Starting phenix.real_space_refine on Sun Jul 5 03:31:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz6_41735/07_2026/8tz6_41735_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz6_41735/07_2026/8tz6_41735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz6_41735/07_2026/8tz6_41735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz6_41735/07_2026/8tz6_41735.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz6_41735/07_2026/8tz6_41735_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz6_41735/07_2026/8tz6_41735_trim.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.113 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: 8 Type Number sf(0) Gaussians P 12 5.49 5 S 87 5.16 5 Na 3 4.78 5 C 8442 2.51 5 N 1932 2.21 5 O 2205 1.98 5 F 3 1.80 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24849 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'LBN': 4, 'U7I': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C Time building chain proxies: 10.32, per 1000 atoms: 0.42 Number of scatterers: 24849 At special positions: 0 Unit cell: (128.52, 126.36, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 87 16.00 P 12 15.00 Na 3 11.00 F 3 9.00 O 2205 8.00 N 1932 7.00 C 8442 6.00 H 12165 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 783.5 milliseconds 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: 84 helices and 3 sheets defined 87.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 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: 4.587A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.956A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.582A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.451A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 294 through 312 Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.571A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.647A pdb=" N ARG A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.335A 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: 3.542A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.117A 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 Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.180A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.764A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 removed outlier: 3.629A pdb=" N CYS A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 removed outlier: 4.139A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 617 removed outlier: 3.658A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) 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: 4.588A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.955A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 4.582A 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: 4.451A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.572A pdb=" N VAL B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.647A pdb=" N ARG B 355 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.335A 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: 3.543A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.118A 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 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.180A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.764A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 567 removed outlier: 3.630A pdb=" N CYS B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 removed outlier: 4.139A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 617 removed outlier: 3.657A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 597 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 203 Proline residue: C 167 - end of helix removed outlier: 4.587A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.955A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 4.582A 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: 4.451A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.572A pdb=" N VAL C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.647A pdb=" N ARG C 355 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 381 through 389 Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.335A 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: 3.542A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.118A 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 Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.180A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.764A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 567 removed outlier: 3.630A pdb=" N CYS C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 586 removed outlier: 4.139A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 617 removed outlier: 3.657A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 597 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA2, first strand: chain 'B' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'C' and resid 546 through 547 979 hydrogen bonds defined for protein. 