR A 152 PHE 0.012 0.001 PHE C 469 TRP 0.008 0.001 TRP B 180 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00335 (13182) covalent geometry : angle 0.45472 (17670) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.31230 ( 6) hydrogen bonds : bond 0.04299 ( 693) hydrogen bonds : angle 3.76786 ( 1980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.428 Fit side-chains REVERT: A 159 GLU cc_start: 0.8394 (tt0) cc_final: 0.8014 (tt0) REVERT: A 233 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7586 (tpp80) REVERT: A 245 ARG cc_start: 0.8454 (mtt-85) cc_final: 0.7951 (mtm110) REVERT: A 524 MET cc_start: 0.5025 (ptp) cc_final: 0.3448 (ptm) REVERT: B 62 MET cc_start: 0.8482 (ttp) cc_final: 0.8132 (ttp) REVERT: B 191 GLN cc_start: 0.8273 (pp30) cc_final: 0.8006 (pt0) REVERT: B 306 ILE cc_start: 0.9042 (mt) cc_final: 0.8743 (mt) REVERT: B 428 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8272 (mt0) REVERT: B 524 MET cc_start: 0.4478 (ptp) cc_final: 0.3536 (ptp) REVERT: C 460 GLN cc_start: 0.8602 (tt0) cc_final: 0.8139 (pt0) outliers start: 13 outliers final: 12 residues processed: 130 average time/residue: 0.1230 time to fit residues: 22.7480 Evaluate side-chains 126 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN B 184 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.108601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.087551 restraints weight = 16304.785| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.31 r_work: 0.2597 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13185 Z= 0.194 Angle : 0.507 6.183 17676 Z= 0.257 Chirality : 0.040 0.136 1878 Planarity : 0.003 0.031 2154 Dihedral : 15.031 89.825 2277 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.78 % Allowed : 9.90 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1443 helix: 1.87 (0.18), residues: 936 sheet: -2.74 (0.65), residues: 60 loop : -1.64 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 125 TYR 0.012 0.001 TYR A 209 PHE 0.011 0.001 PHE C 469 TRP 0.009 0.001 TRP B 180 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00477 (13182) covalent geometry : angle 0.50727 (17670) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.29668 ( 6) hydrogen bonds : bond 0.04821 ( 693) hydrogen bonds : angle 3.87708 ( 1980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.476 Fit side-chains REVERT: A 159 GLU cc_start: 0.8364 (tt0) cc_final: 0.8001 (tt0) REVERT: A 233 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7578 (tpp80) REVERT: A 524 MET cc_start: 0.5038 (ptp) cc_final: 0.3504 (ptm) REVERT: B 62 MET cc_start: 0.8696 (ttp) cc_final: 0.8247 (ttp) REVERT: B 191 GLN cc_start: 0.8203 (pp30) cc_final: 0.7938 (pt0) REVERT: B 245 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7936 (mtp85) REVERT: B 306 ILE cc_start: 0.9044 (mt) cc_final: 0.8765 (mt) REVERT: B 428 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8298 (mt0) REVERT: B 524 MET cc_start: 0.4570 (ptp) cc_final: 0.3584 (ptp) REVERT: C 263 PHE cc_start: 0.9213 (m-80) cc_final: 0.8995 (m-80) REVERT: C 460 GLN cc_start: 0.8621 (tt0) cc_final: 0.8137 (pt0) outliers start: 23 outliers final: 19 residues processed: 136 average time/residue: 0.1265 time to fit residues: 24.2359 Evaluate side-chains 137 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 20.0000 chunk 139 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.112251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.091454 restraints weight = 15957.226| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.30 r_work: 0.2658 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13185 Z= 0.099 Angle : 0.419 5.115 17676 Z= 0.217 Chirality : 0.037 0.131 1878 Planarity : 0.003 0.029 2154 Dihedral : 13.910 86.243 2277 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.31 % Allowed : 10.52 % Favored : 88.17 % 