Starting phenix.real_space_refine on Sat Jun 21 02:59:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz4_41733/06_2025/8tz4_41733_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz4_41733/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz4_41733/06_2025/8tz4_41733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz4_41733/06_2025/8tz4_41733.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz4_41733/06_2025/8tz4_41733_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz4_41733/06_2025/8tz4_41733_trim.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} 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: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} 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: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} 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: 12.24, per 1000 atoms: 0.50 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: 6.66 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.89 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: 8.65 Time building geometry restraints manager: 7.99 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: 1.140 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: 0.440 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 51.880 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP C 316 HIS 0.001 0.000 HIS A 394 PHE 0.009 0.001 PHE B 413 TYR 0.010 0.001 TYR A 519 ARG 0.001 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.13107 ( 979) hydrogen bonds : angle 4.74078 ( 2877) covalent geometry : bond 0.00512 (12581) covalent geometry : angle 0.43379 (17132) *********************** 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 : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8078 (t80) cc_final: 0.7680 (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: 0.7650 (m-30) REVERT: B 124 ILE cc_start: 0.9309 (tt) cc_final: 0.8820 (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: 0.7926 (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: 0.8339 (mt) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.4527 time to fit residues: 216.3187 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 : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.129174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100379 restraints weight = 46886.809| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.85 r_work: 0.2822 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12581 Z= 0.135 Angle : 0.467 5.628 17132 Z= 0.249 Chirality : 0.035 0.213 1987 Planarity : 0.003 0.035 2080 Dihedral : 8.073 135.152 1710 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.03 % Allowed : 8.00 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.21), residues: 1593 helix: 2.98 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.14 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 316 HIS 0.002 0.000 HIS C 132 PHE 0.015 0.001 PHE A 164 TYR 0.008 0.001 TYR B 519 ARG 0.006 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 979) hydrogen bonds : angle 3.89022 ( 2877) covalent geometry : bond 0.00295 (12581) covalent geometry : angle 0.46651 (17132) *********************** 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 216 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 1.839 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8045 (t80) cc_final: 0.7582 (t80) REVERT: A 509 ASP cc_start: 0.9108 (m-30) cc_final: 0.8876 (m-30) REVERT: B 131 PHE cc_start: 0.7233 (t80) cc_final: 0.6865 (t80) REVERT: B 154 MET cc_start: 0.8304 (mmp) cc_final: 0.8072 (mmt) REVERT: B 305 MET cc_start: 0.8767 (mmm) cc_final: 0.8499 (mmt) REVERT: B 497 MET cc_start: 0.8553 (tmt) cc_final: 0.8150 (tmm) REVERT: B 548 ASP cc_start: 0.7927 (t0) cc_final: 0.7668 (t0) outliers start: 13 outliers final: 8 residues processed: 210 average time/residue: 0.4232 time to fit residues: 138.2844 Evaluate side-chains 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 419 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 155 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.126811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098410 restraints weight = 48420.613| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.84 r_work: 0.2771 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12581 Z= 0.195 Angle : 0.497 4.980 17132 Z= 0.271 Chirality : 0.037 0.132 1987 Planarity : 0.003 0.037 2080 Dihedral : 7.886 133.392 1710 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.19 % Allowed : 9.50 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.21), residues: 1593 helix: 2.75 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.47 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 316 HIS 0.003 0.001 HIS B 152 PHE 0.015 0.001 PHE A 259 TYR 0.013 0.001 TYR B 216 ARG 0.008 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 979) hydrogen bonds : angle 3.94142 ( 2877) covalent geometry : bond 0.00459 (12581) covalent geometry : angle 0.49741 (17132) *********************** 