Starting phenix.real_space_refine on Sat May 24 09:36:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz5_41734/05_2025/8tz5_41734_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz5_41734/05_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_41734/05_2025/8tz5_41734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz5_41734/05_2025/8tz5_41734.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz5_41734/05_2025/8tz5_41734_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz5_41734/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 22.78, per 1000 atoms: 0.92 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: 7.03 Conformation dependent library (CDL) restraints added in 1.9 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: 1.65 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: 8.24 Time building geometry restraints manager: 8.28 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: 0.750 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: 0.400 Extract box with map and model: 0.830 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 62.180 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.020 ------------------------------------------------------------------------------- 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 : 1.640 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: 1.8729 time to fit residues: 494.0499 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 : 1.893 ------------------------------------------------------------------------------- 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 = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120438 restraints weight = 36048.885| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.31 r_work: 0.3296 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 1.745 Fit side-chains REVERT: A 129 MET cc_start: 0.7622 (mtp) cc_final: 0.7343 (mtt) REVERT: A 429 LYS cc_start: 0.7415 (ptpt) cc_final: 0.6665 (ptmm) REVERT: A 430 MET cc_start: 0.7371 (mtt) cc_final: 0.6793 (mtt) REVERT: A 502 MET cc_start: 0.7572 (mtm) cc_final: 0.7116 (tpt) REVERT: B 229 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7461 (mmtp) REVERT: B 283 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7411 (mm-30) REVERT: B 313 LEU cc_start: 0.8656 (mt) cc_final: 0.8316 (mp) REVERT: B 429 LYS cc_start: 0.7137 (ptpt) cc_final: 0.6661 (ptmm) REVERT: B 437 ASN cc_start: 0.7189 (p0) cc_final: 0.6963 (p0) REVERT: B 502 MET cc_start: 0.7634 (mtm) cc_final: 0.7163 (mmp) REVERT: B 508 GLN cc_start: 0.8014 (mt0) cc_final: 0.7578 (mm110) REVERT: B 592 ASP cc_start: 0.7942 (m-30) cc_final: 0.7613 (m-30) REVERT: C 229 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7096 (mmtt) REVERT: C 313 LEU cc_start: 0.8731 (mt) cc_final: 0.8489 (mt) REVERT: C 430 MET cc_start: 0.7365 (mtt) cc_final: 0.6974 (mtt) REVERT: C 502 MET cc_start: 0.7969 (mtm) cc_final: 0.7563 (mmp) REVERT: C 508 GLN cc_start: 0.8155 (mt0) cc_final: 0.7485 (mm110) REVERT: C 601 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6698 (tt) outliers start: 9 outliers final: 3 residues processed: 186 average time/residue: 1.9213 time to fit residues: 400.9428 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 : 1.805 ------------------------------------------------------------------------------- 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: 0.7980 chunk 49 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.150619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107706 restraints weight = 35036.420| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.19 r_work: 0.2968 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13005 Z= 0.194 Angle : 0.538 5.934 17628 Z= 0.290 Chirality : 0.039 0.130 2007 Planarity : 0.005 0.059 2118 Dihedral : 15.962 179.504 2064 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.43 % Allowed : 7.84 % Favored : 90.74 % 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: 2.58 (0.21), residues: 1593 helix: 2.31 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.13 (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 0.023 0.002 PHE C 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 0.06589 ( 973) hydrogen bonds : angle 4.10783 ( 2847) covalent geometry : bond 0.00453 (13005) covalent geometry : angle 0.53789 (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 195 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.771 Fit side-chains REVERT: A 129 MET cc_start: 0.7444 (mtp) cc_final: 0.7189 (mtt) REVERT: A 229 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7468 (mmtp) REVERT: A 253 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6572 (mt-10) REVERT: A 305 MET cc_start: 0.8797 (mmm) cc_final: 0.8585 (mmp) REVERT: A 365 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 416 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7123 (tp30) REVERT: A 429 LYS cc_start: 0.7414 (ptpt) cc_final: 0.6654 (ptmm) REVERT: A 430 MET cc_start: 0.7840 (mtt) cc_final: 0.7106 (mtt) REVERT: A 497 MET cc_start: 0.8297 (tmt) cc_final: 0.8034 (tmt) REVERT: A 502 MET cc_start: 0.7734 (mtm) cc_final: 0.7240 (tpt) REVERT: A 590 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7189 (ttpp) REVERT: A 592 ASP cc_start: 0.8017 (m-30) cc_final: 0.7777 (m-30) REVERT: B 229 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7614 (mmtp) REVERT: B 283 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7803 (mm-30) REVERT: B 305 MET cc_start: 0.8849 (mmp) cc_final: 0.8196 (mmt) REVERT: B 429 LYS cc_start: 0.7442 (ptpt) cc_final: 0.6984 (ptmm) REVERT: B 502 MET cc_start: 0.7832 (mtm) cc_final: 0.7424 (mmp) REVERT: B 508 GLN cc_start: 0.8450 (mt0) cc_final: 0.7944 (mm110) REVERT: C 229 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7480 (mmtp) REVERT: C 313 LEU cc_start: 0.8934 (mt) cc_final: 0.8638 (mt) REVERT: C 477 LEU cc_start: 0.8056 (tp) cc_final: 0.7786 (tp) REVERT: C 585 MET cc_start: 0.7659 (mtm) cc_final: 0.7450 (mtm) outliers start: 18 outliers final: 6 residues processed: 190 average time/residue: 2.0488 time to fit residues: 433.9384 Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 314 MET 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: 0.3980 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: 0.9980 chunk 35 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.154984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112228 restraints weight = 35065.243| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.18 r_work: 0.3029 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13005 Z= 0.120 Angle : 0.447 4.502 17628 Z= 0.238 Chirality : 0.036 0.112 2007 Planarity : 0.004 0.054 2118 Dihedral : 15.107 179.118 2064 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.19 % Allowed : 8.63 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.01 (0.22), residues: 1593 helix: 2.61 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.003 0.001 HIS A 288 PHE 0.014 0.001 PHE C 279 TYR 0.006 0.001 TYR C 285 ARG 0.002 0.000 ARG C 589 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 973) hydrogen bonds : angle 3.82178 ( 2847) covalent geometry : bond 0.00261 (13005) covalent geometry : angle 0.44662 (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 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.852 Fit side-chains REVERT: A 129 MET cc_start: 0.7335 (mtp) cc_final: 0.7096 (mtt) REVERT: A 229 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7360 (mmtt) REVERT: A 253 GLU cc_start: 0.6521 (mt-10) cc_final: 0.6289 (mt-10) REVERT: A 365 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7786 (mt-10) REVERT: A 429 LYS cc_start: 0.7288 (ptpt) cc_final: 0.6586 (ptmm) REVERT: A 430 MET cc_start: 0.7894 (mtt) cc_final: 0.7233 (mtt) REVERT: A 502 MET cc_start: 0.7613 (mtm) cc_final: 0.7150 (tpt) REVERT: A 590 LYS cc_start: 0.7603 (ttmt) cc_final: 0.7088 (ttpp) REVERT: A 592 ASP cc_start: 0.7976 (m-30) cc_final: 0.7736 (m-30) REVERT: B 229 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7355 (mmmt) REVERT: B 283 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7748 (mm-30) REVERT: B 305 MET cc_start: 0.8815 (mmp) cc_final: 0.8125 (mmt) REVERT: B 502 MET cc_start: 0.7701 (mtm) cc_final: 0.7327 (mmp) REVERT: B 508 GLN cc_start: 0.8261 (mt0) cc_final: 0.7770 (mm110) REVERT: C 201 LYS cc_start: 0.8076 (mttm) cc_final: 0.7875 (mptm) REVERT: C 229 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7470 (mmtt) REVERT: C 313 LEU cc_start: 0.8837 (mt) cc_final: 0.8599 (mt) REVERT: C 430 MET cc_start: 0.7508 (mtt) cc_final: 0.7124 (mtt) outliers start: 15 outliers final: 5 residues processed: 179 average time/residue: 2.1550 time to fit residues: 428.4339 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 : 1.664 ------------------------------------------------------------------------------- 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: 2.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.154712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111979 restraints weight = 34929.448| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.18 r_work: 0.3023 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13005 Z= 0.123 Angle : 0.444 4.558 17628 Z= 0.237 Chirality : 0.036 0.113 2007 Planarity : 0.004 0.054 2118 Dihedral : 14.638 178.379 2064 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.79 % Allowed : 9.58 % Favored : 89.63 % 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: 3.13 (0.22), residues: 1593 helix: 2.71 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.03 (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 0.006 0.001 TYR C 357 ARG 0.001 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 973) hydrogen bonds : angle 3.77493 ( 2847) covalent geometry : bond 0.00273 (13005) covalent geometry : angle 0.44351 (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 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 1.777 Fit side-chains REVERT: A 129 MET cc_start: 0.7440 (mtp) cc_final: 0.7216 (mtt) REVERT: A 229 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7462 (mmtt) REVERT: A 253 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6305 (mt-10) REVERT: A 365 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7762 (mt-10) REVERT: A 430 MET cc_start: 0.7759 (mtt) cc_final: 0.7141 (mtt) REVERT: A 502 MET cc_start: 0.7655 (mtm) cc_final: 0.7217 (tpt) REVERT: A 590 LYS cc_start: 0.7599 (ttmt) cc_final: 0.7091 (ttpp) REVERT: A 592 ASP cc_start: 0.7969 (m-30) cc_final: 0.7738 (m-30) REVERT: B 229 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7452 (mmmt) REVERT: B 283 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 305 MET cc_start: 0.8838 (mmp) cc_final: 0.8155 (mmt) REVERT: B 485 GLN cc_start: 0.8489 (mp10) cc_final: 0.8082 (mp10) REVERT: B 502 MET cc_start: 0.7705 (mtm) cc_final: 0.7326 (mmp) REVERT: B 508 GLN cc_start: 0.8275 (mt0) cc_final: 0.7779 (mm110) REVERT: C 229 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7559 (mmtt) REVERT: C 313 LEU cc_start: 0.8835 (mt) cc_final: 0.8594 (mt) REVERT: C 430 MET cc_start: 0.7474 (mtt) cc_final: 0.7088 (mtt) outliers start: 10 outliers final: 4 residues processed: 174 average time/residue: 2.1892 time to fit residues: 422.7950 Evaluate side-chains 170 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 30 optimal weight: 2.9990 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: 8.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.152763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109731 restraints weight = 34778.134| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.19 r_work: 0.3092 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3465 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= 0.160 Angle : 0.489 5.376 17628 Z= 0.261 Chirality : 0.037 0.122 2007 Planarity : 0.004 0.058 2118 Dihedral : 14.785 175.764 2064 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.11 % Allowed : 9.58 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.21), residues: 1593 helix: 2.54 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.12 (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 0.015 0.001 PHE A 413 TYR 0.009 0.001 TYR C 553 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05622 ( 973) hydrogen bonds : angle 3.89892 ( 2847) covalent geometry : bond 0.00371 (13005) covalent geometry : angle 0.48926 (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 190 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.691 Fit side-chains REVERT: A 129 MET cc_start: 0.7342 (mtp) cc_final: 0.7142 (mtt) REVERT: A 229 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7507 (mmtp) REVERT: A 253 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6323 (mt-10) REVERT: A 365 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 430 MET cc_start: 0.7791 (mtt) cc_final: 0.7154 (mtt) REVERT: A 502 MET cc_start: 0.7784 (mtm) cc_final: 0.7315 (tpt) REVERT: A 590 LYS cc_start: 0.7624 (ttmt) cc_final: 0.7129 (ttpp) REVERT: A 592 ASP cc_start: 0.7957 (m-30) cc_final: 0.7734 (m-30) REVERT: B 199 THR cc_start: 0.8511 (m) cc_final: 0.8309 (m) REVERT: B 229 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7486 (mmmt) REVERT: B 283 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7595 (mm-30) REVERT: B 305 MET cc_start: 0.8886 (mmp) cc_final: 0.8171 (mmt) REVERT: B 502 MET cc_start: 0.7772 (mtm) cc_final: 0.7374 (mmp) REVERT: B 508 GLN cc_start: 0.8330 (mt0) cc_final: 0.7832 (mm110) REVERT: C 229 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7592 (mmtt) REVERT: C 313 LEU cc_start: 0.8875 (mt) cc_final: 0.8618 (mt) REVERT: C 430 MET cc_start: 0.7446 (mtt) cc_final: 0.6983 (mtt) outliers start: 14 outliers final: 6 residues processed: 186 average time/residue: 2.0920 time to fit residues: 432.6531 Evaluate side-chains 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 63 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- 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 = 0.153933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111638 restraints weight = 34873.904| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.17 r_work: 0.3092 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3540 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 4.855 17628 Z= 0.242 Chirality : 0.036 0.115 2007 Planarity : 0.004 0.055 2118 Dihedral : 14.212 176.522 2064 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.11 % Allowed : 10.13 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.05 (0.22), residues: 1593 helix: 2.66 (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 C 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 