Starting phenix.real_space_refine on Mon Aug 25 01:34:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz4_41733/08_2025/8tz4_41733_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz4_41733/08_2025/8tz4_41733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tz4_41733/08_2025/8tz4_41733_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz4_41733/08_2025/8tz4_41733_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tz4_41733/08_2025/8tz4_41733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz4_41733/08_2025/8tz4_41733.map" } resolution = 3.23 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= 0.004 sd= 0.080 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 8130 2.51 5 N 1931 2.21 5 O 2095 1.98 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 24408 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'U08': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.96, per 1000 atoms: 0.20 Number of scatterers: 24408 At special positions: 0 Unit cell: (126.36, 128.52, 77.76, 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 2095 8.00 N 1931 7.00 C 8130 6.00 H 12165 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: 2.39 Conformation dependent library (CDL) restraints added in 778.0 milliseconds Enol-peptide restraints added in 953.7 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: 88 helices and 3 sheets defined 89.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 203 Proline residue: A 167 - end of helix removed outlier: 4.576A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.923A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.042A pdb=" N VAL A 230 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.536A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 271 removed outlier: 3.656A pdb=" N GLY A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.341A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 312 removed outlier: 4.338A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.659A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 382 through 389 removed outlier: 3.537A pdb=" N PHE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.168A 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 479 removed outlier: 4.099A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.643A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 3.993A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.700A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 589 through 596 removed outlier: 3.650A pdb=" N GLY A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 619 Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 203 Proline residue: C 167 - end of helix removed outlier: 4.564A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.916A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.043A pdb=" N VAL C 230 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 4.555A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 270 Processing helix chain 'C' and resid 272 through 282 removed outlier: 4.302A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 312 removed outlier: 4.345A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 312 through 330 Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.644A pdb=" N ILE C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) 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: 3.559A pdb=" N THR C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 381 through 389 Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.235A 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 479 removed outlier: 4.114A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.634A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 3.982A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.806A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 589 through 596 removed outlier: 3.546A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 619 Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.561A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.936A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.047A pdb=" N VAL B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 4.560A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 270 Processing helix chain 'B' and resid 272 through 282 removed outlier: 4.377A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 312 removed outlier: 