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: 1.17 (0.23), residues: 1443 helix: 2.05 (0.18), residues: 951 sheet: -2.76 (0.63), residues: 60 loop : -1.69 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 125 TYR 0.011 0.001 TYR C 152 PHE 0.009 0.001 PHE A 469 TRP 0.006 0.001 TRP B 180 HIS 0.003 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00218 (13182) covalent geometry : angle 0.41905 (17670) SS BOND : bond 0.00107 ( 3) SS BOND : angle 0.31438 ( 6) hydrogen bonds : bond 0.03795 ( 693) hydrogen bonds : angle 3.64936 ( 1980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.454 Fit side-chains REVERT: A 159 GLU cc_start: 0.8333 (tt0) cc_final: 0.8020 (tt0) REVERT: A 233 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7562 (tpp80) REVERT: A 245 ARG cc_start: 0.8500 (mtt-85) cc_final: 0.8073 (mtm110) REVERT: A 524 MET cc_start: 0.4886 (ptp) cc_final: 0.3407 (ptm) REVERT: B 191 GLN cc_start: 0.8095 (pp30) cc_final: 0.7784 (pt0) REVERT: B 306 ILE cc_start: 0.9015 (mt) cc_final: 0.8729 (mt) REVERT: B 428 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8278 (mt0) REVERT: B 477 LEU cc_start: 0.8952 (tp) cc_final: 0.8448 (mp) REVERT: B 524 MET cc_start: 0.4490 (ptp) cc_final: 0.3552 (ptp) REVERT: C 460 GLN cc_start: 0.8578 (tt0) cc_final: 0.8091 (pt0) REVERT: C 524 MET cc_start: 0.4574 (ptp) cc_final: 0.3666 (ptm) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.1174 time to fit residues: 24.1576 Evaluate side-chains 144 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 31 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 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 184 GLN B 38 HIS ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.113321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.092458 restraints weight = 16010.930| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.31 r_work: 0.2672 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13185 Z= 0.092 Angle : 0.422 6.730 17676 Z= 0.216 Chirality : 0.037 0.133 1878 Planarity : 0.003 0.029 2154 Dihedral : 13.356 83.357 2277 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.16 % Allowed : 11.68 % Favored : 87.16 % 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 (0.23), residues: 1443 helix: 2.30 (0.18), residues: 933 sheet: -1.13 (0.92), residues: 30 loop : -1.62 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 125 TYR 0.010 0.001 TYR C 152 PHE 0.008 0.001 PHE A 469 TRP 0.007 0.001 TRP B 180 HIS 0.003 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00197 (13182) covalent geometry : angle 0.42251 (17670) SS BOND : bond 0.00103 ( 3) SS BOND : angle 0.28695 ( 6) hydrogen bonds : bond 0.03662 ( 693) hydrogen bonds : angle 3.57440 ( 1980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.347 Fit side-chains REVERT: A 125 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7421 (mtp180) REVERT: A 159 GLU cc_start: 0.8316 (tt0) cc_final: 0.8015 (tt0) REVERT: A 233 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7573 (tpp80) REVERT: A 245 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.8058 (mtm110) REVERT: A 524 MET cc_start: 0.4687 (ptp) cc_final: 0.3679 (ptp) REVERT: B 191 GLN cc_start: 0.8108 (pp30) cc_final: 0.7808 (pt0) REVERT: B 306 ILE cc_start: 0.9023 (mt) cc_final: 0.8695 (mt) REVERT: B 428 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8199 (mt0) REVERT: B 477 LEU cc_start: 0.8936 (tp) cc_final: 0.8473 (mp) REVERT: B 524 MET cc_start: 0.4561 (ptp) cc_final: 0.3664 (ptp) REVERT: C 428 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8159 (mt0) REVERT: C 460 GLN cc_start: 0.8592 (tt0) cc_final: 0.8109 (pt0) REVERT: C 524 MET cc_start: 0.4874 (ptp) cc_final: 0.3670 (ptm) outliers start: 15 outliers final: 11 residues processed: 148 average time/residue: 0.1163 time to fit residues: 24.4265 Evaluate