Starting phenix.real_space_refine on Fri Jul 3 07:45:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jlp_22376/07_2026/7jlp_22376.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlp_22376/07_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_22376/07_2026/7jlp_22376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlp_22376/07_2026/7jlp_22376.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jlp_22376/07_2026/7jlp_22376.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jlp_22376/07_2026/7jlp_22376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jlp_22376/07_2026/7jlp_22376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlp_22376/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 353 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: 353 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: 353 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: 3.08, per 1000 atoms: 0.24 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: 1.03 Conformation dependent library (CDL) restraints added in 564.2 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: 0.36 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: 1.79 Time building geometry restraints manager: 1.36 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: 6846 18.36 - 36.73: 714 36.73 - 55.09: 177 55.09 - 73.46: 33 73.46 - 91.82: 39 Dihedral angle restraints: 7809 sinusoidal: 3531 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 7806 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: 0.740 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.080 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 : 17.049 91.820 5028 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/Z covalent geometry : bond 0.00905 / 0.45 (13182) covalent geometry : angle 1.27066 / 0.49 (17670) SS BOND : bond 0.00133 / 0.09 ( 3) SS BOND : angle 0.57835 / 0.33 ( 6) hydrogen bonds : bond 0.14722 / 9.56 ( 693) hydrogen bonds : angle 5.84978 / 4.19 ( 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 : 0.426 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: 0.1247 time to fit residues: 29.7255 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 : 0.427 ------------------------------------------------------------------------------- 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... 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 = 0.3114 r_free = 0.3114 target = 0.112974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.091920 restraints weight = 15990.226| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.32 r_work: 0.2663 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1232 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= 0.100 Angle : 0.442 5.863 17676 Z= 0.229 Chirality : 0.037 0.135 1878 Planarity : 0.004 0.039 2154 Dihedral : 14.504 85.834 2233 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.70 % Allowed : 6.42 % Favored : 92.88 % 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: -0.21 (0.22), residues: 1443 helix: 1.04 (0.17), residues: 942 sheet: -1.72 (0.92), residues: 30 loop : -2.54 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (13182) covalent geometry : angle 0.44169 / 0.23 (17670) SS BOND : bond 0.00103 / 0.07 ( 3) SS BOND : angle 0.31940 / 0.19 ( 6) hydrogen bonds : bond 0.04014 / 2.59 ( 693) hydrogen bonds : angle 3.91862 / 2.77 ( 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 138 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.493 Fit side-chains REVERT: A 159 GLU cc_start: 0.8328 (tt0) cc_final: 0.8098 (tt0) REVERT: A 233 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7567 (tpp80) REVERT: A 245 ARG cc_start: 0.8379 (mtt-85) cc_final: 0.7864 (mtm110) REVERT: A 524 MET cc_start: 0.5039 (ptp) cc_final: 0.3443 (ptm) REVERT: B 62 MET cc_start: 0.8362 (ttp) cc_final: 0.8033 (ttp) REVERT: B 91 ILE cc_start: 0.8793 (pt) cc_final: 0.8579 (pt) REVERT: B 191 GLN cc_start: 0.8292 (pp30) cc_final: 0.8008 (pt0) REVERT: B 306 ILE cc_start: 0.9013 (mt) cc_final: 0.8733 (mt) REVERT: B 375 LEU cc_start: 0.8858 (mt) cc_final: 0.8603 (mt) REVERT: B 477 LEU cc_start: 0.8926 (tp) cc_final: 0.8373 (mp) REVERT: B 479 GLU cc_start: 0.8597 (tp30) cc_final: 0.8316 (mm-30) REVERT: B 524 MET cc_start: 0.4603 (ptp) cc_final: 0.3803 (ptp) REVERT: C 266 GLU cc_start: 0.7809 (tp30) cc_final: 0.7535 (tp30) outliers start: 9 outliers final: 9 residues processed: 138 average time/residue: 0.1250 time to fit residues: 24.7493 Evaluate side-chains 124 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 4.9990 chunk 68 optimal weight: 0.1980 chunk 110 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN A 191 GLN A 379 ASN B 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.108493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.087406 restraints weight = 16362.868| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.31 r_work: 0.2594 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13185 Z= 0.210 Angle : 0.521 5.473 17676 Z= 0.264 Chirality : 0.040 0.150 1878 Planarity : 0.004 0.039 2154 Dihedral : 14.671 84.781 2223 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.08 % Allowed : 8.51 % Favored : 90.41 % 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: 0.12 (0.22), residues: 1443 helix: 1.32 (0.17), residues: 948 sheet: -2.86 (0.63), residues: 60 loop : -2.32 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.012 0.001 TYR A 152 PHE 0.016 0.001 PHE C 469 TRP 0.012 0.001 TRP A 292 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 (13182) covalent geometry : angle 0.52054 / 0.26 (17670) SS BOND : bond 0.00311 / 0.20 ( 3) SS BOND : angle 0.48144 / 0.30 ( 6) hydrogen bonds : bond 0.05007 / 3.22 ( 693) hydrogen bonds : angle 3.97483 / 2.80 ( 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 128 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.489 Fit side-chains REVERT: A 159 GLU cc_start: 0.8407 (tt0) cc_final: 0.8033 (tt0) REVERT: B 91 ILE cc_start: 0.8822 (pt) cc_final: 0.8557 (pt) REVERT: B 191 GLN cc_start: 0.8298 (pp30) cc_final: 0.7977 (pt0) REVERT: B 245 ARG cc_start: 0.8225 (mtt180) cc_final: 0.8017 (mtp85) REVERT: B 306 ILE cc_start: 0.9057 (mt) cc_final: 0.8777 (mt) REVERT: B 524 MET cc_start: 0.4554 (ptp) cc_final: 0.3576 (ptp) outliers start: 14 outliers final: 11 residues processed: 125 average time/residue: 0.1291 time to fit residues: 23.0666 Evaluate side-chains 121 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 131 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3091 r_free = 0.3091 target = 0.111252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.090047 restraints weight = 16107.184| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.33 r_work: 0.2631 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13185 Z= 0.114 Angle : 0.439 5.185 17676 Z= 0.226 Chirality : 0.037 0.131 1878 Planarity : 0.003 0.040 2154 Dihedral : 14.023 88.864 2223 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.08 % Allowed : 9.74 % Favored : 89.17 % 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: 0.78 (0.23), residues: 1443 helix: 1.76 (0.18), residues: 945 sheet: -1.46 (0.90), residues: 30 loop : -2.06 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 125 TYR 0.010 0.001 TYR C 152 PHE 0.011 0.001 PHE A 469 TRP 0.008 0.001 TRP B 180 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (13182) covalent geometry : angle 0.43883 / 0.23 (17670) SS BOND : bond 0.00149 / 0.10 ( 3) SS BOND : angle 0.37051 / 0.23 ( 6) hydrogen bonds : bond 0.04122 / 2.67 ( 693) hydrogen bonds : angle 3.77193 / 2.65 ( 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 135 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.465 Fit side-chains REVERT: A 159 GLU cc_start: 0.8390 (tt0) cc_final: 0.8008 (tt0) REVERT: A 233 ARG cc_start: 0.7840 (mmm-85) cc_final: 0.7577 (tpp80) REVERT: A 245 ARG cc_start: 0.8458 (mtt-85) cc_final: 0.7939 (mtm110) REVERT: A 524 MET cc_start: 0.5007 (ptp) cc_final: 0.3425 (ptm) REVERT: B 91 ILE cc_start: 0.8856 (pt) cc_final: 0.8555 (pt) REVERT: B 191 GLN cc_start: 0.8282 (pp30) cc_final: 0.8013 (pt0) REVERT: B 306 ILE cc_start: 0.9037 (mt) cc_final: 0.8754 (mt) REVERT: B 428 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8282 (mt0) REVERT: B 524 MET cc_start: 0.4488 (ptp) cc_final: 0.3538 (ptp) REVERT: C 263 PHE cc_start: 0.9191 (m-80) cc_final: 0.8983 (m-80) REVERT: C 524 MET cc_start: 0.4620 (ptp) cc_final: 0.3672 (ptm) outliers start: 14 outliers final: 12 residues processed: 130 average time/residue: 0.1278 time to fit residues: 23.8595 Evaluate side-chains 125 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 269 LEU 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: 3.9990 chunk 117 optimal weight: 0.0370 chunk 61 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3100 r_free = 0.3100 target = 0.112119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.091149 restraints weight = 16107.774| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.31 r_work: 0.2649 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1724 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= 0.107 Angle : 0.427 5.150 17676 Z= 0.221 Chirality : 0.037 0.133 1878 Planarity : 0.003 0.040 2154 Dihedral : 13.473 87.939 2223 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.31 % Allowed : 9.82 % Favored : 88.86 % 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: 1.12 (0.23), residues: 1443 helix: 1.98 (0.18), residues: 945 sheet: -1.40 (0.89), residues: 30 loop : -1.81 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 125 TYR 0.011 0.001 TYR C 152 PHE 0.010 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/Z covalent geometry : bond 0.00244 / 0.11 (13182) covalent geometry : angle 0.42733 / 0.22 (17670) SS BOND : bond 0.00156 / 0.10 ( 3) SS BOND : angle 0.34674 / 0.21 ( 6) hydrogen bonds : bond 0.03923 / 2.54 ( 693) hydrogen bonds : angle 3.67812 / 2.59 ( 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 137 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.415 Fit side-chains REVERT: A 159 GLU cc_start: 0.8300 (tt0) cc_final: 0.7976 (tt0) REVERT: A 233 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7571 (tpp80) REVERT: A 245 ARG cc_start: 0.8490 (mtt-85) cc_final: 0.7971 (mtm110) REVERT: A 524 MET cc_start: 0.4904 (ptp) cc_final: 0.3374 (ptm) REVERT: B 191 GLN cc_start: 0.8193 (pp30) cc_final: 0.7881 (pt0) REVERT: B 306 ILE cc_start: 0.9042 (mt) cc_final: 0.8749 (mt) REVERT: B 428 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8203 (mt0) REVERT: B 479 GLU cc_start: 0.8712 (tp30) cc_final: 0.8432 (tp30) REVERT: B 524 MET cc_start: 0.4477 (ptp) cc_final: 0.3542 (ptp) REVERT: C 428 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8097 (mt0) REVERT: C 524 MET cc_start: 0.4587 (ptp) cc_final: 0.3660 (ptm) outliers start: 17 outliers final: 11 residues processed: 133 average time/residue: 0.1180 time to fit residues: 22.8571 Evaluate side-chains 134 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 430 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN B 38 HIS B 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.109621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.088608 restraints weight = 16111.037| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.31 r_work: 0.2606 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13185 Z= 0.180 Angle : 0.493 6.607 17676 Z= 0.250 Chirality : 0.040 0.133 1878 Planarity : 0.003 0.039 2154 Dihedral : 13.916 89.121 2223 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.31 % Allowed : 11.06 % Favored : 87.63 % 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: 1.21 (0.23), residues: 1443 helix: 1.97 (0.18), residues: 939 sheet: -1.31 (0.91), residues: 30 loop : -1.52 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 125 TYR 0.012 0.001 TYR B 209 PHE 0.010 0.001 PHE C 469 TRP 0.009 