Starting phenix.real_space_refine on Sun Jul 5 03:38:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz5_41734/07_2026/8tz5_41734_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz5_41734/07_2026/8tz5_41734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz5_41734/07_2026/8tz5_41734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz5_41734/07_2026/8tz5_41734.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz5_41734/07_2026/8tz5_41734_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz5_41734/07_2026/8tz5_41734_trim.cif" } resolution = 2.74 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= 0.010 sd= 0.235 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 87 5.16 5 Na 3 4.78 5 C 8439 2.51 5 N 1935 2.21 5 O 2205 1.98 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 24846 Number of models: 1 Model: "" Number of chains: 2 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, 'U56': 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 Restraints were copied for chains: B, C Time building chain proxies: 8.97, per 1000 atoms: 0.36 Number of scatterers: 24846 At special positions: 0 Unit cell: (127.65, 129.87, 75.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 12 15.00 Na 3 11.00 O 2205 8.00 N 1935 7.00 C 8439 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: 2.47 Conformation dependent library (CDL) restraints added in 568.5 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: 90 helices and 3 sheets defined 90.3% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 removed outlier: 3.577A pdb=" N ILE A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 198 Proline residue: A 167 - end of helix removed outlier: 4.797A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.984A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.161A pdb=" N VAL A 230 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.557A 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 281 removed outlier: 4.340A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.391A pdb=" N THR A 286 " --> pdb=" O GLU A 283 " (cutoff:3.500A) 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: 3.589A pdb=" N TRP A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 349 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.278A 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: 3.610A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.621A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.101A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.907A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 586 removed outlier: 4.018A pdb=" N GLY A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.710A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.362A 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 removed outlier: 3.577A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 198 Proline residue: B 167 - end of helix removed outlier: 4.796A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.984A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.160A pdb=" N VAL B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 4.557A 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 281 removed outlier: 4.339A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 4.391A pdb=" N THR B 286 " --> pdb=" O GLU B 283 " (cutoff:3.500A) 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: 3.588A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.278A 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: 3.610A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.622A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.101A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.906A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 586 removed outlier: 4.017A pdb=" N GLY B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.710A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 597 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 5.362A 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 removed outlier: 3.577A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 198 Proline residue: C 167 - end of helix removed outlier: 4.796A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.984A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.161A pdb=" N VAL C 230 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 4.558A 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 281 removed outlier: 