side-chains 141 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN C 507 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.111117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.089972 restraints weight = 15931.656| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.31 r_work: 0.2628 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13185 Z= 0.139 Angle : 0.467 7.299 17676 Z= 0.236 Chirality : 0.038 0.133 1878 Planarity : 0.003 0.029 2154 Dihedral : 13.563 83.700 2277 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.08 % Allowed : 11.91 % Favored : 87.01 % 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: 1.63 (0.23), residues: 1443 helix: 2.33 (0.18), residues: 933 sheet: -1.07 (0.92), residues: 30 loop : -1.40 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 125 TYR 0.011 0.001 TYR C 152 PHE 0.009 0.001 PHE B 475 TRP 0.010 0.001 TRP C 180 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00336 (13182) covalent geometry : angle 0.46669 (17670) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.19312 ( 6) hydrogen bonds : bond 0.04173 ( 693) hydrogen bonds : angle 3.66965 ( 1980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.437 Fit side-chains REVERT: A 125 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7423 (mtp180) REVERT: A 159 GLU cc_start: 0.8342 (tt0) cc_final: 0.8016 (tt0) REVERT: A 233 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7562 (tpp80) REVERT: A 245 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.8084 (mtm110) REVERT: A 524 MET cc_start: 0.4776 (ptp) cc_final: 0.3705 (ptp) REVERT: B 191 GLN cc_start: 0.8119 (pp30) cc_final: 0.7808 (pt0) REVERT: B 306 ILE cc_start: 0.9024 (mt) cc_final: 0.8711 (mt) REVERT: B 428 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8247 (mt0) REVERT: B 477 LEU cc_start: 0.8918 (tp) cc_final: 0.8431 (mp) REVERT: B 524 MET cc_start: 0.4594 (ptp) cc_final: 0.3677 (ptp) REVERT: C 428 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8167 (mt0) REVERT: C 460 GLN cc_start: 0.8599 (tt0) cc_final: 0.8142 (pt0) REVERT: C 524 MET cc_start: 0.4773 (ptp) cc_final: 0.3556 (ptm) outliers start: 14 outliers final: 13 residues processed: 142 average time/residue: 0.1156 time to fit residues: 23.4502 Evaluate side-chains 143 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.112550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.091719 restraints weight = 15987.607| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.30 r_work: 0.2660 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13185 Z= 0.102 Angle : 0.435 6.865 17676 Z= 0.222 Chirality : 0.037 0.133 1878 Planarity : 0.003 0.030 2154 Dihedral : 13.138 81.613 2277 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.16 % Allowed : 12.06 % Favored : 86.77 % 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: 1.77 (0.23), residues: 1443 helix: 2.51 (0.18), residues: 918 sheet: -1.00 (0.93), residues: 30 loop : -1.38 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 231 TYR 0.012 0.001 TYR C 152 PHE 0.009 0.001 PHE A 469 TRP 0.007 0.001 TRP B 180 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00232 (13182) covalent geometry : angle 0.43480 (17670) SS BOND : bond 0.00139 ( 3) SS BOND : angle 0.27904 ( 6) hydrogen bonds : bond 0.03776 ( 693) hydrogen bonds : angle 3.58410 ( 1980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.356 Fit side-chains REVERT: A 125 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7374 (mtp180) REVERT: A 159 GLU cc_start: 0.8366 (tt0) cc_final: 0.8051 (tt0) REVERT: A 233 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7546 (tpp80) REVERT: A 245 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.7970 (mtm110) REVERT: A 266 GLU cc_start: 0.7902 (tp30) cc_final: 0.7614 (tp30) REVERT: A 524 MET cc_start: 0.4699 (ptp) cc_final: 0.3724 (ptp) REVERT: B 