Starting phenix.real_space_refine on Sat Jun 21 22:09:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz6_41735/06_2025/8tz6_41735_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz6_41735/06_2025/8tz6_41735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz6_41735/06_2025/8tz6_41735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz6_41735/06_2025/8tz6_41735.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz6_41735/06_2025/8tz6_41735_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz6_41735/06_2025/8tz6_41735_trim.cif" } resolution = 2.69 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= 0.003 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 12 5.49 5 S 87 5.16 5 Na 3 4.78 5 C 8442 2.51 5 N 1932 2.21 5 O 2205 1.98 5 F 3 1.80 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24849 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'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, 'U7I': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: C, B Time building chain proxies: 22.69, per 1000 atoms: 0.91 Number of scatterers: 24849 At special positions: 0 Unit cell: (128.52, 126.36, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 87 16.00 P 12 15.00 Na 3 11.00 F 3 9.00 O 2205 8.00 N 1932 7.00 C 8442 6.00 H 12165 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.30 Conformation dependent library (CDL) restraints added in 2.2 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 3 sheets defined 87.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 203 Proline residue: A 167 - end of helix removed outlier: 4.587A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.956A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.582A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.451A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 294 through 312 Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.571A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.647A pdb=" N ARG A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.335A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 479 removed outlier: 3.542A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.180A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.764A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 removed outlier: 3.629A pdb=" N CYS A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 removed outlier: 4.139A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 617 removed outlier: 3.658A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.588A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.955A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 4.582A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 270 Processing helix chain 'B' and resid 272 through 282 removed outlier: 4.451A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.572A pdb=" N VAL B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.647A pdb=" N ARG B 355 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.335A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 479 removed outlier: 3.543A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.180A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.764A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 567 removed outlier: 3.630A pdb=" N CYS B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 removed outlier: 4.139A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 617 removed outlier: 3.657A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 597 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 203 Proline residue: C 167 - end of helix removed outlier: 4.587A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.955A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 4.582A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 270 Processing helix chain 'C' and resid 272 through 282 removed outlier: 4.451A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.572A pdb=" N VAL C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.647A pdb=" N ARG C 355 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 381 through 389 Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.335A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 479 removed outlier: 3.542A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 487 through 496 Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.180A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.764A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 567 removed outlier: 3.630A pdb=" N CYS C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 586 removed outlier: 4.139A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 617 removed outlier: 3.657A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 597 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA2, first strand: chain 'B' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'C' and resid 546 through 547 979 hydrogen bonds defined for protein. 2883 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.55 Time building geometry restraints manager: 8.