2883 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: 5.57 Time building geometry restraints manager: 3.03 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: 48 1.22 - 1.42: 5415 1.42 - 1.61: 7377 1.61 - 1.81: 183 Bond restraints: 25170 Sorted by residual: bond pdb=" C02 U7I A 801 " pdb=" C03 U7I A 801 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C02 U7I B 801 " pdb=" C03 U7I B 801 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C02 U7I C 801 " pdb=" C03 U7I C 801 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C04 U7I B 801 " pdb=" O05 U7I B 801 " ideal model delta sigma weight residual 1.427 1.270 0.157 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C04 U7I A 801 " pdb=" O05 U7I A 801 " ideal model delta sigma weight residual 1.427 1.271 0.156 2.00e-02 2.50e+03 6.12e+01 ... (remaining 25165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 44898 3.25 - 6.49: 201 6.49 - 9.74: 35 9.74 - 12.99: 10 12.99 - 16.23: 12 Bond angle restraints: 45156 Sorted by residual: angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 109.68 -16.23 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 109.68 -16.23 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O1 LBN C 803 " pdb=" P1 LBN C 803 " pdb=" O2 LBN C 803 " ideal model delta sigma weight residual 93.45 109.67 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1 LBN A 806 " pdb=" P1 LBN A 806 " pdb=" O2 LBN A 806 " ideal model delta sigma weight residual 93.45 109.65 -16.20 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1 LBN B 806 " pdb=" P1 LBN B 806 " pdb=" O2 LBN B 806 " ideal model delta sigma weight residual 93.45 109.62 -16.17 3.00e+00 1.11e-01 2.91e+01 ... (remaining 45151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 11672 35.53 - 71.06: 427 71.06 - 106.59: 9 106.59 - 142.12: 3 142.12 - 177.66: 9 Dihedral angle restraints: 12120 sinusoidal: 6390 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN A 803 " pdb=" C2 LBN A 803 " pdb=" C3 LBN A 803 " pdb=" O7 LBN A 803 " ideal model delta sinusoidal sigma weight residual 62.67 -114.99 177.66 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN B 803 " pdb=" C2 LBN B 803 " pdb=" C3 LBN B 803 " pdb=" O7 LBN B 803 " ideal model delta sinusoidal sigma weight residual 62.67 -114.98 177.65 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN C 803 " pdb=" C2 LBN C 803 " pdb=" C3 LBN C 803 " pdb=" O7 LBN C 803 " ideal model delta sinusoidal sigma weight residual 62.67 -114.95 177.62 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1976 0.108 - 0.216: 28 0.216 - 0.324: 0 0.324 - 0.433: 0 0.433 - 0.541: 3 Chirality restraints: 2007 Sorted by residual: chirality pdb=" C02 U7I B 801 " pdb=" C03 U7I B 801 " pdb=" C06 U7I B 801 " pdb=" F18 U7I B 801 " both_signs ideal model delta sigma weight residual False 2.88 2.33 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" C02 U7I C 801 " pdb=" C03 U7I C 801 " pdb=" C06 U7I C 801 " pdb=" F18 U7I C 801 " both_signs ideal model delta sigma weight residual False 2.88 2.34 0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" C02 U7I A 801 " pdb=" C03 U7I A 801 " pdb=" C06 U7I A 801 " pdb=" F18 U7I A 801 " both_signs ideal model delta sigma weight residual False 2.88 2.34 0.54 2.00e-01 2.50e+01 7.21e+00 ... (remaining 2004 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 195 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C LEU C 195 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU C 195 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 196 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 195 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C LEU A 195 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A 195 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 196 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 195 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C LEU B 195 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU B 195 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 196 " -0.010 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1556 2.22 - 2.81: 51238 2.81 - 3.41: 64625 3.41 - 4.00: 86662 4.00 - 4.60: 139147 Nonbonded interactions: 343228 Sorted by model distance: nonbonded pdb=" OE1 GLU C 489 " pdb=" H GLU C 489 " model vdw 1.622 2.450 nonbonded pdb=" OE1 GLU A 489 " pdb=" H GLU A 489 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU B 489 " pdb=" H GLU B 489 " model vdw 1.624 2.450 nonbonded pdb=" OE1 GLN C 206 " pdb=" H GLN C 206 " model vdw 1.630 2.450 nonbonded pdb=" OE1 GLN B 206 " pdb=" H GLN B 206 " model vdw 1.630 2.450 ... (remaining 343223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.510 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.012 0.295 13005 Z= 0.577 Angle : 0.908 16.233 17634 Z= 0.361 Chirality : 0.046 0.541 2007 Planarity : 0.003 0.034 2118 Dihedral : 15.812 177.656 4626 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.48 % Allowed : 2.61 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.21), residues: 1593 helix: 2.51 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -1.01 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 599 TYR 0.010 0.001 TYR C 231 PHE 0.016 0.001 PHE C 413 TRP 0.010 0.001 TRP C 316 HIS 0.001 0.000 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.01180 / 0.58 (13005) covalent geometry : angle 0.90775 / 0.36 (17634) hydrogen bonds : bond 0.14056 / 9.24 ( 979) hydrogen bonds : angle 5.15226 / 3.80 ( 2883) *********************** 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 261 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 255 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8171 (mt0) cc_final: 0.7949 (mt0) REVERT: A 267 GLN cc_start: 0.7613 (tt0) cc_final: 0.7364 (mt0) REVERT: A 305 MET cc_start: 0.7699 (mmm) cc_final: 0.7322 (mmp) REVERT: A 477 LEU cc_start: 0.7925 (tp) cc_final: 0.7712 (tt) REVERT: A 497 MET cc_start: 0.6252 (tmt) cc_final: 0.5442 (tmt) REVERT: A 526 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: B 264 LYS cc_start: 0.7405 (mttt) cc_final: 0.7005 (mtpt) REVERT: B 420 PRO cc_start: 0.8720 (Cg_endo) cc_final: 0.8459 (Cg_exo) REVERT: B 428 MET cc_start: 0.7433 (mmt) cc_final: 0.6906 (mmt) REVERT: B 526 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: B 534 LYS cc_start: 0.7596 (mttt) cc_final: 0.7312 (mtpp) REVERT: C 131 PHE cc_start: 0.7585 (t80) cc_final: 0.7238 (t80) REVERT: C 264 LYS cc_start: 0.7358 (mttt) cc_final: 0.6991 (mtpt) REVERT: C 267 GLN cc_start: 0.7408 (tt0) cc_final: 0.7119 (mt0) REVERT: C 418 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7501 (mt-10) REVERT: C 497 MET cc_start: 0.6617 (tmt) cc_final: 0.6211 (tmt) REVERT: C 534 LYS cc_start: 0.7600 (mttt) cc_final: 0.7319 (mtpp) outliers start: 6 outliers final: 2 residues processed: 261 average time/residue: 0.9275 time to fit residues: 270.1765 Evaluate side-chains 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain C residue 526 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 ASN A 423 ASN B 423 ASN C 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.149089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107925 restraints weight = 37621.587| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.55 r_work: 0.3111 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13005 Z= 0.114 Angle : 0.471 4.292 17634 Z= 0.246 Chirality : 0.036 0.116 2007 Planarity : 0.003 0.042 2118 Dihedral : 14.675 157.152 2084 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.71 % Allowed : 9.03 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.21), residues: 1593 helix: 2.77 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -1.01 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 251 TYR 0.011 0.001 TYR B 231 PHE 0.012 0.001 PHE B 146 TRP 0.007 0.001 TRP C 261 HIS 0.002 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13005) covalent geometry : angle 0.47089 / 0.25 (17634) hydrogen bonds : bond 0.04411 / 3.00 ( 979) hydrogen bonds : angle 3.87500 / 2.88 ( 2883) *********************** 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 198 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8002 (mt0) cc_final: 0.7792 (mt0) REVERT: A 305 MET cc_start: 0.8213 (mmm) cc_final: 0.8006 (mmm) REVERT: A 327 VAL cc_start: 0.7486 (t) cc_final: 0.7271 (p) REVERT: A 444 GLN cc_start: 0.7302 (mt0) cc_final: 0.7048 (mt0) REVERT: B 262 LEU cc_start: 0.7661 (mt) cc_final: 0.7363 (mt) REVERT: B 264 LYS cc_start: 0.6794 (mttt) cc_final: 0.6346 (mtpt) REVERT: B 497 MET cc_start: 0.6367 (tmt) cc_final: 0.5849 (tmt) REVERT: B 534 LYS cc_start: 0.7267 (mttt) cc_final: 0.7016 (mttt) REVERT: C 264 LYS cc_start: 0.6940 (mttt) cc_final: 0.6320 (mtpt) REVERT: C 349 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: C 418 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6516 (mt-10) REVERT: C 534 LYS cc_start: 0.7227 (mttt) cc_final: 0.6906 (mtpp) outliers start: 9 outliers final: 2 residues processed: 194 average