Starting phenix.real_space_refine on Mon Aug 25 01:28:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz9_41738/08_2025/8tz9_41738_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz9_41738/08_2025/8tz9_41738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz9_41738/08_2025/8tz9_41738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz9_41738/08_2025/8tz9_41738.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz9_41738/08_2025/8tz9_41738_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz9_41738/08_2025/8tz9_41738_trim.cif" } resolution = 3.67 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= 0.008 sd= 0.045 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 S 87 5.16 5 C 8103 2.51 5 N 1923 2.21 5 O 2115 1.98 5 H 12069 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24297 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.62, per 1000 atoms: 0.19 Number of scatterers: 24297 At special positions: 0 Unit cell: (128.52, 130.68, 75.6, 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 87 16.00 O 2115 8.00 N 1923 7.00 C 8103 6.00 H 12069 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 797.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 90.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 130 through 157 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.683A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.711A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.437A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 277 removed outlier: 3.534A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 283 through 287 removed outlier: 4.369A pdb=" N THR B 286 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 313 through 330 removed outlier: 3.511A pdb=" N GLY B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.563A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 3.978A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 3.981A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 481 removed outlier: 3.660A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.522A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 496 " --> pdb=" O CYS B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.227A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.969A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 586 Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.595A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 612 " --> pdb=" O CYS B 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 130 through 157 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 157 through 203 Proline residue: A 167 - end of helix removed outlier: 4.683A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.712A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.436A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 277 removed outlier: 3.535A pdb=" N ALA A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.368A pdb=" N THR A 286 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 293 through 312 Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.510A pdb=" N GLY A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 349 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.563A pdb=" N THR A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.978A pdb=" N GLY A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 3.981A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 481 removed outlier: 3.659A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.521A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 496 " --> pdb=" O CYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.227A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.971A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 586 Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.595A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 612 " --> pdb=" O CYS A 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 130 through 157 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 157 through 201 Proline residue: C 167 - end of helix removed outlier: 4.682A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.712A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.438A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 277 removed outlier: 3.534A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 283 through 287 removed outlier: 4.369A pdb=" N THR C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 293 through 312 Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.511A pdb=" N GLY C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 376 removed outlier: 3.564A pdb=" N THR C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.978A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 389 " --> pdb=" O TYR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 3.980A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 481 removed outlier: 3.660A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.522A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 496 " --> pdb=" O CYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.226A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.971A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 586 Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.593A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 612 " --> pdb=" O CYS C 608 " (cutoff:3.500A) 992 hydrogen bonds defined for protein. 