4.378A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 312 through 330 Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.625A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) 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: 3.577A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.184A 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 479 removed outlier: 3.516A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.624A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.010A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.829A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 589 through 596 removed outlier: 3.506A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 619 Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA2, first strand: chain 'C' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 547 979 hydrogen bonds defined for protein. 2877 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: 6.12 Time building geometry restraints manager: 3.23 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: 12147 1.03 - 1.22: 19 1.22 - 1.42: 5353 1.42 - 1.61: 7070 1.61 - 1.81: 157 Bond restraints: 24746 Sorted by residual: bond pdb=" C3 U08 A 801 " pdb=" C4 U08 A 801 " ideal model delta sigma weight residual 1.520 1.252 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C1 U08 A 801 " pdb=" C2 U08 A 801 " ideal model delta sigma weight residual 1.552 1.297 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C11 U08 A 801 " pdb=" N5 U08 A 801 " ideal model delta sigma weight residual 1.328 1.509 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C4 U08 A 801 " pdb=" O1 U08 A 801 " ideal model delta sigma weight residual 1.435 1.607 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" C2 U08 A 801 " pdb=" C3 U08 A 801 " ideal model delta sigma weight residual 1.527 1.699 -0.172 2.00e-02 2.50e+03 7.35e+01 ... (remaining 24741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 44430 1.73 - 3.46: 179 3.46 - 5.19: 41 5.19 - 6.92: 3 6.92 - 8.65: 1 Bond angle restraints: 44654 Sorted by residual: angle pdb=" N2 U08 A 801 " pdb=" C12 U08 A 801 " pdb=" N4 U08 A 801 " ideal model delta sigma weight residual 128.80 120.15 8.65 3.00e+00 1.11e-01 8.30e+00 angle pdb=" CA GLY B 568 " pdb=" C GLY B 568 " pdb=" N PHE B 569 " ideal model delta sigma weight residual 114.58 116.66 -2.08 8.60e-01 1.35e+00 5.83e+00 angle pdb=" CA GLY C 568 " pdb=" C GLY C 568 " pdb=" N PHE C 569 " ideal model delta sigma weight residual 114.58 116.64 -2.06 8.60e-01 1.35e+00 5.75e+00 angle pdb=" N GLY C 568 " pdb=" CA GLY C 568 " pdb=" C GLY C 568 " ideal model delta sigma weight residual 110.38 113.56 -3.18 1.48e+00 4.57e-01 4.63e+00 angle pdb=" C12 U08 A 801 " pdb=" N2 U08 A 801 " pdb=" N1 U08 A 801 " ideal model delta sigma weight residual 113.47 119.81 -6.34 3.00e+00 1.11e-01 4.46e+00 ... (remaining 44649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.24: 11359 28.24 - 56.48: 341 56.48 - 84.72: 47 84.72 - 112.96: 5 112.96 - 141.20: 2 Dihedral angle restraints: 11754 sinusoidal: 6024 harmonic: 5730 Sorted by residual: dihedral pdb=" O1 U08 A 801 " pdb=" C4 U08 A 801 " pdb=" C6 U08 A 801 " pdb=" O4 U08 A 801 " ideal model delta sinusoidal sigma weight residual 172.60 -46.20 -141.20 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C3 U08 A 801 " pdb=" C4 U08 A 801 " pdb=" C6 U08 A 801 " pdb=" O4 U08 A 801 " ideal model delta sinusoidal sigma weight residual -69.46 69.06 -138.52 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" N3 U08 A 801 " pdb=" C1 U08 A 801 " pdb=" C8 U08 A 801 " pdb=" O1 U08 A 801 " ideal model delta sinusoidal sigma weight residual -124.25 -23.10 -101.15 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 11751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1656 0.047 - 0.094: 296 0.094 - 0.141: 34 0.141 - 0.188: 0 0.188 - 0.235: 1 Chirality restraints: 1987 Sorted by residual: chirality pdb=" C3 U08 A 801 " pdb=" C2 U08 A 801 " pdb=" C4 U08 A 801 " pdb=" O3 U08 A 801 " both_signs ideal model delta sigma weight residual False -2.67 -2.44 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PRO A 234 " pdb=" N PRO A 234 " pdb=" C PRO A 234 " pdb=" CB PRO A 234 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA PRO B 234 " pdb=" N PRO B 234 " pdb=" C PRO B 234 " pdb=" CB PRO B 234 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 1984 not shown) Planarity