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 216 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8149 (t80) cc_final: 0.7774 (t80) REVERT: A 307 MET cc_start: 0.8963 (mtm) cc_final: 0.8752 (mtm) REVERT: A 509 ASP cc_start: 0.9074 (m-30) cc_final: 0.8857 (m-30) REVERT: C 257 MET cc_start: 0.8087 (mtt) cc_final: 0.7813 (mtp) REVERT: B 131 PHE cc_start: 0.7515 (t80) cc_final: 0.7129 (t80) REVERT: B 305 MET cc_start: 0.8805 (mmm) cc_final: 0.8408 (mmt) REVERT: B 497 MET cc_start: 0.8764 (tmt) cc_final: 0.8359 (tmm) REVERT: B 548 ASP cc_start: 0.8013 (t0) cc_final: 0.7796 (t0) outliers start: 15 outliers final: 10 residues processed: 207 average time/residue: 0.4221 time to fit residues: 135.8493 Evaluate side-chains 207 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 123 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 617 MET 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 65 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 146 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 = 0.129534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101235 restraints weight = 48409.983| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.87 r_work: 0.2804 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12581 Z= 0.107 Angle : 0.437 4.615 17132 Z= 0.233 Chirality : 0.035 0.111 1987 Planarity : 0.003 0.035 2080 Dihedral : 7.650 127.185 1710 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.79 % Allowed : 10.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.21), residues: 1593 helix: 2.91 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.39 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.001 0.000 HIS A 288 PHE 0.011 0.001 PHE C 177 TYR 0.008 0.001 TYR A 519 ARG 0.003 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 979) hydrogen bonds : angle 3.68596 ( 2877) covalent geometry : bond 0.00228 (12581) covalent geometry : angle 0.43720 (17132) *********************** 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 212 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7991 (t80) cc_final: 0.7611 (t80) REVERT: A 509 ASP cc_start: 0.9131 (m-30) cc_final: 0.8877 (m-30) REVERT: C 489 GLU cc_start: 0.8545 (mp0) cc_final: 0.8319 (mp0) REVERT: B 131 PHE cc_start: 0.7241 (t80) cc_final: 0.6880 (t80) REVERT: B 176 TRP cc_start: 0.6765 (t-100) cc_final: 0.6489 (t-100) REVERT: B 305 MET cc_start: 0.8751 (mmm) cc_final: 0.8355 (mmt) REVERT: B 497 MET cc_start: 0.8713 (tmt) cc_final: 0.8370 (tmm) REVERT: B 548 ASP cc_start: 0.8145 (t0) cc_final: 0.7859 (t0) outliers start: 10 outliers final: 9 residues processed: 206 average time/residue: 0.4189 time to fit residues: 135.7635 Evaluate side-chains 199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU 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 617 MET 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 100 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 135 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.127273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099652 restraints weight = 48170.885| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.71 r_work: 0.2848 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12581 Z= 0.107 Angle : 0.437 4.615 17132 Z= 0.233 Chirality : 0.035 0.111 1987 Planarity : 0.003 0.035 2080 Dihedral : 7.650 127.185 1710 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.71 % Allowed : 11.32 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.21), residues: 1593 helix: 2.91 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.39 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.001 0.000 HIS A 288 PHE 0.011 0.001 PHE C 177 TYR 0.008 0.001 TYR A 519 ARG 0.003 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 979) hydrogen bonds : angle 3.68596 ( 2877) covalent geometry : bond 0.00228 (12581) covalent geometry : angle 0.43720 (17132) *********************** 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 199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8036 (t80) cc_final: 0.7646 (t80) REVERT: A 509 ASP cc_start: 0.9241 (m-30) cc_final: 0.9001 (m-30) REVERT: B 131 PHE cc_start: 0.7239 (t80) cc_final: 0.6868 (t80) REVERT: B 176 TRP cc_start: 0.6774 (t-100) cc_final: 0.6497 (t-100) REVERT: B 305 MET cc_start: 0.8858 (mmm) cc_final: 0.8462 (mmt) REVERT: B 497 MET cc_start: 0.8811 (tmt) cc_final: 0.8425 (tmm) REVERT: B 548 ASP cc_start: 0.8212 (t0) cc_final: 0.7912 (t0) outliers start: 9 outliers final: 9 residues processed: 194 average time/residue: 0.4161 time to fit residues: 126.9064 Evaluate side-chains 199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU 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 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 6 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 57 optimal weight: 0.1980 chunk 149 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.127496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099915 restraints weight = 48002.652| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.67 