2931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12051 1.03 - 1.23: 27 1.23 - 1.42: 5325 1.42 - 1.62: 7071 1.62 - 1.81: 159 Bond restraints: 24633 Sorted by residual: bond pdb=" C11 XMO B 801 " pdb=" O12 XMO B 801 " ideal model delta sigma weight residual 1.398 1.678 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C11 XMO A 801 " pdb=" O12 XMO A 801 " ideal model delta sigma weight residual 1.398 1.677 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C11 XMO C 801 " pdb=" O12 XMO C 801 " ideal model delta sigma weight residual 1.398 1.677 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C10 XMO B 801 " pdb=" C11 XMO B 801 " ideal model delta sigma weight residual 1.534 1.287 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C10 XMO A 801 " pdb=" C11 XMO A 801 " ideal model delta sigma weight residual 1.534 1.288 0.246 2.00e-02 2.50e+03 1.52e+02 ... (remaining 24628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 43768 1.79 - 3.58: 589 3.58 - 5.38: 70 5.38 - 7.17: 6 7.17 - 8.96: 3 Bond angle restraints: 44436 Sorted by residual: angle pdb=" N ASP B 548 " pdb=" CA ASP B 548 " pdb=" C ASP B 548 " ideal model delta sigma weight residual 108.19 103.35 4.84 1.29e+00 6.01e-01 1.41e+01 angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" C ASP A 548 " ideal model delta sigma weight residual 108.19 103.35 4.84 1.29e+00 6.01e-01 1.41e+01 angle pdb=" N ASP C 548 " pdb=" CA ASP C 548 " pdb=" C ASP C 548 " ideal model delta sigma weight residual 108.19 103.40 4.79 1.29e+00 6.01e-01 1.38e+01 angle pdb=" C THR B 252 " pdb=" N GLU B 253 " pdb=" CA GLU B 253 " ideal model delta sigma weight residual 119.78 124.07 -4.29 1.24e+00 6.50e-01 1.20e+01 angle pdb=" C THR A 252 " pdb=" N GLU A 253 " pdb=" CA GLU A 253 " ideal model delta sigma weight residual 119.78 124.07 -4.29 1.24e+00 6.50e-01 1.20e+01 ... (remaining 44431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.35: 11306 32.35 - 64.70: 409 64.70 - 97.06: 15 97.06 - 129.41: 3 129.41 - 161.76: 12 Dihedral angle restraints: 11745 sinusoidal: 6015 harmonic: 5730 Sorted by residual: dihedral pdb=" C01 XMO B 801 " pdb=" C02 XMO B 801 " pdb=" C04 XMO B 801 " pdb=" O06 XMO B 801 " ideal model delta sinusoidal sigma weight residual 296.92 135.16 161.76 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C01 XMO C 801 " pdb=" C02 XMO C 801 " pdb=" C04 XMO C 801 " pdb=" O06 XMO C 801 " ideal model delta sinusoidal sigma weight residual 296.92 135.23 161.69 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C01 XMO A 801 " pdb=" C02 XMO A 801 " pdb=" C04 XMO A 801 " pdb=" O06 XMO A 801 " ideal model delta sinusoidal sigma weight residual 296.92 135.31 161.61 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 11742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1764 0.067 - 0.135: 219 0.135 - 0.202: 0 0.202 - 0.270: 0 0.270 - 0.337: 3 Chirality restraints: 1986 Sorted by residual: chirality pdb=" C10 XMO B 801 " pdb=" C09 XMO B 801 " pdb=" C11 XMO B 801 " pdb=" O22 XMO B 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C10 XMO A 801 " pdb=" C09 XMO A 801 " pdb=" C11 XMO A 801 " pdb=" O22 XMO A 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C10 XMO C 801 " pdb=" C09 XMO C 801 " pdb=" C11 XMO C 801 " pdb=" O22 XMO C 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1983 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 196 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C VAL C 196 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL C 196 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE C 197 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 196 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C VAL B 196 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL B 196 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 197 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 196 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C VAL A 196 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 196 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 197 " -0.009 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 942 2.18 - 2.78: 46802 2.78 - 3.39: 67605 3.39 - 3.99: 84316 3.99 - 4.60: 134630 Nonbonded interactions: 334295 Sorted by model distance: nonbonded pdb=" O LEU A 195 " pdb=" HG1 THR A 199 " model vdw 1.569 2.450 nonbonded pdb=" O LEU B 195 " pdb=" HG1 THR B 199 " model vdw 1.569 2.450 