time/residue: 0.9930 time to fit residues: 214.6485 Evaluate side-chains 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 349 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 135 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN C 508 GLN C 620 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099536 restraints weight = 38326.683| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.56 r_work: 0.3015 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13005 Z= 0.156 Angle : 0.494 5.494 17634 Z= 0.260 Chirality : 0.037 0.118 2007 Planarity : 0.004 0.044 2118 Dihedral : 14.221 151.276 2076 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.58 % Allowed : 9.98 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.21), residues: 1593 helix: 2.67 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -1.40 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 539 TYR 0.009 0.001 TYR B 231 PHE 0.016 0.001 PHE C 146 TRP 0.008 0.001 TRP C 194 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (13005) covalent geometry : angle 0.49436 / 0.26 (17634) hydrogen bonds : bond 0.05574 / 3.79 ( 979) hydrogen bonds : angle 3.93147 / 2.91 ( 2883) *********************** 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 218 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8281 (mmm) cc_final: 0.8030 (mmm) REVERT: A 335 GLU cc_start: 0.7531 (pt0) cc_final: 0.7282 (pt0) REVERT: A 508 GLN cc_start: 0.8080 (mt0) cc_final: 0.7207 (mm-40) REVERT: A 601 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6929 (tt) REVERT: B 231 TYR cc_start: 0.7151 (t80) cc_final: 0.6939 (t80) REVERT: B 242 GLN cc_start: 0.8236 (mt0) cc_final: 0.7974 (mt0) REVERT: B 262 LEU cc_start: 0.7799 (mt) cc_final: 0.7479 (mt) REVERT: B 264 LYS cc_start: 0.6777 (mttt) cc_final: 0.6363 (mtpt) REVERT: C 264 LYS cc_start: 0.6950 (mttt) cc_final: 0.6472 (mtpt) REVERT: C 313 LEU cc_start: 0.7743 (mt) cc_final: 0.7539 (mt) REVERT: C 335 GLU cc_start: 0.7480 (pt0) cc_final: 0.7189 (pt0) REVERT: C 349 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: C 418 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6697 (mt-10) REVERT: C 534 LYS cc_start: 0.7422 (mttt) cc_final: 0.7034 (mttm) outliers start: 20 outliers final: 7 residues processed: 209 average time/residue: 1.0077 time to fit residues: 235.1982 Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 104 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 423 ASN A 479 ASN A 620 ASN C 508 GLN C 620 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100258 restraints weight = 39215.535| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.55 r_work: 0.3032 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13005 Z= 0.200 Angle : 0.535 5.935 17634 Z= 0.282 Chirality : 0.038 0.122 2007 Planarity : 0.004 0.049 2118 Dihedral : 14.318 144.124 2076 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.43 % Allowed : 11.72 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.21), residues: 1593 helix: 2.33 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 589 TYR 0.012 0.001 TYR C 553 PHE 0.015 0.001 PHE C 146 TRP 0.008 0.001 TRP A 178 HIS 0.006 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (13005) covalent geometry : angle 0.53502 / 0.28 (17634) hydrogen bonds : bond 0.06074 / 4.13 ( 979) hydrogen bonds : angle 4.07145 / 3.01 ( 2883) *********************** 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 195 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8346 (mt0) cc_final: 0.8029 (mt0) REVERT: A 313 LEU cc_start: 0.8179 (mt) cc_final: 0.7955 (mt) REVERT: A 335 GLU cc_start: 0.7681 (pt0) cc_final: 0.7455 (pt0) REVERT: A 482 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7136 (t0) REVERT: A 508 GLN cc_start: 0.8400 (mt0) cc_final: 0.7688 (mm-40) REVERT: B 151 ASP cc_start: 0.7558 (m-30) cc_final: 0.7066 (m-30) REVERT: B 260 ASP cc_start: 0.8000 (t0) cc_final: 0.7665 (t0) REVERT: B 262 LEU cc_start: 0.8120 (mt) cc_final: 0.7820 (mt) REVERT: B 264 LYS cc_start: 0.7338 (mttt) cc_final: 0.6946 (mtpt) REVERT: B 497 MET cc_start: 0.7222 (tmt) cc_final: 0.6729 (tmt) REVERT: C 264 LYS cc_start: 0.7372 (mttt) cc_final: 0.6995 (mtpt) REVERT: C 335 GLU cc_start: 0.7778 (pt0) cc_final: 0.7427 (pt0) REVERT: C 349 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: C 428 MET cc_start: 0.7904 (mmt) cc_final: 0.7576 (mmt) REVERT: C 534 LYS cc_start: 0.7886 (mttt) cc_final: 0.7474 (mttm) outliers start: 18 outliers final: 10 residues processed: 190 average time/residue: 0.9923 time to fit residues: 211.3876 Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 526 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN C 423 ASN C 426 ASN C 508 GLN C 620 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101851 restraints weight = 39146.267| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.55 r_work: 0.3055 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13005 Z= 0.147 Angle : 0.473 5.207 17634 Z= 0.249 Chirality : 0.036 0.114 2007 Planarity : 0.004 0.045 2118 Dihedral : 13.432 140.239 2076 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.58 % Allowed : 12.51 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.21), residues: 1593 helix: 2.50 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -1.48 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 539 TYR 0.009 0.001 TYR C 553 PHE 0.016 0.001 PHE C 146 TRP 0.007 0.001 TRP C 323 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (13005) covalent geometry : angle 0.47340 / 0.25 (17634) hydrogen bonds : bond 0.05124 / 3.48 ( 979) hydrogen bonds : angle 3.89758 / 2.88 ( 2883) *********************** 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 196 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 LEU cc_start: 0.8062 (mt) cc_final: 0.7839 (mt) REVERT: A 335 GLU cc_start: 0.7648 (pt0) cc_final: 0.7417 (pt0) REVERT: A 482 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7066 (t0) REVERT: A 508 GLN cc_start: 0.8322 (mt0) cc_final: 0.7626 (mm-40) REVERT: A 601 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7260 (tt) REVERT: B 151 ASP cc_start: 0.7529 (m-30) cc_final: 0.7021 (m-30) REVERT: B 242 GLN cc_start: 0.8423 (mt0) cc_final: 0.8144 (mt0) REVERT: B 260 ASP cc_start: 0.7955 (t0) cc_final: 0.7604 (t0) REVERT: B 262 LEU cc_start: 0.8075 (mt) cc_final: 0.7779 (mt) REVERT: B 264 LYS cc_start: 0.7279 (mttt) cc_final: 0.6893 (mtpt) REVERT: C 264 LYS cc_start: 0.7328 (mttt) cc_final: 0.6949 (mtpt) REVERT: C 335 GLU cc_start: 0.7757 (pt0) cc_final: 0.7417 (pt0) REVERT: C 349 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: C 428 MET cc_start: 0.7891 (mmt) cc_final: 0.7598 (mmt) REVERT: C 547 VAL cc_start: 0.6864 (OUTLIER) cc_final: 0.6644 (t) outliers start: 20 outliers final: 10 residues processed: 191 average time/residue: 0.9002 time to fit residues: 194.0492 Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 140 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN B 423 ASN C 423 ASN C 508 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.100351 restraints weight = 39097.650| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.55 r_work: 0.3033 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13005 Z= 0.187 Angle : 0.514 5.907 17634 Z= 0.269 Chirality : 0.038 0.119 2007 Planarity : 0.004 0.047 2118 Dihedral : 13.372 139.216 2076 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.82 % Allowed : 12.59 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.21), residues: 1593 helix: 2.33 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -1.52 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 539 TYR 0.011 0.001 TYR C 553 PHE 0.017 0.001 PHE C 146 TRP 0.009 0.001 TRP A 178 HIS 0.005 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (13005) covalent geometry : angle 0.51369 / 0.27 (17634) hydrogen bonds : bond 0.05877 / 3.99 ( 979) hydrogen bonds : angle 4.01974 / 2.96 ( 2883) *********************** 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 203 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 LEU cc_start: 0.8107 (mt) cc_final: 0.7881 (mt) REVERT: A 335 GLU cc_start: 0.7651 (pt0) cc_final: 0.7325 (pt0) REVERT: A 482 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7141 (t0) REVERT: A 508 GLN cc_start: 0.8319 (mt0) cc_final: 0.7623 (mm-40) REVERT: A 601 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7399 (tt) REVERT: B 151 ASP cc_start: 0.7568 (m-30) cc_final: 0.7049 (m-30) REVERT: B 242 GLN cc_start: 0.8479 (mt0) cc_final: 0.8194 (mt0) REVERT: B 260 ASP cc_start: 0.8009 (t0) cc_final: 0.7657 (t0) REVERT: B 262 LEU cc_start: 0.8193 (mt) cc_final: 0.7895 (mt) REVERT: B 264 LYS cc_start: 0.7295 (mttt) cc_final: 0.6905 (mtpt) REVERT: B 497 MET cc_start: 0.7319 (tmt) cc_final: 0.6822 (tmt) REVERT: C 195 LEU cc_start: 0.6685 (mt) cc_final: 0.6386 (mt) REVERT: C 264 LYS cc_start: 0.7363 (mttt) cc_final: 0.6979 (mtpt) REVERT: C 335 GLU cc_start: 0.7739 (pt0) cc_final: 0.7356 (pt0) REVERT: C 349 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: C 428 MET cc_start: 0.7884 (mmt) cc_final: 0.7565 (mmt) REVERT: C 534 LYS cc_start: 0.7848 (mttt) cc_final: 0.7532 (mttm) outliers start: 23 outliers final: 13 residues processed: 194 average time/residue: 0.8672 time to fit residues: 189.9281 Evaluate side-chains 