restraints: 3622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 195 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C LEU B 195 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU B 195 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 196 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 195 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C LEU C 195 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU C 195 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL C 196 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 195 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C LEU A 195 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 195 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.012 2.00e-02 2.50e+03 ... (remaining 3619 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 907 2.19 - 2.80: 48106 2.80 - 3.40: 69112 3.40 - 4.00: 87284 4.00 - 4.60: 137866 Nonbonded interactions: 343275 Sorted by model distance: nonbonded pdb=" OE1 GLU C 525 " pdb=" H GLU C 525 " model vdw 1.592 2.450 nonbonded pdb=" OE1 GLU B 525 " pdb=" H GLU B 525 " model vdw 1.616 2.450 nonbonded pdb=" O VAL B 490 " pdb=" HG SER B 493 " model vdw 1.680 2.450 nonbonded pdb=" O SER A 451 " pdb="HD22 ASN A 455 " model vdw 1.682 2.450 nonbonded pdb=" O VAL C 490 " pdb=" HG SER C 493 " model vdw 1.682 2.450 ... (remaining 343270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 90 through 622) selection = chain 'B' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.140 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.740 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.005 0.268 12581 Z= 0.258 Angle : 0.434 8.645 17132 Z= 0.235 Chirality : 0.035 0.235 1987 Planarity : 0.003 0.025 2080 Dihedral : 12.312 141.200 4260 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 3.71 (0.21), residues: 1593 helix: 3.00 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 539 TYR 0.010 0.001 TYR A 519 PHE 0.009 0.001 PHE B 413 TRP 0.005 0.001 TRP C 316 HIS 0.001 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00512 (12581) covalent geometry : angle 0.43379 (17132) hydrogen bonds : bond 0.13107 ( 979) hydrogen bonds : angle 4.74078 ( 2877) *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 316 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8078 (t80) cc_final: 0.7685 (t80) REVERT: A 509 ASP cc_start: 0.8800 (m-30) cc_final: 0.8479 (m-30) REVERT: C 145 ILE cc_start: 0.9110 (mt) cc_final: 0.8904 (mm) REVERT: C 305 MET cc_start: 0.8074 (mmm) cc_final: 0.7813 (mmt) REVERT: C 489 GLU cc_start: 0.8207 (mp0) cc_final: 0.7925 (mp0) REVERT: C 592 ASP cc_start: 0.7869 (m-30) cc_final: 0.7664 (m-30) REVERT: B 124 ILE cc_start: 0.9309 (tt) cc_final: 0.8821 (tp) REVERT: B 131 PHE cc_start: 0.7450 (t80) cc_final: 0.7166 (t80) REVERT: B 138 PHE cc_start: 0.8410 (t80) cc_final: 0.8164 (t80) REVERT: B 248 LEU cc_start: 0.8207 (tp) cc_final: 0.7927 (mm) REVERT: B 305 MET cc_start: 0.8423 (mmm) cc_final: 0.8047 (mmt) REVERT: B 497 MET cc_start: 0.8191 (tmt) cc_final: 0.7963 (tmm) REVERT: B 575 LEU cc_start: 0.8554 (tp) cc_final: 0.8344 (mt) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2216 time to fit residues: 106.3714 Evaluate side-chains 194 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN C 479 ASN B 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.098692 restraints weight = 47852.301| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.81 r_work: 0.2808 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12581 Z= 0.172 Angle : 0.490 5.198 17132 Z= 0.266 Chirality : 0.036 0.111 1987 Planarity : 0.003 0.036 2080 Dihedral : 8.129 139.556 1710 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 8.23 % Favored : 90.34 % 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: 2.82 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.29 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 355 TYR 0.010 0.001 TYR A 529 PHE 0.016 0.001 PHE A 164 TRP 0.007 0.001 TRP A 414 HIS 0.002 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00395 (12581) covalent geometry : angle 0.48957 (17132) hydrogen bonds : bond 0.04640 ( 979) hydrogen bonds : angle 3.95417 ( 2877) *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8166 (t80) cc_final: 0.7647 (t80) REVERT: A 307 MET cc_start: 0.9069 (mtm) cc_final: 0.8792 (mtm) REVERT: B 131 PHE cc_start: 0.7324 (t80) cc_final: 