nonbonded pdb=" O LEU C 195 " pdb=" HG1 THR C 199 " model vdw 1.573 2.450 nonbonded pdb=" O LEU B 248 " pdb=" HG1 THR B 252 " model vdw 1.584 2.450 nonbonded pdb=" O LEU A 248 " pdb=" HG1 THR A 252 " model vdw 1.588 2.450 ... (remaining 334290 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.770 Find NCS groups from input model: 0.170 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 0.280 12564 Z= 0.452 Angle : 0.604 8.962 17118 Z= 0.337 Chirality : 0.041 0.337 1986 Planarity : 0.003 0.036 2082 Dihedral : 15.653 161.760 4275 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.72 % Allowed : 4.57 % Favored : 94.71 % 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 aren not related in a simple way. whole: 3.31 (0.21), residues: 1593 helix: 2.78 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.89 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 557 TYR 0.007 0.001 TYR C 519 PHE 0.012 0.001 PHE A 413 TRP 0.012 0.001 TRP B 316 HIS 0.004 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00900 (12564) covalent geometry : angle 0.60375 (17118) hydrogen bonds : bond 0.14750 ( 992) hydrogen bonds : angle 5.36592 ( 2931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 370 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.9005 (t) cc_final: 0.8776 (p) outliers start: 9 outliers final: 3 residues processed: 378 average time/residue: 0.2178 time to fit residues: 125.5730 Evaluate side-chains 214 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.110398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089186 restraints weight = 86592.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.092858 restraints weight = 33522.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095126 restraints weight = 18391.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.096467 restraints weight = 12803.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097052 restraints weight = 10342.442| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12564 Z= 0.186 Angle : 0.590 6.258 17118 Z= 0.323 Chirality : 0.037 0.117 1986 Planarity : 0.004 0.042 2082 Dihedral : 7.819 76.963 1770 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.84 % Allowed : 11.70 % Favored : 86.46 % 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 aren not related in a simple way. whole: 3.38 (0.21), residues: 1593 helix: 2.83 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.87 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 163 TYR 0.010 0.001 TYR C 483 PHE 0.019 0.002 PHE B 131 TRP 0.008 0.001 TRP C 316 HIS 0.003 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00396 (12564) covalent geometry : angle 0.59002 (17118) hydrogen bonds : bond 0.05591 ( 992) hydrogen bonds : angle 4.73129 ( 2931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 497 MET cc_start: 0.8142 (tmt) cc_final: 0.7854 (tmm) REVERT: A 349 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6824 (mm-30) REVERT: A 440 GLU cc_start: 0.7772 (tp30) cc_final: 0.7317 (tp30) REVERT: A 497 MET cc_start: 0.8402 (tmt) cc_final: 0.8128 (tmm) REVERT: A 556 MET cc_start: 0.7662 (tpp) cc_final: 0.7422 (mmm) REVERT: C 482 ASP cc_start: 0.8393 (t0) cc_final: 0.7973 (t0) REVERT: C 483 TYR cc_start: 0.7972 (t80) cc_final: 0.7319 (m-80) outliers start: 23 outliers final: 16 residues processed: 231 average time/residue: 0.2092 time to fit residues: 75.7340 Evaluate side-chains 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS A 175 HIS C 169 GLN C 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.085124 restraints weight = 86694.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088641 restraints weight = 34538.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.090775 restraints weight = 19351.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091974 restraints weight = 13709.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.092525 restraints weight = 11341.675| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12564 Z= 0.199 Angle : 0.549 5.179 17118 Z= 0.307 Chirality : 0.037 0.136 1986 Planarity : 0.003 0.039 2082 Dihedral : 6.683 83.079 1770 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.21 % Allowed : 11.54 % Favored : 85.26 % 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 aren not related in a simple way. whole: 3.25 (0.21), residues: 1593 helix: 2.75 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.98 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 163 TYR 0.012 0.001 TYR B 310 PHE 0.018 0.002 PHE A 501 TRP 0.007 0.001 TRP A 316 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00421 (12564) covalent geometry : angle 0.54933 (17118) hydrogen bonds : bond 0.05735 ( 992) hydrogen bonds : angle 4.64805 ( 2931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 267 GLN cc_start: 0.8396 (tt0) cc_final: 0.8150 (tp40) REVERT: C 207 LEU cc_start: 0.8754 (mt) cc_final: 0.8485 (tt) REVERT: C 283 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: C 483 TYR cc_start: 0.7713 (t80) cc_final: 0.7083 (m-80) outliers start: 40 outliers final: 27 residues processed: 202 average time/residue: 0.1808 time to fit residues: 59.9890 Evaluate side-chains 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 132 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.106172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.085159 restraints weight = 87496.