Starting phenix.real_space_refine on Mon Aug 25 04:40:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz5_41734/08_2025/8tz5_41734_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz5_41734/08_2025/8tz5_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tz5_41734/08_2025/8tz5_41734_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz5_41734/08_2025/8tz5_41734_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tz5_41734/08_2025/8tz5_41734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz5_41734/08_2025/8tz5_41734.map" } 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-2.0-5787/lib/python3.9/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, 153 Unusual residues: {' NA': 1, 'LBN': 4, 'U56': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 7.56, per 1000 atoms: 0.30 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: 1.81 Conformation dependent library (CDL) restraints added in 556.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 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: 0.71 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: 5.16 Time building geometry restraints manager: 2.59 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: 0.04 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.150 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 aren 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 covalent geometry : bond 0.01108 (13005) covalent geometry : angle 0.86143 (17628) hydrogen bonds : bond 0.14112 ( 973) hydrogen bonds : angle 4.91618 ( 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 : 0.476 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: 0.7483 (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: 0.8233 time to fit residues: 216.3203 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 : 0.511 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3813 r_free = 0.3813 target = 0.160703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120674 restraints weight = 36260.908| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.30 r_work: 0.3300 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1886 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= 0.114 Angle : 0.456 4.497 17628 Z= 0.239 Chirality : 0.035 0.115 2007 Planarity : 0.004 0.051 2118 Dihedral : 16.479 179.881 2064 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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 aren not related in a simple way. whole: 3.12 (0.22), residues: 1593 helix: 2.59 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -0.73 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 589 TYR 0.005 0.001 TYR A 231 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 covalent geometry : bond 0.00236 (13005) covalent geometry : angle 0.45581 (17628) hydrogen bonds : bond 0.04463 ( 973) hydrogen bonds : angle 3.84663 ( 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 190 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.541 Fit side-chains REVERT: A 129 MET cc_start: 0.7568 (mtp) cc_final: 0.7292 (mtt) REVERT: A 429 LYS cc_start: 0.7398 (ptpt) cc_final: 0.6653 (ptmm) REVERT: A 430 MET cc_start: 0.7394 (mtt) cc_final: 0.6836 (mtt) REVERT: A 502 MET cc_start: 0.7449 (mtm) cc_final: 0.7022 (tpt) REVERT: B 229 LYS cc_start: 0.7843 (mmtt) cc_final: 0.7455 (mmtp) REVERT: B 283 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 313 LEU cc_start: 0.8671 (mt) cc_final: 0.8334 (mp) REVERT: B 429 LYS cc_start: 0.7115 (ptpt) cc_final: 0.6643 (ptmm) REVERT: B 437 ASN cc_start: 0.7164 (p0) cc_final: 0.6903 (p0) REVERT: B 502 MET cc_start: 0.7605 (mtm) cc_final: 0.7138 (mmp) REVERT: B 508 GLN cc_start: 0.8006 (mt0) cc_final: 0.7568 (mm110) REVERT: B 592 ASP cc_start: 0.7941 (m-30) cc_final: 0.7612 (m-30) REVERT: C 229 LYS cc_start: 0.7535 (mmtt) cc_final: 0.7091 (mmtt) REVERT: C 313 LEU cc_start: 0.8724 (mt) cc_final: 0.8484 (mt) REVERT: C 430 MET cc_start: 0.7366 (mtt) cc_final: 0.6977 (mtt) REVERT: C 502 MET cc_start: 0.7875 (mtm) cc_final: 0.7451 (mmp) REVERT: C 508 GLN cc_start: 0.8133 (mt0) cc_final: 0.7477 (mm110) REVERT: C 601 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6719 (tt) outliers start: 9 outliers final: 3 residues processed: 187 average time/residue: 0.8614 time to fit residues: 