Starting phenix.real_space_refine on Sat Jun 21 22:59:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz5_41734/06_2025/8tz5_41734_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz5_41734/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz5_41734/06_2025/8tz5_41734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz5_41734/06_2025/8tz5_41734.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz5_41734/06_2025/8tz5_41734_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz5_41734/06_2025/8tz5_41734_trim.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 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: C, B Time building chain proxies: 23.15, per 1000 atoms: 0.93 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: 6.27 Conformation dependent library (CDL) restraints added in 2.2 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 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: 1.79 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: 9.40 Time building geometry restraints manager: 7.66 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 13.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.430 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 64.200 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP A 414 HIS 0.001 0.000 HIS B 394 PHE 0.011 0.001 PHE B 413 TYR 0.006 0.001 TYR B 285 ARG 0.002 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.14112 ( 973) hydrogen bonds : angle 4.91618 ( 2847) covalent geometry : bond 0.01108 (13005) covalent geometry : angle 0.86143 (17628) *********************** 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 : 2.032 Fit side-chains revert: symmetry clash REVERT: A 429 LYS cc_start: 0.7730 (ptpt) cc_final: 0.7135 (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: 0.8375 (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: 1.9352 time to fit residues: 510.7394 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 : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 571 ASN B 471 ASN B 479 ASN B 571 ASN C 571 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.160542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120480 restraints weight = 36048.886| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.29 r_work: 0.3296 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1864 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 : 0.457 4.508 17628 Z= 0.240 Chirality : 0.035 0.115 2007 Planarity : 0.004 0.051 2118 Dihedral : 16.535 179.780 2064 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.71 % Allowed : 7.60 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.22), residues: 1593 helix: 2.51 (0.15), residues: 1335 sheet: None (None), residues: 0 loop : -0.59 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 316 HIS 0.004 0.001 HIS B 288 PHE 0.013 0.001 PHE B 413 TYR 0.005 0.001 TYR C 553 ARG 0.003 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 973) hydrogen bonds : angle 3.86559 ( 2847) covalent geometry : bond 0.00235 (13005) covalent geometry : angle 0.45681 (17628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 2.114 Fit side-chains REVERT: A 129 MET cc_start: 0.7598 (mtp) cc_final: 0.7320 (mtt) REVERT: A 429 LYS cc_start: 0.7400 (ptpt) cc_final: 0.6647 (ptmm) REVERT: A 430 MET cc_start: 0.7363 (mtt) cc_final: 0.6780 (mtt) REVERT: A 502 MET cc_start: 0.7556 (mtm) cc_final: 0.7100 (tpt) REVERT: B 229 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7449 (mmtp) REVERT: B 283 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7404 (mm-30) REVERT: B 313 LEU cc_start: 0.8650 (mt) cc_final: 0.8310 (mp) REVERT: B 429 LYS cc_start: 0.7121 (ptpt) cc_final: 0.6644 (ptmm) REVERT: B 437 ASN cc_start: 0.7174 (p0) cc_final: 0.6947 (p0) REVERT: B 502 MET cc_start: 0.7619 (mtm) cc_final: 0.7147 (mmp) REVERT: B 508 GLN cc_start: 0.8005 (mt0) cc_final: 0.7566 (mm110) REVERT: B 592 ASP cc_start: 0.7936 (m-30) cc_final: 0.7606 (m-30) REVERT: C 229 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7081 (mmtt) REVERT: C 313 LEU cc_start: 0.8727 (mt) cc_final: 0.8481 (mt) REVERT: C 430 MET cc_start: 0.7358 (mtt) cc_final: 0.6965 (mtt) REVERT: C 502 MET cc_start: 0.7951 (mtm) cc_final: 0.7545 (mmp) REVERT: C 508 GLN cc_start: 0.8143 (mt0) cc_final: 0.7469 (mm110) REVERT: C 601 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6688 (tt) outliers start: 9 outliers final: 3 residues processed: 186 average time/residue: 1.9699 time to fit residues: 412.0962 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 78 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 508 GLN 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 = 0.152703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109886 restraints weight = 34897.979| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.18 r_work: 0.2982 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13005 Z= 0.176 Angle : 0.515 5.704 17628 Z= 0.278 Chirality : 0.038 0.126 2007 Planarity : 0.005 0.058 2118 Dihedral : 15.779 179.647 2064 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.19 % Allowed : 8.00 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.21), residues: 1593 helix: 2.41 (0.15), residues: 1296 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.004 0.001 HIS C 288 PHE 0.022 0.002 PHE A 413 TYR 0.009 0.002 TYR C 357 ARG 0.004 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.06235 ( 973) hydrogen bonds : angle 4.04664 ( 2847) covalent geometry : bond 0.00407 (13005) covalent geometry : angle 0.51539 (17628) *********************** 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 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 1.743 Fit side-chains REVERT: A 129 MET cc_start: 0.7516 (mtp) cc_final: 0.7266 (mtt) REVERT: A 229 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7447 (mmtp) REVERT: A 305 MET cc_start: 0.8749 (mmm) cc_final: 0.8537 (mmp) REVERT: A 365 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 429 LYS cc_start: 0.7461 (ptpt) cc_final: 0.6721 (ptmm) REVERT: A 430 MET cc_start: 0.7855 (mtt) cc_final: 0.7099 (mtt) REVERT: A 502 MET cc_start: 0.7679 (mtm) cc_final: 0.7230 (tpt) REVERT: A 590 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7219 (ttpp) REVERT: A 592 ASP cc_start: 0.7998 (m-30) cc_final: 0.7757 (m-30) REVERT: B 229 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7633 (mmtp) REVERT: B 305 MET cc_start: 0.8794 (mmp) cc_final: 0.8172 (mmt) REVERT: B 429 LYS cc_start: 0.7433 (ptpt) cc_final: 0.7012 (ptmm) REVERT: B 502 MET cc_start: 0.7828 (mtm) cc_final: 0.7439 (mmp) REVERT: B 508 GLN cc_start: 0.8444 (mt0) cc_final: 0.7952 (mm110) REVERT: C 229 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7503 (mmtp) REVERT: C 313 LEU cc_start: 0.8926 (mt) cc_final: 0.8637 (mt) REVERT: C 477 LEU cc_start: 0.8029 (tp) cc_final: 0.7756 (tp) REVERT: C 585 MET cc_start: 0.7678 (mtm) cc_final: 0.7473 (mtm) outliers start: 15 outliers final: 4 residues processed: 184 average time/residue: 2.1145 time to fit residues: 434.1820 Evaluate side-chains 172 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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 340 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 2 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.154289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111509 restraints weight = 35078.602| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.18 r_work: 0.3033 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13005 Z= 0.134 Angle : 0.459 4.802 17628 Z= 0.245 Chirality : 0.036 0.115 2007 Planarity : 0.004 0.056 2118 Dihedral : 15.192 179.050 2064 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.11 % Allowed : 8.39 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.21), residues: 1593 helix: 2.57 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.004 0.001 HIS B 288 PHE 0.014 0.001 PHE C 279 TYR 0.006 0.001 TYR C 285 ARG 0.002 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 973) hydrogen bonds : angle 3.85681 ( 2847) covalent geometry : bond 0.00299 (13005) covalent geometry : angle 0.45905 (17628) *********************** 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 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 3.031 Fit side-chains REVERT: A 129 MET cc_start: 0.7344 (mtp) cc_final: 0.7108 (mtt) REVERT: A 229 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7393 (mmtt) REVERT: A 365 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 429 LYS cc_start: 0.7314 (ptpt) cc_final: 