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088658 restraints weight = 33773.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.090826 restraints weight = 18761.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.092043 restraints weight = 13243.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.092770 restraints weight = 10894.794| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12564 Z= 0.138 Angle : 0.482 4.786 17118 Z= 0.262 Chirality : 0.035 0.121 1986 Planarity : 0.003 0.042 2082 Dihedral : 5.743 74.591 1770 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.32 % Allowed : 12.58 % Favored : 85.10 % 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 aren not related in a simple way. whole: 3.50 (0.21), residues: 1593 helix: 2.93 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.97 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 163 TYR 0.010 0.001 TYR B 564 PHE 0.013 0.001 PHE B 138 TRP 0.007 0.001 TRP B 176 HIS 0.002 0.001 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00289 (12564) covalent geometry : angle 0.48189 (17118) hydrogen bonds : bond 0.04716 ( 992) hydrogen bonds : angle 4.28597 ( 2931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 267 GLN cc_start: 0.8355 (tt0) cc_final: 0.7969 (tp40) REVERT: B 585 MET cc_start: 0.7387 (mtt) cc_final: 0.7147 (mtt) REVERT: A 257 MET cc_start: 0.7187 (tmm) cc_final: 0.6877 (tmm) REVERT: C 207 LEU cc_start: 0.8675 (mt) cc_final: 0.8406 (tt) REVERT: C 533 SER cc_start: 0.9007 (p) cc_final: 0.8800 (p) REVERT: C 554 MET cc_start: 0.7133 (ptm) cc_final: 0.6902 (ptm) outliers start: 29 outliers final: 24 residues processed: 182 average time/residue: 0.1942 time to fit residues: 58.0655 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 2 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 111 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.103506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.082522 restraints weight = 87400.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.085932 restraints weight = 34103.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087970 restraints weight = 19072.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089202 restraints weight = 13641.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089887 restraints weight = 11222.460| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12564 Z= 0.188 Angle : 0.524 6.532 17118 Z= 0.290 Chirality : 0.036 0.127 1986 Planarity : 0.004 0.040 2082 Dihedral : 5.997 68.409 1766 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.40 % Allowed : 13.70 % Favored : 83.89 % 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 aren not related in a simple way. whole: 3.20 (0.21), residues: 1593 helix: 2.73 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.08 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 163 TYR 0.014 0.001 TYR B 564 PHE 0.017 0.002 PHE B 501 TRP 0.007 0.001 TRP B 176 HIS 0.004 0.001 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00404 (12564) covalent geometry : angle 0.52438 (17118) hydrogen bonds : bond 0.05253 ( 992) hydrogen bonds : angle 4.48290 ( 2931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8875 (mt) cc_final: 0.8645 (tt) REVERT: B 257 MET cc_start: 0.7216 (tmm) cc_final: 0.6912 (tmm) REVERT: A 257 MET cc_start: 0.7171 (tmm) cc_final: 0.6866 (tmm) REVERT: A 501 PHE cc_start: 0.9005 (t80) cc_final: 0.8789 (t80) REVERT: C 207 LEU cc_start: 0.8748 (mt) cc_final: 0.8449 (tt) REVERT: C 283 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7390 (mp0) outliers start: 30 outliers final: 23 residues processed: 181 average time/residue: 0.1877 time to fit residues: 55.6804 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 107 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.104937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084152 restraints weight = 87427.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087611 restraints weight = 33644.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089746 restraints weight = 18696.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090753 restraints weight = 13186.