180.0992 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.156400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113795 restraints weight = 35086.988| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.20 r_work: 0.3145 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13005 Z= 0.123 Angle : 0.448 4.453 17628 Z= 0.239 Chirality : 0.036 0.115 2007 Planarity : 0.004 0.052 2118 Dihedral : 15.161 179.819 2064 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.19 % Allowed : 7.92 % 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 aren not related in a simple way. whole: 3.20 (0.22), residues: 1593 helix: 2.73 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 589 TYR 0.007 0.001 TYR C 285 PHE 0.016 0.001 PHE C 413 TRP 0.009 0.001 TRP B 316 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00268 (13005) covalent geometry : angle 0.44752 (17628) hydrogen bonds : bond 0.04955 ( 973) hydrogen bonds : angle 3.80343 ( 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 193 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.386 Fit side-chains REVERT: A 129 MET cc_start: 0.7427 (mtp) cc_final: 0.7148 (mtt) REVERT: A 229 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7335 (mmtt) REVERT: A 253 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6557 (mt-10) REVERT: A 365 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7806 (mt-10) REVERT: A 416 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: A 429 LYS cc_start: 0.7492 (ptpt) cc_final: 0.6750 (ptmm) REVERT: A 430 MET cc_start: 0.7782 (mtt) cc_final: 0.6929 (mtt) REVERT: A 502 MET cc_start: 0.7635 (mtm) cc_final: 0.7214 (tpt) REVERT: A 590 LYS cc_start: 0.7574 (ttmt) cc_final: 0.7055 (ttpp) REVERT: B 229 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7504 (mmtp) REVERT: B 305 MET cc_start: 0.8769 (mmp) cc_final: 0.8158 (mmt) REVERT: B 429 LYS cc_start: 0.7370 (ptpt) cc_final: 0.6939 (ptmm) REVERT: B 502 MET cc_start: 0.7716 (mtm) cc_final: 0.7320 (mmp) REVERT: B 508 GLN cc_start: 0.8294 (mt0) cc_final: 0.7788 (mm110) REVERT: C 229 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7342 (mmtt) REVERT: C 313 LEU cc_start: 0.8856 (mt) cc_final: 0.8589 (mt) REVERT: C 430 MET cc_start: 0.7570 (mtt) cc_final: 0.7130 (mtt) REVERT: C 477 LEU cc_start: 0.7861 (tp) cc_final: 0.7587 (tp) REVERT: C 524 ASN cc_start: 0.8063 (p0) cc_final: 0.7808 (p0) outliers start: 15 outliers final: 5 residues processed: 186 average time/residue: 0.9381 time to fit residues: 194.1241 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 416 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 0.0010 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN B 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110841 restraints weight = 34913.447| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.18 r_work: 0.3009 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3118 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= 0.152 Angle : 0.480 5.367 17628 Z= 0.257 Chirality : 0.037 0.120 2007 Planarity : 0.004 0.056 2118 Dihedral : 15.209 178.984 2064 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.95 % Allowed : 8.71 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.98 (0.21), residues: 1593 helix: 2.59 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 589 TYR 0.007 0.001 TYR C 285 PHE 0.016 0.001 PHE A 413 TRP 0.009 0.001 TRP A 316 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00350 (13005) covalent geometry : angle 0.47977 (17628) hydrogen bonds : bond 0.05461 ( 973) hydrogen bonds : angle 3.89021 ( 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 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.676 Fit side-chains REVERT: A 129 MET cc_start: 0.7336 (mtp) cc_final: 0.7099 (mtt) REVERT: A 229 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7406 (mmtt) REVERT: A 365 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 416 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7127 (tp30) REVERT: A 429 LYS cc_start: 0.7338 (ptpt) cc_final: 0.6638 (ptmm) REVERT: A 430 MET cc_start: 0.7790 (mtt) cc_final: 0.7201 (mtt) REVERT: A 502 MET cc_start: 0.7677 (mtm) cc_final: 0.7210 (tpt) REVERT: A 590 LYS cc_start: 0.7611 (ttmt) cc_final: 0.7107 (ttpp) REVERT: A 592 ASP cc_start: 0.8011 (m-30) cc_final: 0.7763 (m-30) REVERT: B 229 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7371 (mmmt) REVERT: B 283 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 305 MET cc_start: 0.8832 (mmp) cc_final: 0.8169 (mmt) REVERT: B 502 MET cc_start: 0.7731 (mtm) cc_final: 0.7346 (mmp) REVERT: B 508 GLN cc_start: 0.8328 (mt0) cc_final: 0.7846 (mm110) REVERT: C 229 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7463 (mmtt) REVERT: C 313 LEU cc_start: 0.8897 (mt) cc_final: 0.8636 (mt) REVERT: C 430 MET cc_start: 0.7449 (mtt) cc_final: 0.7074 (mtt) REVERT: C 477 LEU cc_start: 0.8025 (tp) cc_final: 0.7787 (tp) REVERT: C 524 ASN cc_start: 0.8542 (p0) cc_final: 0.8339 (p0) outliers start: 12 outliers final: 4 residues processed: 178 average time/residue: 0.9309 time to fit residues: 184.5944 Evaluate side-chains 170 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 165 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU 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: 2.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN C 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109197 restraints weight = 34794.753| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.17 r_work: 0.3002 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13005 Z= 0.177 Angle : 0.507 5.696 17628 Z= 0.272 Chirality : 0.038 0.125 2007 Planarity : 0.004 0.060 2118 Dihedral : 15.282 177.726 2064 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.19 % Allowed : 9.11 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.21), residues: 1593 helix: 2.45 (0.15), residues: 1296 sheet: None (None), residues: 0 loop : -1.19 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.008 0.002 TYR B 494 PHE 0.017 0.002 PHE A 413 TRP 0.007 0.001 TRP B 261 HIS 0.005 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00414 (13005) covalent geometry : angle 0.50703 (17628) hydrogen bonds : bond 0.05970 ( 973) hydrogen bonds : angle 3.98728 ( 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 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.657 Fit side-chains REVERT: A 129 MET cc_start: 0.7284 (mtp) cc_final: 0.7059 (mtt) REVERT: A 229 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7527 (mmtp) REVERT: A 365 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 430 MET cc_start: 0.7737 (mtt) cc_final: 0.7062 (mtt) REVERT: A 497 MET cc_start: 0.8315 (tmt) cc_final: 0.8009 (tmt) REVERT: A 502 MET cc_start: 0.7788 (mtm) cc_final: 0.7276 (tpt) REVERT: A 590 LYS cc_start: 0.7649 (ttmt) cc_final: 0.7152 (ttpp) REVERT: A 592 ASP cc_start: 0.7912 (m-30) cc_final: 0.7692 (m-30) REVERT: B 229 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7524 (mmmt) REVERT: B 283 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7778 (mm-30) REVERT: B 305 MET cc_start: 0.8865 (mmp) cc_final: 0.8201 (mmt) REVERT: B 502 MET cc_start: 0.7817 (mtm) cc_final: 0.7412 (mmp) REVERT: B 508 GLN cc_start: 0.8354 (mt0) cc_final: 0.7859 (mm110) REVERT: C 201 LYS cc_start: 0.8002 (mttm) cc_final: 0.7801 (mptm) REVERT: C 229 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7588 (mmtt) REVERT: C 313 LEU cc_start: 0.8911 (mt) cc_final: 0.8650 (mt) REVERT: C 524 ASN cc_start: 0.8603 (p0) cc_final: 0.8389 (p0) outliers start: 15 outliers final: 7 residues processed: 179 average time/residue: 0.9191 time to fit residues: 182.7949 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 : 0.539 ------------------------------------------------------------------------------- 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 314 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 79 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.154243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.111546 restraints weight = 34690.323| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.18 r_work: 0.3019 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13005 Z= 0.124 Angle : 0.448 4.788 17628 Z= 0.239 Chirality : 0.036 0.115 2007 Planarity : 0.004 0.055 2118 Dihedral : 14.576 177.358 2064 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.11 % Allowed : 9.50 % Favored : 89.39 % 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 aren not related in a simple way. whole: 3.05 (0.22), residues: 1593 helix: 