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 27 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN B 423 ASN C 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.103998 restraints weight = 38790.527| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.53 r_work: 0.3098 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13005 Z= 0.109 Angle : 0.438 4.655 17634 Z= 0.229 Chirality : 0.035 0.113 2007 Planarity : 0.003 0.041 2118 Dihedral : 12.298 131.111 2076 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.19 % Allowed : 13.46 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.22), residues: 1593 helix: 2.72 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -1.35 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 539 TYR 0.007 0.001 TYR C 553 PHE 0.017 0.001 PHE C 146 TRP 0.007 0.001 TRP C 323 HIS 0.002 0.000 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (13005) covalent geometry : angle 0.43766 / 0.23 (17634) hydrogen bonds : bond 0.04303 / 2.93 ( 979) hydrogen bonds : angle 3.74734 / 2.77 ( 2883) *********************** 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 195 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 482 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7145 (t0) REVERT: A 508 GLN cc_start: 0.8262 (mt0) cc_final: 0.7568 (mm-40) REVERT: A 601 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7171 (tt) REVERT: B 151 ASP cc_start: 0.7458 (m-30) cc_final: 0.6986 (m-30) REVERT: B 242 GLN cc_start: 0.8337 (mt0) cc_final: 0.8095 (mt0) REVERT: B 262 LEU cc_start: 0.8091 (mt) cc_final: 0.7830 (mt) REVERT: B 264 LYS cc_start: 0.7160 (mttt) cc_final: 0.6776 (mtpt) REVERT: C 195 LEU cc_start: 0.6630 (mt) cc_final: 0.6358 (mt) REVERT: C 264 LYS cc_start: 0.7272 (mttt) cc_final: 0.6857 (mtpt) REVERT: C 335 GLU cc_start: 0.7717 (pt0) cc_final: 0.7373 (pt0) REVERT: C 349 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: C 428 MET cc_start: 0.7808 (mmt) cc_final: 0.7489 (mmt) REVERT: C 534 LYS cc_start: 0.7771 (mttt) cc_final: 0.7377 (mttm) outliers start: 15 outliers final: 7 residues processed: 193 average time/residue: 0.8645 time to fit residues: 188.8218 Evaluate side-chains 187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN B 423 ASN B 426 ASN C 423 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102869 restraints weight = 38848.376| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.55 r_work: 0.3071 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13005 Z= 0.127 Angle : 0.454 4.999 17634 Z= 0.236 Chirality : 0.035 0.115 2007 Planarity : 0.004 0.042 2118 Dihedral : 12.158 130.378 2076 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.11 % Allowed : 14.09 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.22), residues: 1593 helix: 2.73 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -1.34 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 539 TYR 0.008 0.001 TYR C 553 PHE 0.017 0.001 PHE A 146 TRP 0.008 0.001 TRP A 178 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13005) covalent geometry : angle 0.45404 / 0.24 (17634) hydrogen bonds : bond 0.04657 / 3.17 ( 979) hydrogen bonds : angle 3.76427 / 2.78 ( 2883) *********************** 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 191 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8272 (mt0) cc_final: 0.8052 (mt0) REVERT: A 335 GLU cc_start: 0.7774 (pt0) cc_final: 0.7553 (pt0) REVERT: A 482 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7111 (t0) REVERT: A 601 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7183 (tt) REVERT: B 151 ASP cc_start: 0.7452 (m-30) cc_final: 0.6923 (m-30) REVERT: B 242 GLN cc_start: 0.8350 (mt0) cc_final: 0.8097 (mt0) REVERT: B 260 ASP cc_start: 0.7907 (t0) cc_final: 0.7544 (t0) REVERT: B 262 LEU cc_start: 0.8120 (mt) cc_final: 0.7851 (mt) REVERT: B 264 LYS cc_start: 0.7145 (mttt) cc_final: 0.6743 (mtpt) REVERT: C 264 LYS cc_start: 0.7256 (mttt) cc_final: 0.6828 (mtpt) REVERT: C 349 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: C 428 MET cc_start: 0.7784 (mmt) cc_final: 0.7464 (mmt) REVERT: C 534 LYS cc_start: 0.7727 (mttt) cc_final: 0.7391 (mttm) outliers start: 14 outliers final: 8 residues processed: 188 average time/residue: 0.8889 time to fit residues: 189.5394 Evaluate side-chains 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 73 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN B 423 ASN C 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.100409 restraints weight = 39143.912| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.55 r_work: 0.3053 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13005 Z= 0.185 Angle : 0.513 5.881 