0.001 TRP C 180 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (13182) covalent geometry : angle 0.49341 / 0.25 (17670) SS BOND : bond 0.00297 / 0.19 ( 3) SS BOND : angle 0.36607 / 0.21 ( 6) hydrogen bonds : bond 0.04651 / 3.00 ( 693) hydrogen bonds : angle 3.81171 / 2.68 ( 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 134 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.462 Fit side-chains REVERT: A 159 GLU cc_start: 0.8345 (tt0) cc_final: 0.8008 (tt0) REVERT: A 233 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7580 (tpp80) REVERT: A 524 MET cc_start: 0.5015 (ptp) cc_final: 0.3455 (ptm) REVERT: B 191 GLN cc_start: 0.8176 (pp30) cc_final: 0.7910 (pt0) REVERT: B 306 ILE cc_start: 0.9034 (mt) cc_final: 0.8754 (mt) REVERT: B 428 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8281 (mt0) REVERT: B 479 GLU cc_start: 0.8769 (tp30) cc_final: 0.8469 (tp30) REVERT: B 524 MET cc_start: 0.4509 (ptp) cc_final: 0.3544 (ptp) REVERT: C 193 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.5881 (mp0) REVERT: C 428 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8156 (mt0) REVERT: C 460 GLN cc_start: 0.8624 (tt0) cc_final: 0.8141 (pt0) outliers start: 17 outliers final: 13 residues processed: 130 average time/residue: 0.1166 time to fit residues: 21.7391 Evaluate side-chains 126 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 B residue 431 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 GLU 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: 1.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3103 r_free = 0.3103 target = 0.112300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.091247 restraints weight = 16047.406| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.32 r_work: 0.2656 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1867 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= 0.096 Angle : 0.422 5.540 17676 Z= 0.217 Chirality : 0.037 0.135 1878 Planarity : 0.003 0.039 2154 Dihedral : 13.218 89.467 2223 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.93 % Allowed : 11.68 % Favored : 87.39 % 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: 1.53 (0.23), residues: 1443 helix: 2.26 (0.18), residues: 933 sheet: -1.25 (0.90), residues: 30 loop : -1.46 (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/Z covalent geometry : bond 0.00208 / 0.10 (13182) covalent geometry : angle 0.42199 / 0.22 (17670) SS BOND : bond 0.00123 / 0.08 ( 3) SS BOND : angle 0.35964 / 0.21 ( 6) hydrogen bonds : bond 0.03819 / 2.48 ( 693) hydrogen bonds : angle 3.64886 / 2.57 ( 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 143 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.348 Fit side-chains REVERT: A 159 GLU cc_start: 0.8322 (tt0) cc_final: 0.8014 (tt0) REVERT: A 233 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7567 (tpp80) REVERT: A 245 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.8098 (mtm110) REVERT: A 524 MET cc_start: 0.4778 (ptp) cc_final: 0.3708 (ptp) REVERT: B 191 GLN cc_start: 0.8118 (pp30) cc_final: 0.7812 (pt0) REVERT: B 306 ILE cc_start: 0.9030 (mt) cc_final: 0.8742 (mt) REVERT: B 428 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8251 (mt0) REVERT: B 479 GLU cc_start: 0.8697 (tp30) cc_final: 0.8360 (tp30) REVERT: B 524 MET cc_start: 0.4505 (ptp) cc_final: 0.3563 (ptp) REVERT: C 428 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8122 (mt0) REVERT: C 460 GLN cc_start: 0.8578 (tt0) cc_final: 0.8134 (pt0) REVERT: C 524 MET cc_start: 0.4763 (ptp) cc_final: 0.3548 (ptm) outliers start: 12 outliers final: 11 residues processed: 140 average time/residue: 0.1079 time to fit residues: 21.8808 Evaluate side-chains 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.112948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.092124 restraints weight = 15898.994| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.31 r_work: 0.2663 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13185 