2.65 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.06 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.006 0.001 TYR C 553 PHE 0.012 0.001 PHE C 279 TRP 0.009 0.001 TRP A 316 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00273 (13005) covalent geometry : angle 0.44841 (17628) hydrogen bonds : bond 0.04852 ( 973) hydrogen bonds : angle 3.80753 ( 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: 14 poor density : 173 time to evaluate : 0.637 Fit side-chains REVERT: A 129 MET cc_start: 0.7348 (mtp) cc_final: 0.7143 (mtt) REVERT: A 229 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7452 (mmtp) REVERT: A 365 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 430 MET cc_start: 0.7727 (mtt) cc_final: 0.7118 (mtt) REVERT: A 502 MET cc_start: 0.7695 (mtm) cc_final: 0.7227 (tpt) REVERT: A 590 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7040 (ttpp) REVERT: A 592 ASP cc_start: 0.7907 (m-30) cc_final: 0.7677 (m-30) REVERT: B 199 THR cc_start: 0.8429 (m) cc_final: 0.8229 (m) REVERT: B 229 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7425 (mmmt) REVERT: B 283 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 305 MET cc_start: 0.8853 (mmp) cc_final: 0.8161 (mmt) REVERT: B 485 GLN cc_start: 0.8492 (mp10) cc_final: 0.8102 (mp10) REVERT: B 502 MET cc_start: 0.7706 (mtm) cc_final: 0.7304 (mmp) REVERT: B 508 GLN cc_start: 0.8238 (mt0) cc_final: 0.7732 (mm110) REVERT: C 229 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7551 (mmtt) REVERT: C 313 LEU cc_start: 0.8839 (mt) cc_final: 0.8603 (mt) REVERT: C 430 MET cc_start: 0.7436 (mtt) cc_final: 0.7046 (mtt) REVERT: C 524 ASN cc_start: 0.8474 (p0) cc_final: 0.8247 (p0) outliers start: 14 outliers final: 5 residues processed: 182 average time/residue: 0.9899 time to fit residues: 200.7703 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 166 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 132 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110485 restraints weight = 34776.143| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.18 r_work: 0.3015 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3575 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= 0.148 Angle : 0.475 5.275 17628 Z= 0.254 Chirality : 0.037 0.119 2007 Planarity : 0.004 0.058 2118 Dihedral : 14.303 176.088 2064 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.27 % Allowed : 9.66 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.21), residues: 1593 helix: 2.58 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.09 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.008 0.001 TYR C 553 PHE 0.014 0.001 PHE A 413 TRP 0.008 0.001 TRP B 261 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00341 (13005) covalent geometry : angle 0.47462 (17628) hydrogen bonds : bond 0.05402 ( 973) hydrogen bonds : angle 3.86819 ( 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: 16 poor density : 172 time to evaluate : 0.506 Fit side-chains REVERT: A 129 MET cc_start: 0.7401 (mtp) cc_final: 0.7190 (mtt) REVERT: A 229 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7676 (mmtt) REVERT: A 365 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7760 (mt-10) REVERT: A 430 MET cc_start: 0.7774 (mtt) cc_final: 0.7174 (mtt) REVERT: A 502 MET cc_start: 0.7759 (mtm) cc_final: 0.7314 (tpt) REVERT: A 590 LYS cc_start: 0.7624 (ttmt) cc_final: 0.7130 (ttpp) REVERT: A 592 ASP cc_start: 0.7898 (m-30) cc_final: 0.7676 (m-30) REVERT: B 199 THR cc_start: 0.8516 (m) cc_final: 0.8310 (m) REVERT: B 229 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7493 (mmmt) REVERT: B 283 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7784 (mm-30) REVERT: B 305 MET cc_start: 0.8920 (mmp) cc_final: 0.8231 (mmt) REVERT: B 502 MET cc_start: 0.7790 (mtm) cc_final: 0.7400 (mmp) REVERT: B 508 GLN cc_start: 0.8349 (mt0) cc_final: 0.7849 (mm110) REVERT: C 229 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7594 (mmtt) REVERT: C 313 LEU cc_start: 0.8892 (mt) cc_final: 0.8648 (mt) REVERT: C 524 ASN cc_start: 0.8580 (p0) cc_final: 0.8371 (p0) outliers start: 16 outliers final: 8 residues processed: 180 average time/residue: 0.9263 time to fit residues: 185.2191 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 : 0.596 