r_work: 0.2853 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12581 Z= 0.108 Angle : 0.436 4.751 17132 Z= 0.232 Chirality : 0.034 0.112 1987 Planarity : 0.003 0.036 2080 Dihedral : 7.503 120.828 1710 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.79 % Allowed : 11.24 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.21), residues: 1593 helix: 2.97 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.37 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 150 HIS 0.002 0.000 HIS C 367 PHE 0.012 0.001 PHE C 164 TYR 0.006 0.001 TYR C 231 ARG 0.002 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 979) hydrogen bonds : angle 3.64949 ( 2877) covalent geometry : bond 0.00229 (12581) covalent geometry : angle 0.43588 (17132) *********************** 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 201 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8038 (t80) cc_final: 0.7629 (t80) REVERT: A 157 TYR cc_start: 0.7305 (m-10) cc_final: 0.7065 (m-10) REVERT: A 509 ASP cc_start: 0.9243 (m-30) cc_final: 0.9001 (m-30) REVERT: B 131 PHE cc_start: 0.7201 (t80) cc_final: 0.6856 (t80) REVERT: B 176 TRP cc_start: 0.6852 (t-100) cc_final: 0.6610 (t-100) REVERT: B 305 MET cc_start: 0.8843 (mmm) cc_final: 0.8435 (mmt) REVERT: B 497 MET cc_start: 0.8828 (tmt) cc_final: 0.8444 (tmm) REVERT: B 548 ASP cc_start: 0.8205 (t0) cc_final: 0.7895 (t0) outliers start: 10 outliers final: 8 residues processed: 194 average time/residue: 0.5487 time to fit residues: 172.7787 Evaluate side-chains 198 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 617 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 0.0770 chunk 93 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.127136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099572 restraints weight = 48388.807| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.63 r_work: 0.2837 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12581 Z= 0.134 Angle : 0.443 4.650 17132 Z= 0.237 Chirality : 0.035 0.118 1987 Planarity : 0.003 0.036 2080 Dihedral : 7.481 119.679 1710 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.79 % Allowed : 11.24 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.21), residues: 1593 helix: 2.95 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 150 HIS 0.001 0.000 HIS A 288 PHE 0.009 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 979) hydrogen bonds : angle 3.66101 ( 2877) covalent geometry : bond 0.00300 (12581) covalent geometry : angle 0.44312 (17132) *********************** 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 199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8056 (t80) cc_final: 0.7656 (t80) REVERT: A 157 TYR cc_start: 0.7424 (m-10) cc_final: 0.7169 (m-10) REVERT: A 509 ASP cc_start: 0.9272 (m-30) cc_final: 0.9021 (m-30) REVERT: B 131 PHE cc_start: 0.7293 (t80) cc_final: 0.6950 (t80) REVERT: B 176 TRP cc_start: 0.7008 (t-100) cc_final: 0.6765 (t-100) REVERT: B 305 MET cc_start: 0.8911 (mmm) cc_final: 0.8556 (mmt) REVERT: B 497 MET cc_start: 0.8908 (tmt) cc_final: 0.8589 (tmm) REVERT: B 548 ASP cc_start: 0.8201 (t0) cc_final: 0.7858 (t0) outliers start: 10 outliers final: 9 residues processed: 194 average time/residue: 0.4502 time to fit residues: 137.7790 Evaluate side-chains 197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 123 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 617 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 116 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 155 optimal weight: 0.0970 chunk 86 optimal weight: 0.0670 chunk 146 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 158 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 overall best weight: 0.7556 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.127162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099558 restraints weight = 48058.175| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.64 r_work: 0.2845 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12581 Z= 0.133 Angle : 0.443 4.650 17132 Z= 0.237 Chirality : 0.035 0.118 1987 Planarity : 0.003 0.036 2080 Dihedral : 7.491 119.674 1710 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.71 % Allowed : 11.48 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.21), residues: 1593 helix: 2.95 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 150 HIS 0.001 0.000 HIS A 288 PHE 0.009 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 979) hydrogen bonds : angle 3.66106 ( 2877) covalent geometry : bond 0.00299 (12581) covalent geometry : angle 0.44309 (17132) *********************** 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 197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8043 (t80) cc_final: 0.7628 (t80) REVERT: A 157 TYR cc_start: 0.7307 (m-10) cc_final: 0.7062 (m-10) REVERT: A 509 ASP cc_start: 0.9268 (m-30) cc_final: 0.9014 (m-30) REVERT: B 131 PHE cc_start: 0.7209 (t80) cc_final: 0.6863 (t80) REVERT: B 176 TRP cc_start: 0.6886 (t-100) cc_final: 0.6650 (t-100) REVERT: B 305 MET cc_start: 0.8853 (mmm) cc_final: 0.8449 (mmt) REVERT: B 497 MET cc_start: 0.8837 (tmt) cc_final: 0.8458 (tmm) REVERT: B 548 ASP cc_start: 0.8196 (t0) cc_final: 0.7860 (t0) outliers start: 9 outliers final: 9 residues processed: 192 average time/residue: 0.5286 time to fit residues: 161.7872 Evaluate side-chains 197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 123 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 617 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 114 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3470 r_free = 0.3470 target = 0.127128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099802 restraints weight = 48305.281| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.67 r_work: 0.2845 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12581 Z= 0.141 Angle : 0.441 4.643 17132 Z= 0.237 Chirality : 0.035 0.111 1987 Planarity : 0.003 0.036 2080 Dihedral : 7.482 119.617 1710 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.71 % Allowed : 11.40 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.21), residues: 1593 helix: 2.95 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 150 HIS 0.001 0.000 HIS B 132 PHE 0.009 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 979) hydrogen bonds : angle 3.66122 ( 2877) covalent geometry : bond 0.00312 (12581) covalent geometry : angle 0.44113 (17132) *********************** 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 198 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8054 (t80) cc_final: 0.7657 (t80) REVERT: A 157 TYR cc_start: 0.7420 (m-10) cc_final: 0.7166 (m-10) REVERT: A 509 ASP cc_start: 0.9270 (m-30) cc_final: 0.9017 (m-30) REVERT: B 131 PHE cc_start: 0.7284 (t80) cc_final: 0.6943 (t80) REVERT: B 176 TRP cc_start: 0.6986 (t-100) cc_final: 0.6747 (t-100) REVERT: B 305 MET cc_start: 0.8914 (mmm) cc_final: 0.8559 (mmt) REVERT: B 497 MET cc_start: 0.8903 (tmt) cc_final: 0.8584 (tmm) REVERT: B 548 ASP cc_start: 0.8196 (t0) cc_final: 0.7855 (t0) outliers start: 9 outliers final: 9 residues processed: 193 average time/residue: 0.4393 time to fit residues: 134.7969 Evaluate side-chains 197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 123 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 617 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3470 r_free = 0.3470 target = 0.127125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099477 restraints weight = 48208.153| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.63 r_work: 0.2843 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12581 Z= 0.141 Angle : 0.441 4.643 17132 Z= 0.237 Chirality : 0.035 0.111 1987 Planarity : 0.003 0.036 2080 Dihedral : 7.482 119.617 1710 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.71 % Allowed : 11.40 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.21), residues: 1593 helix: 2.95 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 150 HIS 0.001 0.000 HIS B 132 PHE 0.009 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 979) hydrogen bonds : angle 3.66122 ( 2877) covalent geometry : bond 0.00312 (12581) covalent geometry : angle 0.44113 (17132) ********************** 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 197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8045 (t80) cc_final: 0.7630 (t80) REVERT: A 157 TYR cc_start: 0.7304 (m-10) cc_final: 0.7060 (m-10) REVERT: A 509 ASP cc_start: 0.9273 (m-30) cc_final: 0.9020 (m-30) REVERT: B 131 PHE cc_start: 0.7210 (t80) cc_final: 0.6863 (t80) REVERT: B 176 TRP cc_start: 0.6876 (t-100) cc_final: 0.6641 (t-100) REVERT: B 305 MET cc_start: 0.8855 (mmm) cc_final: 0.8453 (mmt) REVERT: B 497 MET cc_start: 0.8840 (tmt) cc_final: 0.8460 (tmm) REVERT: B 548 ASP cc_start: 0.8198 (t0) cc_final: 0.7862 (t0) outliers start: 9 outliers final: 9 residues processed: 192 average time/residue: 0.4205 time to fit residues: 127.1156 Evaluate side-chains 197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 123 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 617 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.127125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099477 restraints weight = 48199.725| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.63 r_work: 0.2844 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12581 Z= 0.141 Angle : 0.441 4.643 17132 Z= 0.237 Chirality : 0.035 0.111 1987 Planarity : 0.003 0.036 2080 Dihedral : 7.482 119.617 1710 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.71 % Allowed : 11.40 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.21), residues: 1593 helix: 2.95 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 150 HIS 0.001 0.000 HIS B 132 PHE 0.009 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 979) hydrogen bonds : angle 3.66122 ( 2877) covalent geometry : bond 0.00312 (12581) covalent geometry : angle 0.44113 (17132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13674.56 seconds wall clock time: 240 minutes 42.51 seconds (14442.51 seconds total)