4.340A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.390A pdb=" N THR C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) 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: 3.587A pdb=" N TRP C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 381 through 389 Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.279A 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: 3.610A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.621A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.101A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.906A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 586 removed outlier: 4.017A pdb=" N GLY C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.709A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 597 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.361A 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 547 973 hydrogen bonds defined for protein. 2847 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: 5.08 Time building geometry restraints manager: 2.70 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: 45 1.22 - 1.42: 5418 1.42 - 1.61: 7377 1.61 - 1.81: 183 Bond restraints: 25170 Sorted by residual: bond pdb=" C15 U56 C 801 " pdb=" C17 U56 C 801 " ideal model delta sigma weight residual 1.527 1.249 0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C15 U56 B 801 " pdb=" C17 U56 B 801 " ideal model delta sigma weight residual 1.527 1.249 0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C15 U56 A 801 " pdb=" C17 U56 A 801 " ideal model delta sigma weight residual 1.527 1.250 0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" O4 LBN A 805 " pdb=" P1 LBN A 805 " ideal model delta sigma weight residual 1.497 1.647 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" O4 LBN A 806 " pdb=" P1 LBN A 806 " ideal model delta sigma weight residual 1.497 1.647 -0.150 2.00e-02 2.50e+03 5.60e+01 ... (remaining 25165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 44937 3.31 - 6.62: 162 6.62 - 9.94: 36 9.94 - 13.25: 3 13.25 - 16.56: 12 Bond angle restraints: 45150 Sorted by residual: angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 110.01 -16.56 3.00e+00 1.11e-01 3.05e+01 angle pdb=" O1 LBN C 803 " pdb=" P1 LBN C 803 " pdb=" O2 LBN C 803 " ideal model delta sigma weight residual 93.45 110.00 -16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 109.98 -16.53 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O1 LBN B 806 " pdb=" P1 LBN B 806 " pdb=" O2 LBN B 806 " ideal model delta sigma weight residual 93.45 109.57 -16.12 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O1 LBN B 804 " pdb=" P1 LBN B 804 " pdb=" O2 LBN B 804 " ideal model delta sigma weight residual 93.45 109.55 -16.10 3.00e+00 1.11e-01 2.88e+01 ... (remaining 45145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 11677 34.45 - 68.89: 404 68.89 - 103.34: 15 103.34 - 137.78: 3 137.78 - 172.23: 9 Dihedral angle restraints: 12108 sinusoidal: 6378 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN C 804 " pdb=" C2 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " ideal model delta sinusoidal sigma weight residual 62.67 -125.10 -172.23 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O5 LBN B 804 " pdb=" C2 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " ideal model delta sinusoidal sigma weight residual 62.67 -125.11 -172.22 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O5 LBN A 804 " pdb=" C2 LBN A 804 " pdb=" C3 LBN A 804 " pdb=" O7 LBN A 804 " ideal model delta sinusoidal sigma weight residual 62.67 -125.17 -172.16 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1869 0.074 - 0.148: 117 0.148 - 0.222: 15 0.222 - 0.295: 3 0.295 - 0.369: 3 Chirality restraints: 2007 Sorted by residual: chirality pdb=" C17 U56 B 801 " pdb=" C10 U56 B 801 " pdb=" C15 U56 B 801 " pdb=" O18 U56 B 801 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C17 U56 C 801 " pdb=" C10 U56 C 801 " pdb=" C15 U56 C 801 " pdb=" O18 U56 C 801 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C17 U56 A 801 " pdb=" C10 U56 A 801 " pdb=" C15 U56 A 801 " pdb=" O18 U56 A 801 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 2004 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 195 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C LEU A 195 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU A 195 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 195 