0.04982 ( 973) hydrogen bonds : angle 3.80189 ( 2847) covalent geometry : bond 0.00299 (13005) covalent geometry : angle 0.45536 (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 : 1.683 Fit side-chains REVERT: A 129 MET cc_start: 0.7427 (mtp) cc_final: 0.7217 (mtt) REVERT: A 229 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7554 (mmtt) REVERT: A 365 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 430 MET cc_start: 0.7826 (mtt) cc_final: 0.7203 (mtt) REVERT: A 502 MET cc_start: 0.7748 (mtm) cc_final: 0.7299 (tpt) REVERT: A 590 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7183 (ttpp) REVERT: A 592 ASP cc_start: 0.7928 (m-30) cc_final: 0.7710 (m-30) REVERT: B 199 THR cc_start: 0.8502 (m) cc_final: 0.8298 (m) REVERT: B 229 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7516 (mmmt) REVERT: B 283 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 305 MET cc_start: 0.8932 (mmp) cc_final: 0.8253 (mmt) REVERT: B 502 MET cc_start: 0.7773 (mtm) cc_final: 0.7401 (mmp) REVERT: B 508 GLN cc_start: 0.8299 (mt0) cc_final: 0.7823 (mm110) REVERT: C 229 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7634 (mmtt) REVERT: C 313 LEU cc_start: 0.8853 (mt) cc_final: 0.8631 (mt) REVERT: C 428 MET cc_start: 0.7743 (mmp) cc_final: 0.7213 (mmp) outliers start: 14 outliers final: 5 residues processed: 183 average time/residue: 2.0742 time to fit residues: 421.6880 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 : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 340 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.152149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109651 restraints weight = 34867.710| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.16 r_work: 0.3003 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13005 Z= 0.172 Angle : 0.504 5.621 17628 Z= 0.269 Chirality : 0.038 0.125 2007 Planarity : 0.004 0.059 2118 Dihedral : 14.244 174.491 2064 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.71 % Allowed : 10.37 % 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: 2.78 (0.21), residues: 1593 helix: 2.47 (0.14), residues: 1299 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 261 HIS 0.005 0.001 HIS B 288 PHE 0.016 0.002 PHE C 413 TYR 0.009 0.002 TYR C 553 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05852 ( 973) hydrogen bonds : angle 3.94063 ( 2847) covalent geometry : bond 0.00401 (13005) covalent geometry : angle 0.50397 (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 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 1.723 Fit side-chains REVERT: A 229 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7651 (mmtt) REVERT: A 365 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 430 MET cc_start: 0.7758 (mtt) cc_final: 0.7167 (mtt) REVERT: A 497 MET cc_start: 0.8318 (tmt) cc_final: 0.7928 (tmt) REVERT: A 502 MET cc_start: 0.7808 (mtm) cc_final: 0.7346 (tpt) REVERT: A 590 LYS cc_start: 0.7594 (ttmt) cc_final: 0.7097 (ttpp) REVERT: A 592 ASP cc_start: 0.7887 (m-30) cc_final: 0.7669 (m-30) REVERT: B 229 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7498 (mmmt) REVERT: B 283 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 305 MET cc_start: 0.8922 (mmp) cc_final: 0.8237 (mmt) REVERT: B 502 MET cc_start: 0.7800 (mtm) cc_final: 0.7405 (mmp) REVERT: B 508 GLN cc_start: 0.8393 (mt0) cc_final: 0.7904 (mm110) REVERT: C 229 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7599 (mmtt) REVERT: C 313 LEU cc_start: 0.8891 (mt) cc_final: 0.8638 (mt) REVERT: C 428 MET cc_start: 0.7697 (mmp) cc_final: 0.7133 (mmp) outliers start: 9 outliers final: 5 residues processed: 177 average time/residue: 2.1399 time to fit residues: 419.8959 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 340 SER 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: 1.9990 chunk 149 optimal weight: 1.9990 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: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.151809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109355 restraints weight = 34861.279| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.18 r_work: 0.3006 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13005 Z= 0.149 Angle : 0.473 5.241 17628 Z= 0.252 Chirality : 0.037 0.118 2007 Planarity : 0.004 0.057 2118 Dihedral : 14.004 175.680 2064 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.63 % Allowed : 10.69 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.89 (0.21), residues: 1593 helix: 2.55 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -1.16 (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 0.013 0.001 PHE C 279 TYR 0.008 0.001 TYR C 553 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05338 ( 973) hydrogen bonds : angle 3.86532 ( 2847) covalent geometry : bond 0.00342 (13005) covalent geometry : angle 0.47271 (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 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 1.829 Fit side-chains REVERT: A 229 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7678 (mmtt) REVERT: A 365 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 430 MET cc_start: 0.7813 (mtt) cc_final: 0.7228 (mtt) REVERT: A 497 MET cc_start: 0.8292 (tmt) cc_final: 0.7890 (tmt) REVERT: A 502 MET cc_start: 0.7731 (mtm) cc_final: 0.7277 (tpt) REVERT: A 590 LYS cc_start: 0.7569 (ttmt) cc_final: 0.7045 (ttpp) REVERT: A 592 ASP cc_start: 0.7898 (m-30) cc_final: 0.7675 (m-30) REVERT: B 229 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7475 (mmmt) REVERT: B 283 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 305 MET cc_start: 0.8893 (mmp) cc_final: 0.8174 (mmt) REVERT: B 502 MET cc_start: 0.7710 (mtm) cc_final: 0.7356 (mmp) REVERT: B 508 GLN cc_start: 0.8285 (mt0) cc_final: 0.7796 (mm110) REVERT: C 229 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7562 (mmtt) REVERT: C 313 LEU cc_start: 0.8852 (mt) cc_final: 0.8614 (mt) REVERT: C 428 MET cc_start: 0.7673 (mmp) cc_final: 0.7109 (mmp) outliers start: 8 outliers final: 5 residues processed: 177 average time/residue: 2.1748 time to fit residues: 426.9368 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain C residue 340 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 85 optimal weight: 0.0010 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.156404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114667 restraints weight = 34993.614| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.19 r_work: 0.3079 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3674 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= 0.088 Angle : 0.405 4.370 17628 Z= 0.214 Chirality : 0.035 0.115 2007 Planarity : 0.003 0.050 2118 Dihedral : 13.197 179.960 2064 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.40 % Allowed : 11.01 % 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: 3.50 (0.22), residues: 1593 helix: 2.96 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.90 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 316 HIS 0.002 0.000 HIS C 288 PHE 0.009 0.001 PHE C 259 TYR 0.004 0.001 TYR B 519 ARG 0.002 0.000 ARG C 233 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 973) hydrogen bonds : angle 3.55812 ( 2847) covalent geometry : bond 0.00180 (13005) covalent geometry : angle 0.40468 (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 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 1.832 Fit side-chains REVERT: A 229 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7718 (mmtt) REVERT: A 365 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 497 MET cc_start: 0.8406 (tmt) cc_final: 0.7883 (tmt) REVERT: A 502 MET cc_start: 0.7516 (mtm) cc_final: 0.7184 (tpt) REVERT: A 590 LYS cc_start: 0.7556 (ttmt) cc_final: 0.7070 (ttpp) REVERT: A 592 ASP cc_start: 0.8027 (m-30) cc_final: 0.7780 (m-30) REVERT: B 147 PHE cc_start: 0.7687 (m-80) cc_final: 0.7461 (m-10) REVERT: B 229 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7462 (mmmt) REVERT: B 283 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 305 MET cc_start: 0.8872 (mmp) cc_final: 0.8165 (mmt) REVERT: B 485 GLN cc_start: 0.8358 (mp10) cc_final: 0.8015 (mp10) REVERT: B 502 MET cc_start: 0.7656 (mtm) cc_final: 0.7303 (mmp) REVERT: B 508 GLN cc_start: 0.8274 (mt0) cc_final: 0.7812 (mm110) REVERT: B 524 ASN cc_start: 0.8285 (p0) cc_final: 0.8050 (p0) REVERT: C 229 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7540 (mmtt) REVERT: C 428 MET cc_start: 0.7695 (mmp) cc_final: 0.7427 (mmp) outliers start: 5 outliers final: 3 residues processed: 179 average time/residue: 2.0834 time to fit residues: 414.6683 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.153352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111106 restraints weight = 34968.025| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.18 r_work: 0.3029 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13005 Z= 0.122 Angle : 0.445 4.986 17628 Z= 0.236 Chirality : 0.036 0.115 2007 Planarity : 0.004 0.054 2118 Dihedral : 13.366 177.016 2064 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.32 % Allowed : 11.64 % Favored : 88.04 % 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: 3.37 (0.22), residues: 1593 helix: 2.88 (0.15), residues: 1299 sheet: None (None), residues: 0 loop : -0.97 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.004 0.001 HIS A 288 PHE 0.012 0.001 PHE A 488 TYR 0.008 0.001 TYR A 357 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 973) hydrogen bonds : angle 3.70969 ( 2847) covalent geometry : bond 0.00270 (13005) covalent geometry : angle 0.44525 (17628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15956.78 seconds wall clock time: 273 minutes 16.99 seconds (16396.99 seconds total)