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 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: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.153384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111062 restraints weight = 34915.068| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.19 r_work: 0.3039 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13005 Z= 0.121 Angle : 0.443 4.760 17628 Z= 0.235 Chirality : 0.036 0.114 2007 Planarity : 0.004 0.055 2118 Dihedral : 13.906 177.957 2064 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.95 % Allowed : 10.06 % 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 aren not related in a simple way. whole: 3.17 (0.22), residues: 1593 helix: 2.74 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.02 (0.33), 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 B 316 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00269 (13005) covalent geometry : angle 0.44335 (17628) hydrogen bonds : bond 0.04716 ( 973) hydrogen bonds : angle 3.75750 ( 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 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.486 Fit side-chains REVERT: A 129 MET cc_start: 0.7314 (mtp) cc_final: 0.7111 (mtt) REVERT: A 229 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7633 (mmtt) REVERT: A 365 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 430 MET cc_start: 0.7713 (mtt) cc_final: 0.7124 (mtt) REVERT: A 502 MET cc_start: 0.7634 (mtm) cc_final: 0.7218 (tpt) REVERT: A 590 LYS cc_start: 0.7539 (ttmt) cc_final: 0.7006 (ttpp) REVERT: A 592 ASP cc_start: 0.7929 (m-30) cc_final: 0.7705 (m-30) REVERT: B 229 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7434 (mmmt) REVERT: B 283 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 305 MET cc_start: 0.8880 (mmp) cc_final: 0.8192 (mmt) REVERT: B 485 GLN cc_start: 0.8495 (mp10) cc_final: 0.8114 (mp10) REVERT: B 502 MET cc_start: 0.7648 (mtm) cc_final: 0.7314 (mmp) REVERT: B 508 GLN cc_start: 0.8239 (mt0) cc_final: 0.7724 (mm-40) REVERT: C 229 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7540 (mmtt) REVERT: C 313 LEU cc_start: 0.8834 (mt) cc_final: 0.8617 (mt) REVERT: C 524 ASN cc_start: 0.8459 (p0) cc_final: 0.8212 (p0) outliers start: 12 outliers final: 8 residues processed: 179 average time/residue: 0.9491 time to fit residues: 188.7349 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 : 0.621 ------------------------------------------------------------------------------- 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=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: 3.9990 chunk 139 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 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: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.152115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109693 restraints weight = 34677.680| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.19 r_work: 0.3009 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13005 Z= 0.146 Angle : 0.473 5.285 17628 Z= 0.252 Chirality : 0.037 0.120 2007 Planarity : 0.004 0.057 2118 Dihedral : 13.975 175.904 2064 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.95 % Allowed : 10.29 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.21), residues: 1593 helix: 2.63 (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 0.008 0.001 TYR C 553 PHE 0.014 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 covalent geometry : bond 0.00335 (13005) covalent geometry : angle 0.47250 (17628) hydrogen bonds : bond 0.05307 ( 973) hydrogen bonds : angle 3.84548 ( 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 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.673 Fit side-chains REVERT: A 129 MET cc_start: 0.7324 (mtp) cc_final: 0.7122 (mtt) REVERT: A 229 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7728 (mmtt) REVERT: A 365 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 430 MET cc_start: 0.7717 (mtt) cc_final: 0.7136 (mtt) REVERT: A 502 MET cc_start: 0.7692 (mtm) cc_final: 0.7274 (tpt) REVERT: A 590 LYS cc_start: 0.7583 (ttmt) cc_final: 0.7052 (ttpp) REVERT: A 592 ASP cc_start: 0.7904 (m-30) cc_final: 0.7681 (m-30) REVERT: B 229 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7453 (mmmt) REVERT: B 283 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 305 MET cc_start: 0.8896 (mmp) cc_final: 0.8204 (mmt) REVERT: B 485 GLN cc_start: 0.8541 (mp10) cc_final: 0.8119 (mp10) REVERT: B 502 MET cc_start: 0.7707 (mtm) cc_final: 0.7358 (mmp) REVERT: B 508 GLN cc_start: 0.8295 (mt0) cc_final: 0.7793 (mm110) REVERT: C 229 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7546 (mmtt) REVERT: C 313 LEU cc_start: 0.8867 (mt) cc_final: 0.8637 (mt) REVERT: C 524 ASN cc_start: 0.8584 (p0) cc_final: 0.8366 (p0) outliers start: 12 outliers final: 8 residues processed: 178 average time/residue: 1.0489 time to fit residues: 206.3563 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 : 0.584 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 117 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.153016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110847 restraints weight = 34925.408| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.18 r_work: 0.3026 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13005 Z= 0.124 Angle : 0.448 4.837 17628 Z= 0.238 Chirality : 0.036 0.115 2007 Planarity : 0.004 0.055 2118 Dihedral : 13.764 177.780 2064 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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 aren not related in a simple way. whole: 3.19 (0.22), residues: 1593 helix: 2.75 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.006 0.001 TYR C 553 PHE 0.012 0.001 PHE C 279 TRP 0.008 0.001 TRP B 316 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00278 (13005) covalent geometry : angle 0.44820 (17628) hydrogen bonds : bond 0.04785 ( 973) hydrogen bonds : angle 3.75990 ( 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 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.630 Fit side-chains REVERT: A 229 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7643 (mmtt) REVERT: A 365 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 430 MET cc_start: 0.7714 (mtt) cc_final: 0.7124 (mtt) REVERT: A 502 MET cc_start: 0.7650 (mtm) cc_final: 0.7233 (tpt) REVERT: A 590 LYS cc_start: 0.7563 (ttmt) cc_final: 0.7034 (ttpp) REVERT: A 592 ASP cc_start: 0.7904 (m-30) cc_final: 0.7680 (m-30) REVERT: B 229 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7438 (mmmt) REVERT: B 283 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 305 MET cc_start: 0.8896 (mmp) cc_final: 0.8227 (mmt) REVERT: B 485 GLN cc_start: 0.8508 (mp10) cc_final: 0.8122 (mp10) REVERT: B 502 MET cc_start: 0.7651 (mtm) cc_final: 0.7326 (mmp) REVERT: B 508 GLN cc_start: 0.8243 (mt0) cc_final: 0.7740 (mm-40) REVERT: C 229 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7545 (mmtt) REVERT: C 313 LEU cc_start: 0.8837 (mt) cc_final: 0.8620 (mt) REVERT: C 524 ASN cc_start: 0.8475 (p0) cc_final: 0.8225 (p0) outliers start: 8 outliers final: 7 residues processed: 175 average time/residue: 1.0104 time to fit residues: 196.0926 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 : 0.530 ------------------------------------------------------------------------------- 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 508 GLN 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: 2.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.154260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112102 restraints weight = 35002.995| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.19 r_work: 0.3054 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3722 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= 0.108 Angle : 0.426 4.445 17628 Z= 0.226 Chirality : 0.035 0.112 2007 Planarity : 0.004 0.054 2118 Dihedral : 13.426 179.092 2064 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.71 % Allowed : 10.61 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.39 (0.22), residues: 1593 helix: 2.87 (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 A 557 TYR 0.006 0.001 TYR C 519 PHE 0.011 0.001 PHE C 259 TRP 0.009 0.001 TRP B 316 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00235 (13005) covalent geometry : angle 0.42644 (17628) hydrogen bonds : bond 0.04316 ( 973) hydrogen bonds : angle 3.66477 ( 2847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7146.52 seconds wall clock time: 121 minutes 28.83 seconds (7288.83 seconds total)