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C LEU C 195 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU C 195 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL C 196 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 195 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C LEU B 195 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU B 195 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 196 " -0.009 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1209 2.21 - 2.81: 49909 2.81 - 3.41: 67094 3.41 - 4.00: 87989 4.00 - 4.60: 139562 Nonbonded interactions: 345763 Sorted by model distance: nonbonded pdb="HH21 ARG A 436 " pdb=" OE2 GLU A 440 " model vdw 1.615 2.450 nonbonded pdb="HH21 ARG C 436 " pdb=" OE2 GLU C 440 " model vdw 1.615 2.450 nonbonded pdb="HH21 ARG B 436 " pdb=" OE2 GLU B 440 " model vdw 1.616 2.450 nonbonded pdb=" O LEU B 248 " pdb=" HG1 THR B 252 " model vdw 1.647 2.450 nonbonded pdb=" O LEU A 248 " pdb=" HG1 THR A 252 " model vdw 1.647 2.450 ... (remaining 345758 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: 0.05 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: 1.230 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: 0.180 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 25.730 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.011 0.278 13005 Z= 0.554 Angle : 0.861 16.562 17628 Z= 0.342 Chirality : 0.042 0.369 2007 Planarity : 0.003 0.036 2118 Dihedral : 15.925 172.227 4614 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.24 % Allowed : 2.38 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.21), residues: 1593 helix: 2.18 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.78 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 539 TYR 0.006 0.001 TYR B 285 PHE 0.011 0.001 PHE B 413 TRP 0.006 0.001 TRP A 414 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd/Z covalent geometry : bond 0.01108 / 0.55 (13005) covalent geometry : angle 0.86143 / 0.34 (17628) hydrogen bonds : bond 0.14112 / 9.68 ( 973) hydrogen bonds : angle 4.91618 / 3.58 ( 2847) *********************** 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 235 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 232 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 429 LYS cc_start: 0.7730 (ptpt) cc_final: 0.7134 (ptmm) REVERT: A 502 MET cc_start: 0.7747 (mtm) cc_final: 0.7396 (mmp) REVERT: B 229 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7436 (mmmt) REVERT: B 313 LEU cc_start: 0.8498 (mt) cc_final: 0.8187 (mp) REVERT: B 429 LYS cc_start: 0.7484 (ptpt) cc_final: 0.6874 (ptmm) REVERT: B 444 GLN cc_start: 0.7612 (mt0) cc_final: 0.7262 (tm-30) REVERT: B 502 MET cc_start: 0.7579 (mtm) cc_final: 0.7201 (mmp) REVERT: B 508 GLN cc_start: 0.7724 (mt0) cc_final: 0.7271 (mm110) REVERT: C 229 LYS cc_start: 0.7381 (mmtt) cc_final: 0.7019 (mmtt) REVERT: C 313 LEU cc_start: 0.8663 (mt) cc_final: 0.8376 (mt) REVERT: C 429 LYS cc_start: 0.7596 (ptpt) cc_final: 0.7140 (ptmm) REVERT: C 444 GLN cc_start: 0.7269 (mt0) cc_final: 0.7022 (tm-30) REVERT: C 502 MET cc_start: 0.7615 (mtm) cc_final: 0.7331 (mmp) outliers start: 3 outliers final: 0 residues processed: 235 average time/residue: 0.8131 time to fit residues: 214.6046 Evaluate side-chains 172 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN B 471 ASN B 479 ASN C 571 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120860 restraints weight = 36207.101| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.33 r_work: 0.3306 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13005 Z= 0.112 Angle : 0.455 4.507 17628 Z= 0.239 Chirality : 0.035 0.116 2007 Planarity : 0.004 0.051 2118 Dihedral : 16.490 179.964 2064 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.71 % Allowed : 7.60 % Favored : 91.69 % 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: 3.09 (0.22), residues: 1593 helix: 2.52 (0.15), residues: 1335 sheet: None (None), residues: 0 loop : -0.60 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 589 TYR 0.005 0.001 TYR C 553 PHE 0.013 0.001 PHE B 413 TRP 0.010 0.001 TRP B 316 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (13005) covalent geometry : angle 0.45493 / 0.24 (17628) hydrogen bonds : bond 0.04452 / 3.00 ( 973) hydrogen bonds : angle 3.85032 / 2.80 ( 2847) *********************** 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 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.652 Fit side-chains