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091533 restraints weight = 11136.056| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12564 Z= 0.137 Angle : 0.474 6.123 17118 Z= 0.257 Chirality : 0.034 0.119 1986 Planarity : 0.003 0.042 2082 Dihedral : 5.331 68.086 1764 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.24 % Allowed : 14.02 % Favored : 83.73 % 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 aren not related in a simple way. whole: 3.41 (0.21), residues: 1593 helix: 2.89 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.11 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 163 TYR 0.011 0.001 TYR B 564 PHE 0.014 0.001 PHE B 221 TRP 0.007 0.001 TRP B 176 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00289 (12564) covalent geometry : angle 0.47384 (17118) hydrogen bonds : bond 0.04503 ( 992) hydrogen bonds : angle 4.21589 ( 2931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 MET cc_start: 0.7207 (tmm) cc_final: 0.6894 (tmm) REVERT: B 585 MET cc_start: 0.7436 (mtt) cc_final: 0.7229 (mtt) REVERT: A 257 MET cc_start: 0.7392 (tmm) cc_final: 0.7056 (tmm) REVERT: A 512 MET cc_start: 0.8169 (mtt) cc_final: 0.7698 (mmm) REVERT: C 207 LEU cc_start: 0.8662 (mt) cc_final: 0.8372 (tt) REVERT: C 283 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7465 (mp0) outliers start: 28 outliers final: 23 residues processed: 176 average time/residue: 0.1888 time to fit residues: 53.8969 Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 128 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.102994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.082215 restraints weight = 88129.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085609 restraints weight = 34380.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.087707 restraints weight = 19206.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.088887 restraints weight = 13590.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089548 restraints weight = 11217.946| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12564 Z= 0.188 Angle : 0.516 7.517 17118 Z= 0.285 Chirality : 0.036 0.124 1986 Planarity : 0.004 0.041 2082 Dihedral : 5.684 65.522 1764 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.24 % Allowed : 14.26 % Favored : 83.49 % 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 aren not related in a simple way. whole: 3.16 (0.21), residues: 1593 helix: 2.67 (0.14), residues: 1329 sheet: None (None), residues: 0 loop : -1.15 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 539 TYR 0.012 0.001 TYR B 564 PHE 0.018 0.002 PHE C 221 TRP 0.008 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00406 (12564) covalent geometry : angle 0.51554 (17118) hydrogen bonds : bond 0.05045 ( 992) hydrogen bonds : angle 4.43147 ( 2931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 MET cc_start: 0.7313 (tmm) cc_final: 0.6991 (tmm) REVERT: B 585 MET cc_start: 0.7491 (mtt) cc_final: 0.7278 (mtt) REVERT: A 257 MET cc_start: 0.7371 (tmm) cc_final: 0.7043 (tmm) REVERT: C 207 LEU cc_start: 0.8769 (mt) cc_final: 0.8462 (tt) outliers start: 28 outliers final: 25 residues processed: 170 average time/residue: 0.1775 time to fit residues: 48.5639 Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 139 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 552 GLN C 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084012 restraints weight = 87658.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087460 restraints weight = 33950.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.089590 restraints weight = 18892.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090810 restraints weight = 13311.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091458 restraints weight = 10938.259| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12564 Z= 0.125 Angle : 0.461 7.898 17118 Z= 0.249 Chirality : 0.034 0.128 1986 Planarity : 0.003 0.044 2082 Dihedral : 5.133 65.602 1764 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.92 % Allowed : 14.58 % Favored : 83.49 % 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 aren not related in a simple way. whole: 3.43 (0.21), residues: 1593 helix: 2.92 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.21 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 539 TYR 0.011 0.001 TYR B 564 PHE 0.015 0.001 PHE B 221 TRP 0.016 0.001 TRP C 184 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00263 (12564) covalent geometry : angle 0.46147 (17118) hydrogen bonds : bond 0.04318 ( 992) hydrogen bonds : angle 4.10997 ( 2931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 MET cc_start: 0.7305 (tmm) cc_final: 0.6950 (tmm) REVERT: A 257 MET cc_start: 0.7296 (tmm) cc_final: 0.6967 (tmm) REVERT: C 207 LEU cc_start: 0.8698 (mt) cc_final: 0.8395 (tt) REVERT: C 325 MET cc_start: 0.8786 (ttm) cc_final: 0.8577 (ttm) outliers start: 24 outliers final: 23 residues processed: 171 average time/residue: 0.1643 time to fit residues: 45.8496 Evaluate side-chains 165 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 6 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.103019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082427 restraints weight = 88236.