0.6933 (t80) REVERT: B 305 MET cc_start: 0.8868 (mmm) cc_final: 0.8597 (mmt) REVERT: B 497 MET cc_start: 0.8756 (tmt) cc_final: 0.8442 (tmm) REVERT: B 620 ASN cc_start: 0.8088 (p0) cc_final: 0.7857 (p0) outliers start: 18 outliers final: 12 residues processed: 217 average time/residue: 0.2065 time to fit residues: 70.0169 Evaluate side-chains 205 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 340 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100588 restraints weight = 47721.076| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.85 r_work: 0.2833 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12581 Z= 0.109 Angle : 0.440 4.670 17132 Z= 0.234 Chirality : 0.035 0.122 1987 Planarity : 0.003 0.043 2080 Dihedral : 7.935 139.979 1710 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.27 % Allowed : 9.90 % Favored : 88.84 % 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: 3.72 (0.21), residues: 1593 helix: 2.99 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.29 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.010 0.001 TYR B 216 PHE 0.010 0.001 PHE A 259 TRP 0.007 0.001 TRP B 316 HIS 0.001 0.000 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00233 (12581) covalent geometry : angle 0.44029 (17132) hydrogen bonds : bond 0.04050 ( 979) hydrogen bonds : angle 3.74712 ( 2877) *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7952 (t80) cc_final: 0.7583 (t80) REVERT: A 307 MET cc_start: 0.8901 (mtm) cc_final: 0.8661 (mtm) REVERT: C 489 GLU cc_start: 0.8574 (mp0) cc_final: 0.8369 (mp0) REVERT: B 131 PHE cc_start: 0.7185 (t80) cc_final: 0.6829 (t80) REVERT: B 305 MET cc_start: 0.8747 (mmm) cc_final: 0.8370 (mmt) REVERT: B 497 MET cc_start: 0.8643 (tmt) cc_final: 0.8414 (tmm) outliers start: 16 outliers final: 14 residues processed: 213 average time/residue: 0.2020 time to fit residues: 67.0051 Evaluate side-chains 206 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 14 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100540 restraints weight = 47521.558| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.78 r_work: 0.2837 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12581 Z= 0.109 Angle : 0.440 4.670 17132 Z= 0.234 Chirality : 0.035 0.122 1987 Planarity : 0.003 0.043 2080 Dihedral : 7.935 139.979 1710 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.19 % Allowed : 10.45 % Favored : 88.36 % 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: 3.72 (0.21), residues: 1593 helix: 2.99 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.29 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.010 0.001 TYR B 216 PHE 0.010 0.001 PHE A 259 TRP 0.007 0.001 TRP B 316 HIS 0.001 0.000 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00233 (12581) covalent geometry : angle 0.44029 (17132) hydrogen bonds : bond 0.04050 ( 979) hydrogen bonds : angle 3.74712 ( 2877) *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7942 (t80) cc_final: 0.7579 (t80) REVERT: A 307 MET cc_start: 0.8899 (mtm) cc_final: 0.8666 (mtm) REVERT: B 131 PHE cc_start: 0.7216 (t80) cc_final: 0.6865 (t80) REVERT: B 305 MET cc_start: 0.8754 (mmm) cc_final: 0.8397 (mmt) REVERT: B 497 MET cc_start: 0.8634 (tmt) cc_final: 0.8413 (tmm) outliers start: 15 outliers final: 14 residues processed: 197 average time/residue: 0.1991 time to fit residues: 60.8201 Evaluate side-chains 206 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 108 optimal weight: 0.0770 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100597 restraints weight = 47596.925| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.79 r_work: 0.2829 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12581 Z= 0.120 Angle : 0.448 4.565 17132 Z= 0.239 Chirality : 0.035 0.117 1987 Planarity : 0.003 0.035 2080 Dihedral : 8.077 147.529 1710 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.27 % Allowed : 9.98 % Favored : 88.76 % 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: 3.70 (0.21), residues: 1593 helix: 2.97 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.006 0.001 TYR A 519 PHE 0.010 0.001 PHE C 177 TRP 0.008 0.001 TRP B 150 HIS 0.001 0.000 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00260 (12581) covalent geometry : angle 0.44755 (17132) hydrogen bonds : bond 0.04054 ( 979) hydrogen bonds : angle 3.73568 ( 2877) *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7915 (t80) cc_final: 0.7521 (t80) REVERT: A 307 MET cc_start: 0.8925 (mtm) cc_final: 0.8702 (mtm) REVERT: B 131 PHE cc_start: 0.7214 (t80) cc_final: 0.6879 (t80) REVERT: B 305 MET cc_start: 0.8759 (mmm) cc_final: 0.8387 (mmt) REVERT: B 497 MET cc_start: 0.8651 (tmt) cc_final: 0.8194 (tmm) outliers start: 16 outliers final: 16 residues processed: 202 average time/residue: 0.1706 time to fit residues: 54.1039 Evaluate side-chains 209 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100606 restraints weight = 47641.157| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.79 r_work: 0.2829 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12581 Z= 0.120 Angle : 0.448 4.565 17132 Z= 0.239 Chirality : 0.035 0.117 1987 Planarity : 0.003 0.035 2080 Dihedral : 8.077 147.529 1710 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.27 % Allowed : 10.13 % Favored : 88.60 % 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: 3.70 (0.21), residues: 1593 helix: 2.97 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.006 0.001 TYR A 519 PHE 0.010 0.001 PHE C 177 TRP 0.008 0.001 TRP B 150 HIS 0.001 0.000 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00260 (12581) covalent geometry : angle 0.44755 (17132) hydrogen bonds : bond 0.04054 ( 979) hydrogen bonds : angle 3.73568 ( 2877) *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7917 (t80) cc_final: 0.7521 (t80) REVERT: A 307 MET cc_start: 0.8926 (mtm) cc_final: 0.8698 (mtm) REVERT: B 131 PHE cc_start: 0.7208 (t80) cc_final: 0.6873 (t80) REVERT: B 305 MET cc_start: 0.8761 (mmm) cc_final: 0.8391 (mmt) REVERT: B 497 MET cc_start: 0.8640 (tmt) cc_final: 0.8196 (tmm) outliers start: 16 outliers final: 16 residues processed: 199 average time/residue: 0.1707 time to fit residues: 53.6186 Evaluate side-chains 209 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101732 restraints weight = 47728.221| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.78 r_work: 0.2834 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12581 Z= 0.119 Angle : 0.439 4.550 17132 Z= 0.234 Chirality : 0.035 0.118 1987 Planarity : 0.003 0.035 2080 Dihedral : 8.114 150.219 1710 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 9.90 % Favored : 88.68 % 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: 3.70 (0.21), residues: 1593 helix: 2.98 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.006 0.001 TYR C 231 PHE 0.011 0.001 PHE C 177 TRP 0.008 0.001 TRP B 150 HIS 0.002 0.000 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00260 (12581) covalent geometry : angle 0.43906 (17132) hydrogen bonds : bond 0.04001 ( 979) hydrogen bonds : angle 3.69737 ( 2877) *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7997 (t80) cc_final: 0.7599 (t80) REVERT: B 131 PHE cc_start: 0.7296 (t80) cc_final: 0.6942 (t80) REVERT: B 305 MET cc_start: 0.8908 (mmm) cc_final: 0.8573 (mmt) REVERT: B 497 MET cc_start: 0.8824 (tmt) cc_final: 0.8423 (tmm) REVERT: B 548 ASP cc_start: 0.7955 (t0) cc_final: 0.7753 (t0) outliers start: 18 outliers final: 15 residues processed: 201 average time/residue: 0.1779 time to fit residues: 56.1088 Evaluate side-chains 213 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100588 restraints weight = 47655.458| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.77 r_work: 0.2829 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12581 Z= 0.119 Angle : 0.439 4.550 17132 Z= 0.234 Chirality : 0.035 0.118 1987 Planarity : 0.003 0.035 2080 Dihedral : 8.114 150.219 1710 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.27 % Allowed : 10.06 % Favored : 88.68 % 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: 3.70 (0.21), residues: 1593 helix: 2.98 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.006 0.001 TYR C 231 PHE 0.011 0.001 PHE C 177 TRP 0.008 0.001 TRP B 150 HIS 0.002 0.000 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00260 (12581) covalent geometry : angle 0.43905 (17132) hydrogen bonds : bond 0.04001 ( 979) hydrogen bonds : angle 3.69737 ( 2877) *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7933 (t80) cc_final: 0.7553 (t80) REVERT: C 489 GLU cc_start: 0.8547 (mp0) cc_final: 0.8335 (mp0) REVERT: B 131 PHE cc_start: 0.7221 (t80) cc_final: 0.6881 (t80) REVERT: B 305 MET cc_start: 0.8750 (mmm) cc_final: 0.8383 (mmt) REVERT: B 497 MET cc_start: 0.8661 (tmt) cc_final: 0.8251 (tmm) outliers start: 16 outliers final: 