REVERT: A 129 MET cc_start: 0.7561 (mtp) cc_final: 0.7286 (mtt) REVERT: A 429 LYS cc_start: 0.7389 (ptpt) cc_final: 0.6642 (ptmm) REVERT: A 430 MET cc_start: 0.7409 (mtt) cc_final: 0.6845 (mtt) REVERT: A 502 MET cc_start: 0.7466 (mtm) cc_final: 0.7023 (tpt) REVERT: A 554 MET cc_start: 0.9172 (ptt) cc_final: 0.8927 (ptt) REVERT: B 229 LYS cc_start: 0.7840 (mmtt) cc_final: 0.7452 (mmtp) REVERT: B 283 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 313 LEU cc_start: 0.8633 (mt) cc_final: 0.8294 (mp) REVERT: B 429 LYS cc_start: 0.7110 (ptpt) cc_final: 0.6629 (ptmm) REVERT: B 437 ASN cc_start: 0.7157 (p0) cc_final: 0.6923 (p0) REVERT: B 502 MET cc_start: 0.7617 (mtm) cc_final: 0.7134 (mmp) REVERT: B 508 GLN cc_start: 0.8005 (mt0) cc_final: 0.7565 (mm110) REVERT: B 592 ASP cc_start: 0.7932 (m-30) cc_final: 0.7601 (m-30) REVERT: C 229 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7082 (mmtt) REVERT: C 313 LEU cc_start: 0.8723 (mt) cc_final: 0.8480 (mt) REVERT: C 430 MET cc_start: 0.7366 (mtt) cc_final: 0.6990 (mtt) REVERT: C 502 MET cc_start: 0.7958 (mtm) cc_final: 0.7539 (mmp) REVERT: C 508 GLN cc_start: 0.8133 (mt0) cc_final: 0.7475 (mm110) REVERT: C 601 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6712 (tt) outliers start: 9 outliers final: 3 residues processed: 186 average time/residue: 0.8161 time to fit residues: 171.2630 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 92 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.158407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116355 restraints weight = 35050.470| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.19 r_work: 0.3083 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13005 Z= 0.109 Angle : 0.423 4.432 17628 Z= 0.224 Chirality : 0.035 0.114 2007 Planarity : 0.003 0.050 2118 Dihedral : 15.031 178.879 2064 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.03 % Allowed : 8.08 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.22), residues: 1593 helix: 2.83 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.71 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 589 TYR 0.006 0.001 TYR C 285 PHE 0.012 0.001 PHE C 413 TRP 0.009 0.001 TRP B 316 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (13005) covalent geometry : angle 0.42344 / 0.22 (17628) hydrogen bonds : bond 0.04433 / 2.98 ( 973) hydrogen bonds : angle 3.72058 / 2.70 ( 2847) *********************** 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 197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.484 Fit side-chains REVERT: A 129 MET cc_start: 0.7494 (mtp) cc_final: 0.7221 (mtt) REVERT: A 229 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7287 (mmtt) REVERT: A 365 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 429 LYS cc_start: 0.7459 (ptpt) cc_final: 0.6713 (ptmm) REVERT: A 430 MET cc_start: 0.7741 (mtt) cc_final: 0.7179 (mtt) REVERT: A 502 MET cc_start: 0.7599 (mtm) cc_final: 0.7202 (tpt) REVERT: A 554 MET cc_start: 0.9194 (ptt) cc_final: 0.8937 (ptt) REVERT: A 590 LYS cc_start: 0.7549 (ttmt) cc_final: 0.7033 (ttpp) REVERT: B 229 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7425 (mmmt) REVERT: B 305 MET cc_start: 0.8760 (mmp) cc_final: 0.8167 (mmt) REVERT: B 365 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 429 LYS cc_start: 0.7323 (ptpt) cc_final: 0.6915 (ptmm) REVERT: B 485 GLN cc_start: 0.8291 (mp10) cc_final: 0.7912 (mp10) REVERT: B 502 MET cc_start: 0.7680 (mtm) cc_final: 0.7291 (mmp) REVERT: B 508 GLN cc_start: 0.8305 (mt0) cc_final: 0.7801 (mm110) REVERT: C 229 LYS cc_start: 0.7666 (mmtt) cc_final: 0.7211 (mmtt) REVERT: C 313 LEU cc_start: 0.8830 (mt) cc_final: 0.8595 (mt) REVERT: C 430 MET cc_start: 0.7594 (mtt) cc_final: 0.7229 (mtt) REVERT: C 477 LEU cc_start: 0.7793 (tp) cc_final: 0.7505 (tp) REVERT: C 601 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7167 (tt) outliers start: 13 outliers final: 5 residues processed: 191 average time/residue: 0.8237 time to fit residues: 176.2048 Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 393 SER 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 85 optimal weight: 0.0050 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.153854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110701 restraints weight = 34854.262| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.21 r_work: 0.3040 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13005 Z= 0.155 Angle : 0.485 5.485 17628 Z= 0.260 Chirality : 0.037 0.122 2007 Planarity : 0.004 0.057 2118 Dihedral : 15.264 179.108 2064 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.03 % Allowed : 8.79 % Favored : 90.18 % 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: 3.00 (0.21), residues: 1593 helix: 2.60 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 589 TYR 0.007 0.001 TYR C 357 PHE 0.018 0.001 PHE A 413 TRP 0.008 0.001 TRP A 316 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13005) covalent geometry : angle 0.48456 / 0.26 (17628) hydrogen bonds : bond 0.05573 / 3.74 ( 973) hydrogen bonds : angle 3.90151 / 2.84 ( 2847) *********************** 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 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.446 Fit side-chains REVERT: A 129 MET cc_start: 0.7345 (mtp) cc_final: 0.7105 (mtt) REVERT: A 229 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7402 (mmtt) REVERT: A 365 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 429 LYS cc_start: 0.7373 (ptpt) cc_final: 0.6655 (ptmm) REVERT: A 430 MET cc_start: 0.7787 (mtt) cc_final: 0.7140 (mtt) REVERT: A 502 MET cc_start: 0.7719 (mtm) cc_final: 0.7255 (tpt) REVERT: A 590 LYS cc_start: 0.7639 (ttmt) cc_final: 0.7140 (ttpp) REVERT: A 592 ASP cc_start: 0.7992 (m-30) cc_final: 0.7744 (m-30) REVERT: B 229 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7363 (mmmt) REVERT: B 283 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 305 MET cc_start: 0.8828 (mmp) cc_final: 0.8140 (mmt) REVERT: B 502 MET cc_start: 0.7753 (mtm) cc_final: 0.7363 (mmp) REVERT: B 508 GLN cc_start: 0.8338 (mt0) cc_final: 0.7866 (mm110) REVERT: C 229 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7530 (mmtt) REVERT: C 313 LEU cc_start: 0.8912 (mt) cc_final: 0.8637 (mt) REVERT: C 430 MET cc_start: 0.7490 (mtt) cc_final: 0.7105 (mtt) REVERT: C 477 LEU cc_start: 0.8026 (tp) cc_final: 0.7779 (tp) outliers start: 13 outliers final: 4 residues processed: 180 average time/residue: 0.8634 time to fit residues: 173.4374 Evaluate side-chains 166 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 393 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 135 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 ASN B 265 GLN C 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.154314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111514 restraints weight = 34849.171| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.18 r_work: 0.3020 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13005 Z= 0.137 Angle : 0.457 4.768 17628 Z= 0.244 Chirality : 0.036 0.117 2007 Planarity : 0.004 0.055 2118 Dihedral : 14.807 179.743 2064 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.11 % Allowed : 8.71 % Favored : 90.18 % 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: 3.07 (0.22), residues: 1593 helix: 2.65 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.007 0.001 TYR C 357 PHE 0.013 0.001 PHE C 413 TRP 0.009 0.001 TRP A 316 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (13005) covalent geometry : angle 0.45703 / 0.24 (17628) hydrogen bonds : bond 0.05065 / 3.41 ( 973) hydrogen bonds : angle 3.82189 / 2.78 ( 2847) *********************** 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 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.652 Fit side-chains REVERT: A 129 MET cc_start: 0.7357 (mtp) cc_final: 0.7122 (mtt) REVERT: A 229 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7445 (mmtt) REVERT: A 365 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7783 (mt-10) REVERT: A 430 MET cc_start: 0.7697 (mtt) cc_final: 0.7033 (mtt) REVERT: A 502 MET cc_start: 0.7691 (mtm) cc_final: 0.7210 (tpt) REVERT: A 590 LYS cc_start: 0.7604 (ttmt) cc_final: 0.7092 (ttpp) REVERT: A 592 ASP cc_start: 0.7966 (m-30) cc_final: 0.7732 (m-30) REVERT: B 229 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7458 (mmmt) REVERT: B 283 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 305 MET cc_start: 0.8830 (mmp) cc_final: 0.8144 (mmt) REVERT: B 485 GLN cc_start: 0.8481 (mp10) cc_final: 0.8068 (mp10) REVERT: B 502 MET cc_start: 0.7741 (mtm) cc_final: 0.7343 (mmp) REVERT: B 508 GLN cc_start: 0.8269 (mt0) cc_final: 0.7783 (mm-40) REVERT: C 229 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7536 (mmtt) REVERT: C 313 LEU cc_start: 0.8863 (mt) cc_final: 0.8622 (mt) REVERT: C 430 MET cc_start: 0.7440 (mtt) cc_final: 0.7049 (mtt) REVERT: C 477 LEU cc_start: 0.7956 (tp) cc_final: 0.7717 (tp) outliers start: 14 outliers final: 5 residues processed: 178 average time/residue: 0.9406 time to fit residues: 186.5341 Evaluate side-chains 169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 79 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.153194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110355 restraints weight = 34669.824| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.18 r_work: 0.3100 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13005 Z= 0.152 Angle : 0.479 5.378 17628 Z= 0.257 Chirality : 0.037 0.120 2007 Planarity : 0.004 0.057 2118 Dihedral : 14.678 177.426 2064 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.35 % Allowed : 9.18 % Favored : 89.47 % 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: 2.94 (0.21), residues: 1593 helix: 2.57 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.08 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.007 0.001 TYR C 553 PHE 0.015 0.001 PHE A 413 TRP 0.007 0.001 TRP B 261 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13005) covalent geometry : angle 0.47932 / 0.26 (17628) hydrogen bonds : bond 0.05478 / 3.69 ( 973) hydrogen bonds : angle 3.88234 / 2.83 ( 2847) *********************** 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 187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.621 Fit side-chains REVERT: A 129 MET cc_start: 0.7400 (mtp) cc_final: 0.7192 (mtt) REVERT: A 229 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7495 (mmtp) REVERT: A 365 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 430 MET cc_start: 0.7755 (mtt) cc_final: 0.7065 (mtt) REVERT: A 502 MET cc_start: 0.7765 (mtm) cc_final: 0.7335 (tpt) REVERT: A 590 LYS cc_start: 0.7623 (ttmt) cc_final: 0.7124 (ttpp) REVERT: A 592 ASP cc_start: 0.7915 (m-30) cc_final: 0.7684 (m-30) REVERT: B 229 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7474 (mmmt) REVERT: B 283 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 305 MET cc_start: 0.8858 (mmp) cc_final: 0.8134 (mmt) REVERT: B 485 GLN cc_start: 0.8526 (mp10) cc_final: 0.8134 (mp10) REVERT: B 502 MET cc_start: 0.7768 (mtm) cc_final: 0.7371 (mmp) REVERT: B 508 GLN cc_start: 0.8324 (mt0) cc_final: 0.7827 (mm110) REVERT: C 229 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7573 (mmtt) REVERT: C 313 LEU cc_start: 0.8881 (mt) cc_final: 0.8634 (mt) REVERT: C 430 MET cc_start: 0.7484 (mtt) cc_final: 0.7025 (mtt) outliers start: 17 outliers final: 8 residues processed: 180 average time/residue: 0.8840 time to fit residues: 177.4738 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 508 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 132 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111569 restraints weight = 34771.121| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.18 r_work: 0.3032 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13005 Z= 0.133 Angle : 0.455 4.897 17628 Z= 0.242 Chirality : 0.036 0.116 2007 Planarity : 0.004 0.056 2118 Dihedral : 14.110 176.529 2064 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.03 % Allowed : 9.98 % Favored : 88.99 % 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: 3.10 (0.22), residues: 1593 helix: 2.68 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.03 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.007 0.001 TYR C 553 PHE 0.012 0.001 PHE C 279 TRP 0.008 0.001 TRP A 316 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13005) covalent geometry : angle 0.45515 / 0.24 (17628) hydrogen bonds : bond 0.04970 / 3.34 ( 973) hydrogen bonds : angle 3.80022 / 2.77 ( 2847) *********************** 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 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.537 Fit side-chains REVERT: A 129 MET cc_start: 0.7395 (mtp) cc_final: 0.7185 (mtt) REVERT: A 229 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7527 (mmtt) REVERT: A 365 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 430 MET cc_start: 0.7724 (mtt) cc_final: 0.7066 (mtt) REVERT: A 502 MET cc_start: 0.7755 (mtm) cc_final: 0.7314 (tpt) REVERT: A 590 LYS cc_start: 0.7611 (ttmt) cc_final: 0.7114 (ttpp) REVERT: A 592 ASP cc_start: 0.7911 (m-30) cc_final: 0.7687 (m-30) REVERT: B 199 THR cc_start: 0.8472 (m) cc_final: 0.8261 (m) REVERT: B 229 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7473 (mmmt) REVERT: B 283 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 