17634 Z= 0.268 Chirality : 0.038 0.118 2007 Planarity : 0.004 0.045 2118 Dihedral : 12.846 136.578 2076 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.11 % Allowed : 14.17 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.21), residues: 1593 helix: 2.55 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 539 TYR 0.011 0.001 TYR C 553 PHE 0.017 0.001 PHE C 413 TRP 0.011 0.001 TRP A 178 HIS 0.006 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (13005) covalent geometry : angle 0.51274 / 0.27 (17634) hydrogen bonds : bond 0.05785 / 3.93 ( 979) hydrogen bonds : angle 3.97458 / 2.93 ( 2883) *********************** 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 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8331 (mt0) cc_final: 0.8083 (mt0) REVERT: A 482 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7065 (t0) REVERT: A 601 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7413 (tt) REVERT: B 242 GLN cc_start: 0.8495 (mt0) cc_final: 0.8228 (mt0) REVERT: B 260 ASP cc_start: 0.8006 (t0) cc_final: 0.7647 (t0) REVERT: B 262 LEU cc_start: 0.8193 (mt) cc_final: 0.7894 (mt) REVERT: B 264 LYS cc_start: 0.7277 (mttt) cc_final: 0.6886 (mtpt) REVERT: B 497 MET cc_start: 0.7426 (tmt) cc_final: 0.6938 (tmt) REVERT: C 264 LYS cc_start: 0.7368 (mttt) cc_final: 0.6950 (mtpt) REVERT: C 349 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: C 428 MET cc_start: 0.7892 (mmt) cc_final: 0.7593 (mmt) REVERT: C 534 LYS cc_start: 0.7840 (mttt) cc_final: 0.7495 (mttm) outliers start: 14 outliers final: 7 residues processed: 186 average time/residue: 0.8399 time to fit residues: 177.0485 Evaluate side-chains 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 152 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN B 423 ASN C 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099962 restraints weight = 38237.187| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.49 r_work: 0.2999 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13005 Z= 0.135 Angle : 0.462 5.032 17634 Z= 0.241 Chirality : 0.036 0.111 2007 Planarity : 0.004 0.042 2118 Dihedral : 12.328 131.791 2076 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.79 % Allowed : 14.81 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.22), residues: 1593 helix: 2.63 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -1.38 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 539 TYR 0.008 0.001 TYR C 553 PHE 0.018 0.001 PHE A 146 TRP 0.009 0.001 TRP A 178 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (13005) covalent geometry : angle 0.46181 / 0.24 (17634) hydrogen bonds : bond 0.04796 / 3.26 ( 979) hydrogen bonds : angle 3.82079 / 2.82 ( 2883) ********************** 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 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 482 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7116 (t0) REVERT: A 601 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7048 (tt) REVERT: B 242 GLN cc_start: 0.8317 (mt0) cc_final: 0.8072 (mt0) REVERT: B 260 ASP cc_start: 0.7834 (t0) cc_final: 0.7474 (t0) REVERT: B 262 LEU cc_start: 0.7996 (mt) cc_final: 0.7731 (mt) REVERT: B 264 LYS cc_start: 0.6971 (mttt) cc_final: 0.6576 (mtpt) REVERT: C 264 LYS cc_start: 0.7037 (mttt) cc_final: 0.6617 (mtpt) REVERT: C 349 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: C 428 MET cc_start: 0.7646 (mmt) cc_final: 0.7326 (mmt) REVERT: C 534 LYS cc_start: 0.7612 (mttt) cc_final: 0.7284 (mttm) outliers start: 10 outliers final: 7 residues processed: 183 average time/residue: 0.9081 time to fit residues: 188.0142 Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN B 423 ASN C 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099858 restraints weight = 38310.048| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.49 r_work: 0.2981 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13005 Z= 0.136 Angle : 0.464 5.112 17634 Z= 0.242 Chirality : 0.036 0.113 2007 Planarity : 0.004 0.042 2118 Dihedral : 12.225 131.202 2076 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.87 % Allowed : 14.65 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.22), residues: 1593 helix: 2.76 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 539 TYR 0.008 0.001 TYR C 553 PHE 0.018 0.001 PHE A 146 TRP 0.009 0.001 TRP A 178 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13005) covalent geometry : angle 0.46401 / 0.24 (17634) hydrogen bonds : bond 0.04865 / 3.31 ( 979) hydrogen bonds : angle 3.81071 / 2.82 ( 2883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7845.52 seconds wall clock time: 133 minutes 26.82 seconds (8006.82 seconds total)