Z= 0.098 Angle : 0.427 7.257 17676 Z= 0.219 Chirality : 0.037 0.132 1878 Planarity : 0.003 0.039 2154 Dihedral : 12.844 88.836 2223 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.85 % Allowed : 12.22 % Favored : 86.93 % 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: 1.53 (0.23), residues: 1443 helix: 2.32 (0.18), residues: 933 sheet: -1.14 (0.91), residues: 30 loop : -1.60 (0.27), residues: 480 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 0.008 0.001 TRP B 180 HIS 0.003 0.000 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (13182) covalent geometry : angle 0.42710 / 0.22 (17670) SS BOND : bond 0.00148 / 0.09 ( 3) SS BOND : angle 0.29914 / 0.15 ( 6) hydrogen bonds : bond 0.03748 / 2.43 ( 693) hydrogen bonds : angle 3.59173 / 2.53 ( 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 140 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.456 Fit side-chains REVERT: A 125 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7426 (mtp180) REVERT: A 159 GLU cc_start: 0.8323 (tt0) cc_final: 0.8022 (tt0) REVERT: A 233 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7570 (tpp80) REVERT: A 245 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.7897 (mtm110) REVERT: A 524 MET cc_start: 0.4681 (ptp) cc_final: 0.3696 (ptp) REVERT: B 191 GLN cc_start: 0.8132 (pp30) cc_final: 0.7835 (pt0) REVERT: B 306 ILE cc_start: 0.9031 (mt) cc_final: 0.8698 (mt) REVERT: B 428 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8247 (mt0) REVERT: B 477 LEU cc_start: 0.8901 (tp) cc_final: 0.8457 (mp) REVERT: B 479 GLU cc_start: 0.8701 (tp30) cc_final: 0.8408 (tp30) REVERT: B 524 MET cc_start: 0.4538 (ptp) cc_final: 0.3663 (ptp) REVERT: C 428 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8178 (mt0) REVERT: C 460 GLN cc_start: 0.8592 (tt0) cc_final: 0.8107 (pt0) REVERT: C 524 MET cc_start: 0.4760 (ptp) cc_final: 0.3642 (ptm) outliers start: 11 outliers final: 11 residues processed: 138 average time/residue: 0.1085 time to fit residues: 21.5400 Evaluate side-chains 138 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.111255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.090272 restraints weight = 16064.312| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.31 r_work: 0.2638 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13185 Z= 0.126 Angle : 0.454 7.557 17676 Z= 0.230 Chirality : 0.038 0.132 1878 Planarity : 0.003 0.039 2154 Dihedral : 12.964 89.307 2223 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.08 % Allowed : 12.22 % Favored : 86.70 % 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: 1.68 (0.23), residues: 1443 helix: 2.35 (0.18), residues: 933 sheet: -1.16 (0.91), residues: 30 loop : -1.33 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 125 TYR 0.011 0.001 TYR C 152 PHE 0.009 0.001 PHE B 475 TRP 0.009 0.001 TRP C 180 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13182) covalent geometry : angle 0.45365 / 0.23 (17670) SS BOND : bond 0.00217 / 0.14 ( 3) SS BOND : angle 0.33553 / 0.17 ( 6) hydrogen bonds : bond 0.04061 / 2.63 ( 693) hydrogen bonds : angle 3.64089 / 2.56 ( 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 143 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.439 Fit side-chains REVERT: A 125 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7434 (mtp180) REVERT: A 159 GLU cc_start: 0.8348 (tt0) cc_final: 0.8023 (tt0) REVERT: A 233 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7560 (tpp80) REVERT: A 245 ARG cc_start: 0.8547 (mtt-85) cc_final: 0.8105 (mtm110) REVERT: A 524 MET cc_start: 0.4741 (ptp) cc_final: 0.3749 (ptp) REVERT: B 191 GLN cc_start: 0.8104 (pp30) cc_final: 0.7795 (pt0) REVERT: B 306 ILE cc_start: 0.9035 (mt) cc_final: 0.8725 (mt) REVERT: B 428 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8262 (mt0) REVERT: B 477 LEU cc_start: 0.8874 (tp) cc_final: 0.8415 (mp) REVERT: B 479 GLU cc_start: 0.8701 (tp30) cc_final: 0.8401 (tp30) REVERT: B 524 MET cc_start: 0.4570 (ptp) cc_final: 0.3682 (ptp) REVERT: C 428 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8182 (mt0) REVERT: C 460 GLN cc_start: 0.8595 (tt0) cc_final: 0.8140 (pt0) REVERT: C 524 MET cc_start: 0.4817 (ptp) cc_final: 0.3639 (ptm) outliers start: 14 outliers final: 13 residues processed: 140 average time/residue: 0.1054 time to fit residues: 21.2836 Evaluate side-chains 140 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3118 r_free = 0.3118 target = 0.113581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.092607 restraints weight = 15901.440| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.32 r_work: 0.2670 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2072 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= 0.092 Angle : 0.422 7.228 17676 Z= 0.216 Chirality : 0.037 0.134 1878 Planarity : 0.003 0.039 2154 Dihedral : 12.533 89.815 2223 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.85 % Allowed : 12.37 % 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: 1.70 (0.23), residues: 1443 helix: 2.41 (0.18), residues: 933 sheet: -1.10 (0.92), residues: 30 loop : -1.42 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 125 TYR 0.011 0.001 TYR C 152 PHE 0.008 0.001 PHE A 469 TRP 0.007 0.001 TRP B 180 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (13182) covalent geometry : angle 0.42203 / 0.22 (17670) SS BOND : bond 0.00106 / 0.07 ( 3) SS BOND : angle 0.37001 / 0.21 ( 6) hydrogen bonds : bond 0.03658 / 2.38 ( 693) hydrogen bonds : angle 3.54564 / 2.50 ( 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 139 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.476 Fit side-chains REVERT: A 159 GLU cc_start: 0.8377 (tt0) cc_final: 0.8065 (tt0) REVERT: A 233 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7564 (tpp80) REVERT: A 524 MET cc_start: 0.4584 (ptp) cc_final: 0.3634 (ptp) REVERT: B 62 MET cc_start: 0.8269 (ttm) cc_final: 0.7972 (ttp) REVERT: B 191 GLN cc_start: 0.8083 (pp30) cc_final: 0.7805 (pt0) REVERT: B 306 ILE cc_start: 0.9020 (mt) cc_final: 0.8691 (mt) REVERT: B 428 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8205 (mt0) REVERT: B 477 LEU cc_start: 0.8873 (tp) cc_final: 0.8467 (mp) REVERT: B 479 GLU cc_start: 0.8735 (tp30) cc_final: 0.8430 (tp30) REVERT: B 524 MET cc_start: 0.4846 (ptp) cc_final: 0.3999 (ptp) REVERT: C 428 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8151 (mt0) REVERT: C 460 GLN cc_start: 0.8591 (tt0) cc_final: 0.8116 (pt0) outliers start: 11 outliers final: 11 residues processed: 137 average time/residue: 0.1138 time to fit residues: 22.6794 Evaluate side-chains 139 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 57 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3103 r_free = 0.3103 target = 0.112342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.091204 restraints weight = 15957.987| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.32 r_work: 0.2646 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13185 Z= 0.117 Angle : 0.443 7.641 17676 Z= 0.225 Chirality : 0.038 0.131 1878 Planarity : 0.003 0.039 2154 Dihedral : 12.647 89.249 2223 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.01 % Allowed : 12.45 % Favored : 86.54 % 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: 1.65 (0.23), residues: 1443 helix: 2.24 (0.18), residues: 957 sheet: -1.08 (0.92), residues: 30 loop : -1.34 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 125 TYR 0.012 0.001 TYR C 152 PHE 0.009 0.001 PHE B 475 TRP 0.009 0.001 TRP C 180 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13182) covalent geometry : angle 0.44342 / 0.23 (17670) SS BOND : bond 0.00196 / 0.13 ( 3) SS BOND : angle 0.34882 / 0.17 ( 6) hydrogen bonds : bond 0.03946 / 2.56 ( 693) hydrogen bonds : angle 3.58624 / 2.53 ( 1980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.53 seconds wall clock time: 49 minutes 15.60 seconds (2955.60 seconds total)