305 MET cc_start: 0.8862 (mmp) cc_final: 0.8161 (mmt) REVERT: B 485 GLN cc_start: 0.8506 (mp10) cc_final: 0.8113 (mp10) REVERT: B 502 MET cc_start: 0.7755 (mtm) cc_final: 0.7365 (mmp) REVERT: B 508 GLN cc_start: 0.8268 (mt0) cc_final: 0.7780 (mm110) REVERT: C 229 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7582 (mmtt) REVERT: C 313 LEU cc_start: 0.8864 (mt) cc_final: 0.8638 (mt) REVERT: C 428 MET cc_start: 0.7711 (mmp) cc_final: 0.7151 (mmp) REVERT: C 430 MET cc_start: 0.7479 (mtt) cc_final: 0.7039 (mtt) outliers start: 13 outliers final: 6 residues processed: 183 average time/residue: 0.8641 time to fit residues: 176.6334 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 33 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.155234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112583 restraints weight = 34964.440| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.19 r_work: 0.3048 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13005 Z= 0.114 Angle : 0.434 4.627 17628 Z= 0.230 Chirality : 0.035 0.112 2007 Planarity : 0.004 0.054 2118 Dihedral : 13.583 176.983 2064 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.87 % Allowed : 10.37 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.22), residues: 1593 helix: 2.82 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 557 TYR 0.006 0.001 TYR C 553 PHE 0.011 0.001 PHE B 259 TRP 0.008 0.001 TRP A 316 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13005) covalent geometry : angle 0.43417 / 0.23 (17628) hydrogen bonds : bond 0.04524 / 3.05 ( 973) hydrogen bonds : angle 3.70766 / 2.70 ( 2847) *********************** 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 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.662 Fit side-chains REVERT: A 129 MET cc_start: 0.7351 (mtp) cc_final: 0.7148 (mtt) REVERT: A 229 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7641 (mmtt) REVERT: A 365 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 430 MET cc_start: 0.7713 (mtt) cc_final: 0.7084 (mtt) REVERT: A 502 MET cc_start: 0.7673 (mtm) cc_final: 0.7242 (tpt) REVERT: A 590 LYS cc_start: 0.7586 (ttmt) cc_final: 0.7081 (ttpp) REVERT: A 592 ASP cc_start: 0.7922 (m-30) cc_final: 0.7697 (m-30) REVERT: B 199 THR cc_start: 0.8419 (m) cc_final: 0.8212 (m) REVERT: B 229 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7449 (mmmt) REVERT: B 283 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 305 MET cc_start: 0.8887 (mmp) cc_final: 0.8186 (mmt) REVERT: B 485 GLN cc_start: 0.8433 (mp10) cc_final: 0.8023 (mp10) REVERT: B 502 MET cc_start: 0.7726 (mtm) cc_final: 0.7338 (mmp) REVERT: B 508 GLN cc_start: 0.8262 (mt0) cc_final: 0.7768 (mm110) REVERT: C 229 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7576 (mmtt) REVERT: C 313 LEU cc_start: 0.8843 (mt) cc_final: 0.8639 (mt) REVERT: C 428 MET cc_start: 0.7586 (mmp) cc_final: 0.7110 (mmp) REVERT: C 430 MET cc_start: 0.7402 (mtt) cc_final: 0.6957 (mtt) outliers start: 11 outliers final: 7 residues processed: 178 average time/residue: 0.9054 time to fit residues: 179.8026 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.154317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112092 restraints weight = 34721.690| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.16 r_work: 0.3037 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13005 Z= 0.128 Angle : 0.451 5.006 17628 Z= 0.240 Chirality : 0.036 0.115 2007 Planarity : 0.004 0.054 2118 Dihedral : 13.503 176.151 2064 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.79 % Allowed : 10.29 % Favored : 88.92 % 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: 3.22 (0.22), residues: 1593 helix: 2.77 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.01 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 557 TYR 0.008 0.001 TYR A 357 PHE 0.012 0.001 PHE A 413 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 0.00287 / 0.13 (13005) covalent geometry : angle 0.45135 / 0.24 (17628) hydrogen bonds : bond 0.04883 / 3.29 ( 973) hydrogen bonds : angle 3.76433 / 2.74 ( 2847) *********************** 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 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.621 Fit side-chains REVERT: A 129 MET cc_start: 0.7329 (mtp) cc_final: 0.7124 (mtt) REVERT: A 229 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7720 (mmtt) REVERT: A 365 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 