15 residues processed: 204 average time/residue: 0.1989 time to fit residues: 63.9937 Evaluate side-chains 212 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 130 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.100438 restraints weight = 47942.306| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.78 r_work: 0.2826 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12581 Z= 0.119 Angle : 0.439 4.550 17132 Z= 0.234 Chirality : 0.035 0.118 1987 Planarity : 0.003 0.035 2080 Dihedral : 8.114 150.219 1710 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.27 % Allowed : 10.06 % Favored : 88.68 % 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: 3.70 (0.21), residues: 1593 helix: 2.98 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.006 0.001 TYR C 231 PHE 0.011 0.001 PHE C 177 TRP 0.008 0.001 TRP B 150 HIS 0.002 0.000 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00260 (12581) covalent geometry : angle 0.43905 (17132) hydrogen bonds : bond 0.04001 ( 979) hydrogen bonds : angle 3.69737 ( 2877) *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7936 (t80) cc_final: 0.7552 (t80) REVERT: C 489 GLU cc_start: 0.8556 (mp0) cc_final: 0.8340 (mp0) REVERT: B 131 PHE cc_start: 0.7219 (t80) cc_final: 0.6877 (t80) REVERT: B 305 MET cc_start: 0.8752 (mmm) cc_final: 0.8378 (mmt) REVERT: B 497 MET cc_start: 0.8660 (tmt) cc_final: 0.8242 (tmm) outliers start: 16 outliers final: 15 residues processed: 203 average time/residue: 0.1766 time to fit residues: 56.5989 Evaluate side-chains 212 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.0980 chunk 98 optimal weight: 0.0000 chunk 110 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 139 optimal weight: 0.1980 chunk 140 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102700 restraints weight = 47530.699| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.80 r_work: 0.2843 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12581 Z= 0.099 Angle : 0.441 6.646 17132 Z= 0.234 Chirality : 0.035 0.114 1987 Planarity : 0.003 0.035 2080 Dihedral : 7.987 147.879 1710 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.19 % Allowed : 10.21 % Favored : 88.60 % 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: 3.82 (0.21), residues: 1593 helix: 3.06 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.31 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.007 0.001 TYR C 231 PHE 0.010 0.001 PHE C 177 TRP 0.007 0.001 TRP C 323 HIS 0.002 0.000 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00199 (12581) covalent geometry : angle 0.44104 (17132) hydrogen bonds : bond 0.03688 ( 979) hydrogen bonds : angle 3.58586 ( 2877) ********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.565 Fit side-chains REVERT: A 131 PHE cc_start: 0.7898 (t80) cc_final: 0.7494 (t80) REVERT: A 172 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7732 (mm) REVERT: C 489 GLU cc_start: 0.8546 (mp0) cc_final: 0.8292 (mp0) REVERT: C 497 MET cc_start: 0.8673 (tmm) cc_final: 0.7870 (tmm) REVERT: B 131 PHE cc_start: 0.7147 (t80) cc_final: 0.6808 (t80) REVERT: B 305 MET cc_start: 0.8728 (mmm) cc_final: 0.8346 (mmt) REVERT: B 497 MET cc_start: 0.8633 (tmt) cc_final: 0.8217 (tmm) outliers start: 15 outliers final: 12 residues processed: 206 average time/residue: 0.1794 time to fit residues: 58.0397 Evaluate side-chains 204 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099675 restraints weight = 48003.763| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.74 r_work: 0.2816 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12581 Z= 0.154 Angle : 0.467 5.287 17132 Z= 0.251 Chirality : 0.035 0.111 1987 Planarity : 0.003 0.036 2080 Dihedral : 7.949 143.914 1710 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.11 % Allowed : 10.61 % Favored : 88.28 % 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: 3.70 (0.21), residues: 1593 helix: 2.99 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.47 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.009 0.001 TYR A 529 PHE 0.015 0.001 PHE A 259 TRP 0.009 0.001 TRP B 150 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00351 (12581) covalent geometry : angle 0.46723 (17132) hydrogen bonds : bond 0.04090 ( 979) hydrogen bonds : angle 3.67892 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5265.03 seconds wall clock time: 89 minutes 55.33 seconds (5395.33 seconds total)