0.6628 (ptmm) REVERT: A 430 MET cc_start: 0.7860 (mtt) cc_final: 0.7183 (mtt) REVERT: A 502 MET cc_start: 0.7666 (mtm) cc_final: 0.7202 (tpt) REVERT: A 590 LYS cc_start: 0.7611 (ttmt) cc_final: 0.7114 (ttpp) REVERT: A 592 ASP cc_start: 0.7988 (m-30) cc_final: 0.7750 (m-30) REVERT: B 229 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7410 (mmmt) REVERT: B 305 MET cc_start: 0.8841 (mmp) cc_final: 0.8152 (mmt) REVERT: B 502 MET cc_start: 0.7760 (mtm) cc_final: 0.7376 (mmp) REVERT: B 508 GLN cc_start: 0.8285 (mt0) cc_final: 0.7802 (mm110) REVERT: C 229 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7491 (mmtt) REVERT: C 313 LEU cc_start: 0.8861 (mt) cc_final: 0.8627 (mt) REVERT: C 430 MET cc_start: 0.7506 (mtt) cc_final: 0.7123 (mtt) outliers start: 14 outliers final: 5 residues processed: 180 average time/residue: 2.6255 time to fit residues: 527.9947 Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 340 SER Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 43 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.154040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110978 restraints weight = 34922.382| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.20 r_work: 0.3108 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13005 Z= 0.134 Angle : 0.456 4.912 17628 Z= 0.244 Chirality : 0.036 0.115 2007 Planarity : 0.004 0.056 2118 Dihedral : 14.826 177.902 2064 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.03 % Allowed : 9.18 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.22), residues: 1593 helix: 2.63 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.07 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.004 0.001 HIS B 288 PHE 0.013 0.001 PHE C 279 TYR 0.007 0.001 TYR C 553 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 973) hydrogen bonds : angle 3.82817 ( 2847) covalent geometry : bond 0.00301 (13005) covalent geometry : angle 0.45618 (17628) *********************** 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 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 2.062 Fit side-chains REVERT: A 129 MET cc_start: 0.7415 (mtp) cc_final: 0.7184 (mtt) REVERT: A 229 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7481 (mmtt) REVERT: A 365 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 430 MET cc_start: 0.7796 (mtt) cc_final: 0.7148 (mtt) REVERT: A 502 MET cc_start: 0.7699 (mtm) cc_final: 0.7238 (tpt) REVERT: A 590 LYS cc_start: 0.7615 (ttmt) cc_final: 0.7117 (ttpp) REVERT: A 592 ASP cc_start: 0.7973 (m-30) cc_final: 0.7744 (m-30) REVERT: B 229 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7470 (mmmt) REVERT: B 305 MET cc_start: 0.8846 (mmp) cc_final: 0.8176 (mmt) REVERT: B 485 GLN cc_start: 0.8509 (mp10) cc_final: 0.8103 (mp10) REVERT: B 502 MET cc_start: 0.7741 (mtm) cc_final: 0.7359 (mmp) REVERT: B 508 GLN cc_start: 0.8336 (mt0) cc_final: 0.7846 (mm110) REVERT: C 229 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7571 (mmtt) REVERT: C 313 LEU cc_start: 0.8850 (mt) cc_final: 0.8606 (mt) REVERT: C 430 MET cc_start: 0.7488 (mtt) cc_final: 0.7071 (mtt) outliers start: 13 outliers final: 5 residues processed: 178 average time/residue: 2.1845 time to fit residues: 431.6216 Evaluate side-chains 173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 340 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 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 50.0000 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.152024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109255 restraints weight = 34889.183| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.17 r_work: 0.3007 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: 0.8015 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13005 Z= 0.145 Angle : 0.469 5.194 17628 Z= 0.251 Chirality : 0.037 0.117 2007 Planarity : 0.004 0.057 2118 Dihedral : 14.677 176.281 2064 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.79 % Allowed : 9.74 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.21), residues: 1593 helix: 2.58 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 261 HIS 0.004 0.001 HIS C 288 PHE 0.014 0.001 PHE C 279 TYR 0.007 0.001 TYR C 553 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 