502 MET cc_start: 0.7671 (mtm) cc_final: 0.7237 (tpt) REVERT: A 590 LYS cc_start: 0.7568 (ttmt) cc_final: 0.7053 (ttpp) REVERT: A 592 ASP cc_start: 0.7917 (m-30) cc_final: 0.7690 (m-30) REVERT: B 199 THR cc_start: 0.8414 (m) cc_final: 0.8208 (m) REVERT: B 229 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7438 (mmmt) REVERT: B 283 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 305 MET cc_start: 0.8886 (mmp) cc_final: 0.8176 (mmt) REVERT: B 485 GLN cc_start: 0.8482 (mp10) cc_final: 0.8107 (mp10) REVERT: B 502 MET cc_start: 0.7712 (mtm) cc_final: 0.7324 (mmp) REVERT: B 508 GLN cc_start: 0.8265 (mt0) cc_final: 0.7765 (mm-40) REVERT: C 229 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7541 (mmtt) REVERT: C 313 LEU cc_start: 0.8856 (mt) cc_final: 0.8637 (mt) REVERT: C 428 MET cc_start: 0.7625 (mmp) cc_final: 0.7133 (mmp) REVERT: C 430 MET cc_start: 0.7394 (mtt) cc_final: 0.6944 (mtt) outliers start: 10 outliers final: 7 residues processed: 176 average time/residue: 0.9043 time to fit residues: 177.5857 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 117 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.150192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107568 restraints weight = 35073.229| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.19 r_work: 0.2981 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13005 Z= 0.199 Angle : 0.537 6.192 17628 Z= 0.287 Chirality : 0.039 0.133 2007 Planarity : 0.005 0.059 2118 Dihedral : 14.054 173.861 2064 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.87 % Allowed : 10.29 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.21), residues: 1593 helix: 2.44 (0.14), residues: 1299 sheet: None (None), residues: 0 loop : -1.14 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 251 TYR 0.011 0.002 TYR A 357 PHE 0.019 0.002 PHE C 413 TRP 0.008 0.001 TRP C 507 HIS 0.005 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (13005) covalent geometry : angle 0.53710 / 0.29 (17628) hydrogen bonds : bond 0.06308 / 4.26 ( 973) hydrogen bonds : angle 4.01765 / 2.92 ( 2847) ********************** 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 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.682 Fit side-chains REVERT: A 129 MET cc_start: 0.7323 (mtp) cc_final: 0.7120 (mtt) REVERT: A 229 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7683 (mmtt) REVERT: A 365 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7788 (mt-10) REVERT: A 497 MET cc_start: 0.8306 (tmt) cc_final: 0.7932 (tmt) REVERT: A 502 MET cc_start: 0.7814 (mtm) cc_final: 0.7319 (tpt) REVERT: A 590 LYS cc_start: 0.7589 (ttmt) cc_final: 0.7054 (ttpp) REVERT: A 592 ASP cc_start: 0.7900 (m-30) cc_final: 0.7681 (m-30) REVERT: B 229 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7491 (mmmt) REVERT: B 283 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 305 MET cc_start: 0.8898 (mmp) cc_final: 0.8183 (mmt) REVERT: B 502 MET cc_start: 0.7777 (mtm) cc_final: 0.7394 (mmp) REVERT: B 508 GLN cc_start: 0.8386 (mt0) cc_final: 0.7897 (mm110) REVERT: C 229 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7563 (mmtt) REVERT: C 313 LEU cc_start: 0.8891 (mt) cc_final: 0.8635 (mt) outliers start: 11 outliers final: 7 residues processed: 178 average time/residue: 0.9985 time to fit residues: 198.1848 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 27 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.155155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113315 restraints weight = 35115.457| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.18 r_work: 0.3072 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13005 Z= 0.095 Angle : 0.416 4.324 17628 Z= 0.220 Chirality : 0.035 0.113 2007 Planarity : 0.003 0.051 2118 Dihedral : 13.175 178.972 2064 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.63 % Allowed : 10.69 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.22), residues: 1593 helix: 2.88 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 233 TYR 0.006 0.001 TYR A 357 PHE 0.010 0.001 PHE C 259 TRP 0.012 0.001 TRP A 316 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (13005) covalent geometry : angle 0.41596 / 0.22 (17628) hydrogen bonds : bond 0.03954 / 2.67 ( 973) hydrogen bonds : angle 3.64047 / 2.65 ( 2847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6901.90 seconds wall clock time: 117 minutes 18.56 seconds (7038.56 seconds total)