191 GLN cc_start: 0.8106 (pp30) cc_final: 0.7887 (pt0) REVERT: B 306 ILE cc_start: 0.9024 (mt) cc_final: 0.8692 (mt) REVERT: B 428 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8216 (mt0) REVERT: B 477 LEU cc_start: 0.8904 (tp) cc_final: 0.8460 (mp) REVERT: B 524 MET cc_start: 0.4560 (ptp) cc_final: 0.3683 (ptp) REVERT: C 428 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8156 (mt0) REVERT: C 460 GLN cc_start: 0.8598 (tt0) cc_final: 0.8136 (pt0) outliers start: 15 outliers final: 14 residues processed: 141 average time/residue: 0.1157 time to fit residues: 23.4343 Evaluate side-chains 144 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN C 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.113617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.092669 restraints weight = 15912.229| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.31 r_work: 0.2666 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13185 Z= 0.098 Angle : 0.433 7.608 17676 Z= 0.221 Chirality : 0.037 0.132 1878 Planarity : 0.003 0.030 2154 Dihedral : 12.822 79.848 2277 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.01 % Allowed : 12.76 % Favored : 86.23 % 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: 1.75 (0.23), residues: 1443 helix: 2.44 (0.18), residues: 933 sheet: -0.94 (0.94), residues: 30 loop : -1.41 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.012 0.001 TYR C 152 PHE 0.009 0.001 PHE A 469 TRP 0.008 0.001 TRP C 180 HIS 0.003 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00220 (13182) covalent geometry : angle 0.43293 (17670) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.24964 ( 6) hydrogen bonds : bond 0.03700 ( 693) hydrogen bonds : angle 3.54030 ( 1980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.447 Fit side-chains REVERT: A 159 GLU cc_start: 0.8377 (tt0) cc_final: 0.8055 (tt0) REVERT: A 233 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7540 (tpp80) REVERT: A 524 MET cc_start: 0.4592 (ptp) cc_final: 0.3674 (ptp) REVERT: B 191 GLN cc_start: 0.8096 (pp30) cc_final: 0.7884 (pt0) REVERT: B 306 ILE cc_start: 0.9024 (mt) cc_final: 0.8689 (mt) REVERT: B 428 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8197 (mt0) REVERT: B 477 LEU cc_start: 0.8894 (tp) cc_final: 0.8473 (mp) REVERT: B 524 MET cc_start: 0.4854 (ptp) cc_final: 0.3998 (ptp) REVERT: C 428 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8052 (mt0) REVERT: C 460 GLN cc_start: 0.8597 (tt0) cc_final: 0.8141 (pt0) outliers start: 13 outliers final: 12 residues processed: 147 average time/residue: 0.1077 time to fit residues: 23.0178 Evaluate side-chains 145 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 113 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.113367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.092357 restraints weight = 15884.834| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.30 r_work: 0.2667 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13185 Z= 0.102 Angle : 0.443 7.678 17676 Z= 0.224 Chirality : 0.037 0.132 1878 Planarity : 0.003 0.030 2154 Dihedral : 12.733 79.022 2277 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.01 % Allowed : 12.76 % Favored : 86.23 % 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: 1.78 (0.23), residues: 1443 helix: 2.46 (0.18), residues: 933 sheet: -0.88 (0.95), residues: 30 loop : -1.39 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.013 0.001 TYR C 152 PHE 0.009 0.001 PHE A 469 TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00234 (13182) covalent geometry : angle 0.44283 (17670) SS BOND : bond 0.00157 ( 3) SS BOND : angle 0.25984 ( 6) hydrogen bonds : bond 0.03733 ( 693) hydrogen bonds : angle 3.54122 ( 1980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.53 seconds wall clock time: 46 minutes 38.35 seconds (2798.35 seconds total)