973) hydrogen bonds : angle 3.85588 ( 2847) covalent geometry : bond 0.00330 (13005) covalent geometry : angle 0.46870 (17628) *********************** 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 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 2.574 Fit side-chains REVERT: A 129 MET cc_start: 0.7403 (mtp) cc_final: 0.7199 (mtt) REVERT: A 229 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7497 (mmtp) REVERT: A 365 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 430 MET cc_start: 0.7764 (mtt) cc_final: 0.7138 (mtt) REVERT: A 502 MET cc_start: 0.7722 (mtm) cc_final: 0.7257 (tpt) REVERT: A 590 LYS cc_start: 0.7602 (ttmt) cc_final: 0.7102 (ttpp) REVERT: A 592 ASP cc_start: 0.7952 (m-30) cc_final: 0.7731 (m-30) REVERT: B 199 THR cc_start: 0.8457 (m) cc_final: 0.8252 (m) REVERT: B 229 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7468 (mmmt) REVERT: B 253 GLU cc_start: 0.6393 (mt-10) cc_final: 0.6167 (mt-10) REVERT: B 305 MET cc_start: 0.8877 (mmp) cc_final: 0.8173 (mmt) REVERT: B 502 MET cc_start: 0.7745 (mtm) cc_final: 0.7346 (mmp) REVERT: B 508 GLN cc_start: 0.8285 (mt0) cc_final: 0.7787 (mm110) REVERT: C 229 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7574 (mmtt) REVERT: C 313 LEU cc_start: 0.8866 (mt) cc_final: 0.8621 (mt) REVERT: C 430 MET cc_start: 0.7496 (mtt) cc_final: 0.7047 (mtt) outliers start: 10 outliers final: 5 residues processed: 182 average time/residue: 2.7314 time to fit residues: 554.9445 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 3.579 ------------------------------------------------------------------------------- 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 340 SER Chi-restraints excluded: chain C residue 508 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.153920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.111072 restraints weight = 34894.603| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.21 r_work: 0.3015 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13005 Z= 0.133 Angle : 0.455 4.953 17628 Z= 0.242 Chirality : 0.036 0.115 2007 Planarity : 0.004 0.056 2118 Dihedral : 14.316 176.513 2064 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.11 % Allowed : 9.98 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.22), residues: 1593 helix: 2.67 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.08 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 261 HIS 0.004 0.001 HIS B 288 PHE 0.014 0.001 PHE C 279 TYR 0.007 0.001 TYR C 553 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 973) hydrogen bonds : angle 3.80315 ( 2847) covalent geometry : bond 0.00299 (13005) covalent geometry : angle 0.45477 (17628) *********************** 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 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 2.089 Fit side-chains REVERT: A 129 MET cc_start: 0.7352 (mtp) cc_final: 0.7142 (mtt) REVERT: A 229 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7501 (mmtt) REVERT: A 365 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 502 MET cc_start: 0.7688 (mtm) cc_final: 0.7253 (tpt) REVERT: A 590 LYS cc_start: 0.7572 (ttmt) cc_final: 0.7064 (ttpp) REVERT: A 592 ASP cc_start: 0.7908 (m-30) cc_final: 0.7680 (m-30) REVERT: B 199 THR cc_start: 0.8463 (m) cc_final: 0.8261 (m) REVERT: B 229 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7437 (mmmt) REVERT: B 253 GLU cc_start: 0.6372 (mt-10) cc_final: 0.6164 (mt-10) REVERT: B 305 MET cc_start: 0.8890 (mmp) cc_final: 0.8189 (mmt) REVERT: B 502 MET cc_start: 0.7729 (mtm) cc_final: 0.7321 (mmp) REVERT: B 508 GLN cc_start: 0.8242 (mt0) cc_final: 0.7730 (mm110) REVERT: C 229 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7559 (mmtt) REVERT: C 313 LEU cc_start: 0.8859 (mt) cc_final: 0.8618 (mt) REVERT: C 428 MET cc_start: 0.7633 (mmp) cc_final: 0.7355 (mmp) outliers start: 14 outliers final: 5 residues processed: 184 average time/residue: 2.3395 time to fit residues: 477.4416 Evaluate side-chains 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 172 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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 B residue 590 LYS Chi-restraints excluded: chain C residue 340 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 