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085790 restraints weight = 34163.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087889 restraints weight = 19053.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089052 restraints weight = 13464.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089594 restraints weight = 11130.486| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12564 Z= 0.178 Angle : 0.508 7.886 17118 Z= 0.281 Chirality : 0.035 0.123 1986 Planarity : 0.004 0.043 2082 Dihedral : 5.410 62.852 1764 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.08 % Allowed : 14.74 % Favored : 83.17 % 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 aren not related in a simple way. whole: 3.21 (0.21), residues: 1593 helix: 2.77 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.32 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.013 0.001 TYR B 564 PHE 0.020 0.002 PHE A 301 TRP 0.010 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00386 (12564) covalent geometry : angle 0.50822 (17118) hydrogen bonds : bond 0.04826 ( 992) hydrogen bonds : angle 4.34067 ( 2931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 MET cc_start: 0.7292 (tmm) cc_final: 0.6939 (tmm) REVERT: A 257 MET cc_start: 0.7364 (tmm) cc_final: 0.7024 (tmm) REVERT: A 325 MET cc_start: 0.8831 (ttm) cc_final: 0.8552 (ttm) REVERT: C 205 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8149 (mp10) REVERT: C 207 LEU cc_start: 0.8765 (mt) cc_final: 0.8457 (tt) REVERT: C 325 MET cc_start: 0.8845 (ttm) cc_final: 0.8643 (ttm) outliers start: 26 outliers final: 25 residues processed: 166 average time/residue: 0.1813 time to fit residues: 49.1698 Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 93 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.104518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083985 restraints weight = 87062.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087449 restraints weight = 33611.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.089578 restraints weight = 18633.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090747 restraints weight = 13119.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091295 restraints weight = 10810.976| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12564 Z= 0.126 Angle : 0.470 7.859 17118 Z= 0.254 Chirality : 0.034 0.128 1986 Planarity : 0.003 0.044 2082 Dihedral : 5.015 63.433 1764 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.08 % Allowed : 14.82 % Favored : 83.09 % 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 aren not related in a simple way. whole: 3.39 (0.21), residues: 1593 helix: 2.91 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.32 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 163 TYR 0.010 0.001 TYR B 564 PHE 0.023 0.001 PHE A 301 TRP 0.011 0.001 TRP B 176 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00271 (12564) covalent geometry : angle 0.46971 (17118) hydrogen bonds : bond 0.04248 ( 992) hydrogen bonds : angle 4.10771 ( 2931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 MET cc_start: 0.7315 (tmm) cc_final: 0.6955 (tmm) REVERT: A 257 MET cc_start: 0.7293 (tmm) cc_final: 0.6960 (tmm) REVERT: A 325 MET cc_start: 0.8837 (ttm) cc_final: 0.8582 (ttm) REVERT: C 205 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8067 (mp10) outliers start: 26 outliers final: 24 residues processed: 169 average time/residue: 0.1487 time to fit residues: 41.4207 Evaluate side-chains 170 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 89 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083329 restraints weight = 88229.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086767 restraints weight = 34149.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.088897 restraints weight = 19003.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090115 restraints weight = 13397.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090806 restraints weight = 10968.406| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12564 Z= 0.143 Angle : 0.480 5.914 17118 Z= 0.263 Chirality : 0.035 0.130 1986 Planarity : 0.003 0.044 2082 Dihedral : 5.040 61.561 1764 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.08 % Allowed : 15.62 % Favored : 82.29 % 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 aren not related in a simple way. whole: 3.34 (0.21), residues: 1593 helix: 2.89 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 539 TYR 0.011 0.001 TYR B 564 PHE 0.031 0.001 PHE A 221 TRP 0.010 0.001 TRP B 176 HIS 0.003 0.001 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00308 (12564) covalent geometry : angle 0.48012 (17118) hydrogen bonds : bond 0.04391 ( 992) hydrogen bonds : angle 4.17007 ( 2931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3506.87 seconds wall clock time: 60 minutes 40.78 seconds (3640.78 seconds total)