138 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.152392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109546 restraints weight = 34862.038| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.19 r_work: 0.3005 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13005 Z= 0.165 Angle : 0.495 5.559 17628 Z= 0.264 Chirality : 0.037 0.123 2007 Planarity : 0.004 0.059 2118 Dihedral : 14.319 174.797 2064 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.79 % Allowed : 10.37 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.21), residues: 1593 helix: 2.50 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.15 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 261 HIS 0.004 0.001 HIS B 288 PHE 0.015 0.001 PHE C 413 TYR 0.008 0.001 TYR C 553 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05717 ( 973) hydrogen bonds : angle 3.91929 ( 2847) covalent geometry : bond 0.00384 (13005) covalent geometry : angle 0.49450 (17628) *********************** 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 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 1.926 Fit side-chains REVERT: A 229 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7685 (mmtt) REVERT: A 365 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 430 MET cc_start: 0.7731 (mtt) cc_final: 0.7134 (mtt) REVERT: A 497 MET cc_start: 0.8319 (tmt) cc_final: 0.7926 (tmt) REVERT: A 502 MET cc_start: 0.7815 (mtm) cc_final: 0.7351 (tpt) REVERT: A 590 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7125 (ttpp) REVERT: A 592 ASP cc_start: 0.7895 (m-30) cc_final: 0.7680 (m-30) REVERT: B 199 THR cc_start: 0.8512 (m) cc_final: 0.8311 (m) REVERT: B 229 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7484 (mmmt) REVERT: B 283 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7776 (mm-30) REVERT: B 305 MET cc_start: 0.8925 (mmp) cc_final: 0.8239 (mmt) REVERT: B 502 MET cc_start: 0.7802 (mtm) cc_final: 0.7399 (mmp) REVERT: B 508 GLN cc_start: 0.8394 (mt0) cc_final: 0.7902 (mm110) REVERT: C 229 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7590 (mmtt) REVERT: C 313 LEU cc_start: 0.8886 (mt) cc_final: 0.8639 (mt) outliers start: 10 outliers final: 6 residues processed: 180 average time/residue: 2.2406 time to fit residues: 447.8757 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 B residue 590 LYS Chi-restraints excluded: chain C residue 340 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 115 optimal weight: 4.9990 chunk 53 optimal weight: 50.0000 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.150130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107544 restraints weight = 34888.552| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.18 r_work: 0.2980 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13005 Z= 0.202 Angle : 0.533 6.057 17628 Z= 0.285 Chirality : 0.039 0.133 2007 Planarity : 0.005 0.061 2118 Dihedral : 14.400 173.599 2064 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.87 % Allowed : 10.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.21), residues: 1593 helix: 2.34 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.18 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 261 HIS 0.005 0.001 HIS B 288 PHE 0.017 0.002 PHE A 413 TYR 0.010 0.002 TYR C 553 ARG 0.003 0.001 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.06293 ( 973) hydrogen bonds : angle 4.03174 ( 2847) covalent geometry : bond 0.00480 (13005) covalent geometry : angle 0.53324 (17628) *********************** 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 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.987 Fit side-chains REVERT: A 229 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7712 (mmtt) REVERT: A 365 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 430 MET cc_start: 0.7796 (mtt) cc_final: 0.7212 (mtt) REVERT: A 497 MET cc_start: 0.8297 (tmt) cc_final: 0.7909 (tmt) REVERT: A 502 MET cc_start: 0.7809 (mtm) cc_final: 0.7323 (tpt) REVERT: A 590 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7049 (ttpp) REVERT: A 592 ASP cc_start: 0.7901 (m-30) cc_final: 0.7684 (m-30) REVERT: B 229 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7496 (mmmt) REVERT: B 305 MET cc_start: 0.8893 (mmp) cc_final: 0.8223 (mmt) REVERT: B 502 MET cc_start: 0.7789 (mtm) cc_final: 0.7402 (mmp) REVERT: B 508 GLN cc_start: 0.8393 (mt0) cc_final: 0.7903 (mm110) REVERT: C 229 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7576 (mmtt) REVERT: C 313 LEU cc_start: 0.8891 (mt) cc_final: 0.8630 (mt) outliers start: 11 outliers final: 6 residues processed: 183 average time/residue: 2.2507 time to fit residues: 457.9821 Evaluate side-chains 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 2.223 ------------------------------------------------------------------------------- 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 B residue 590 LYS Chi-restraints excluded: chain C residue 340 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 10 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.154606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112543 restraints weight = 34947.685| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.19 r_work: 0.3122 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13005 Z= 0.099 Angle : 0.420 4.314 17628 Z= 0.223 Chirality : 0.035 0.113 2007 Planarity : 0.004 0.053 2118 Dihedral : 13.560 178.287 2064 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.48 % Allowed : 10.93 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.22), residues: 1593 helix: 2.80 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.002 0.001 HIS C 288 PHE 0.010 0.001 PHE C 279 TYR 0.005 0.001 TYR C 553 ARG 0.001 0.000 ARG C 233 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 973) hydrogen bonds : angle 3.66757 ( 2847) covalent geometry : bond 0.00211 (13005) covalent geometry : angle 0.41999 (17628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 1.793 Fit side-chains REVERT: A 229 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7680 (mmtt) REVERT: A 365 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7756 (mt-10) REVERT: A 430 MET cc_start: 0.7851 (mtt) cc_final: 0.7269 (mtt) REVERT: A 497 MET cc_start: 0.8402 (tmt) cc_final: 0.7923 (tmt) REVERT: A 502 MET cc_start: 0.7623 (mtm) cc_final: 0.7232 (tpt) REVERT: A 524 ASN cc_start: 0.8660 (p0) cc_final: 0.8439 (p0) REVERT: A 590 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7030 (ttpp) REVERT: A 592 ASP cc_start: 0.7942 (m-30) cc_final: 0.7731 (m-30) REVERT: B 229 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7445 (mmmt) REVERT: B 305 MET cc_start: 0.8858 (mmp) cc_final: 0.8164 (mmt) REVERT: B 485 GLN cc_start: 0.8411 (mp10) cc_final: 0.8048 (mp10) REVERT: B 502 MET cc_start: 0.7645 (mtm) cc_final: 0.7320 (mmp) REVERT: B 508 GLN cc_start: 0.8263 (mt0) cc_final: 0.7768 (mm-40) REVERT: C 229 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7562 (mmtt) REVERT: C 428 MET cc_start: 0.7604 (mmp) cc_final: 0.7322 (mmp) outliers start: 6 outliers final: 4 residues processed: 179 average time/residue: 2.2621 time to fit residues: 449.3759 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 : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 590 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.0020 chunk 148 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 143 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.157089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115445 restraints weight = 34937.808| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.18 r_work: 0.3090 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 13005 Z= 0.086 Angle : 0.402 4.569 17628 Z= 0.211 Chirality : 0.034 0.115 2007 Planarity : 0.003 0.050 2118 Dihedral : 12.840 179.985 2064 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.48 % Allowed : 11.16 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.22), residues: 1593 helix: 3.11 (0.15), residues: 1293 sheet: None (None), residues: 0 loop : -0.53 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 316 HIS 0.002 0.000 HIS C 288 PHE 0.009 0.001 PHE C 279 TYR 0.005 0.001 TYR A 357 ARG 0.001 0.000 ARG C 233 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 973) hydrogen bonds : angle 3.49543 ( 2847) covalent geometry : bond 0.00178 (13005) covalent geometry : angle 0.40228 (17628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17720.90 seconds wall clock time: 312 minutes 14.97 seconds (18734.97 seconds total)