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12147 1.03 - 1.22: 48 1.22 - 1.42: 5415 1.42 - 1.61: 7377 1.61 - 1.81: 183 Bond restraints: 25170 Sorted by residual: bond pdb=" C02 U7I A 801 " pdb=" C03 U7I A 801 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C02 U7I B 801 " pdb=" C03 U7I B 801 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C02 U7I C 801 " pdb=" C03 U7I C 801 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C04 U7I B 801 " pdb=" O05 U7I B 801 " ideal model delta sigma weight residual 1.427 1.270 0.157 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C04 U7I A 801 " pdb=" O05 U7I A 801 " ideal model delta sigma weight residual 1.427 1.271 0.156 2.00e-02 2.50e+03 6.12e+01 ... (remaining 25165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 44898 3.25 - 6.49: 201 6.49 - 9.74: 35 9.74 - 12.99: 10 12.99 - 16.23: 12 Bond angle restraints: 45156 Sorted by residual: angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 109.68 -16.23 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 109.68 -16.23 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O1 LBN C 803 " pdb=" P1 LBN C 803 " pdb=" O2 LBN C 803 " ideal model delta sigma weight residual 93.45 109.67 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1 LBN A 806 " pdb=" P1 LBN A 806 " pdb=" O2 LBN A 806 " ideal model delta sigma weight residual 93.45 109.65 -16.20 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1 LBN B 806 " pdb=" P1 LBN B 806 " pdb=" O2 LBN B 806 " ideal model delta sigma weight residual 93.45 109.62 -16.17 3.00e+00 1.11e-01 2.91e+01 ... (remaining 45151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 11672 35.53 - 71.06: 427 71.06 - 106.59: 9 106.59 - 142.12: 3 142.12 - 177.66: 9 Dihedral angle restraints: 12120 sinusoidal: 6390 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN A 803 " pdb=" C2 LBN A 803 " pdb=" C3 LBN A 803 " pdb=" O7 LBN A 803 " ideal model delta sinusoidal sigma weight residual 62.67 -114.99 177.66 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN B 803 " pdb=" C2 LBN B 803 " pdb=" C3 LBN B 803 " pdb=" O7 LBN B 803 " ideal model delta sinusoidal sigma weight residual 62.67 -114.98 177.65 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN C 803 " pdb=" C2 LBN C 803 " pdb=" C3 LBN C 803 " pdb=" O7 LBN C 803 " ideal model delta sinusoidal sigma weight residual 62.67 -114.95 177.62 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1976 0.108 - 0.216: 28 0.216 - 0.324: 0 0.324 - 0.433: 0 0.433 - 0.541: 3 Chirality restraints: 2007 Sorted by residual: chirality pdb=" C02 U7I B 801 " pdb=" C03 U7I B 801 " pdb=" C06 U7I B 801 " pdb=" F18 U7I B 801 " both_signs ideal model delta sigma weight residual False 2.88 2.33 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" C02 U7I C 801 " pdb=" C03 U7I C 801 " pdb=" C06 U7I C 801 " pdb=" F18 U7I C 801 " both_signs ideal model delta sigma weight residual False 2.88 2.34 0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" C02 U7I A 801 " pdb=" C03 U7I A 801 " pdb=" C06 U7I A 801 " pdb=" F18 U7I A 801 " both_signs ideal model delta sigma weight residual False 2.88 2.34 0.54 2.00e-01 2.50e+01 7.21e+00 ... (remaining 2004 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 195 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C LEU C 195 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU C 195 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 196 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 195 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C LEU A 195 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A 195 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 196 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 195 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C LEU B 195 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU B 195 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 196 " -0.010 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1556 2.22 - 2.81: 51238 2.81 - 3.41: 64625 3.41 - 4.00: 86662 4.00 - 4.60: 139147 Nonbonded interactions: 343228 Sorted by model distance: nonbonded pdb=" OE1 GLU C 489 " pdb=" H GLU C 489 " model vdw 1.622 2.450 nonbonded pdb=" OE1 GLU A 489 " pdb=" H GLU A 489 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU B 489 " pdb=" H GLU B 489 " model vdw 1.624 2.450 nonbonded pdb=" OE1 GLN C 206 " pdb=" H GLN C 206 " model vdw 1.630 2.450 nonbonded pdb=" OE1 GLN B 206 " pdb=" H GLN B 206 " model vdw 1.630 2.450 ... (remaining 343223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 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: 108.290 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: 0.440 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 67.140 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.295 13005 Z= 0.577 Angle : 0.908 16.233 17634 Z= 0.361 Chirality : 0.046 0.541 2007 Planarity : 0.003 0.034 2118 Dihedral : 15.812 177.656 4626 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.48 % Allowed : 2.61 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.99 (0.21), residues: 1593 helix: 2.51 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -1.01 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 316 HIS 0.001 0.000 HIS C 367 PHE 0.016 0.001 PHE C 413 TYR 0.010 0.001 TYR C 231 ARG 0.002 0.000 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.14056 ( 979) hydrogen bonds : angle 5.15226 ( 2883) covalent geometry : bond 0.01180 (13005) covalent geometry : angle 0.90775 (17634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 255 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8171 (mt0) cc_final: 0.7950 (mt0) REVERT: A 267 GLN cc_start: 0.7613 (tt0) cc_final: 0.7364 (mt0) REVERT: A 305 MET cc_start: 0.7699 (mmm) cc_final: 0.7322 (mmp) REVERT: A 477 LEU cc_start: 0.7925 (tp) cc_final: 0.7712 (tt) REVERT: A 497 MET cc_start: 0.6252 (tmt) cc_final: 0.5442 (tmt) REVERT: A 526 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: B 264 LYS cc_start: 0.7405 (mttt) cc_final: 0.7005 (mtpt) REVERT: B 420 PRO cc_start: 0.8720 (Cg_endo) cc_final: 0.8459 (Cg_exo) REVERT: B 428 MET cc_start: 0.7433 (mmt) cc_final: 0.6906 (mmt) REVERT: B 526 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: B 534 LYS cc_start: 0.7596 (mttt) cc_final: 0.7312 (mtpp) REVERT: C 131 PHE cc_start: 0.7585 (t80) cc_final: 0.7239 (t80) REVERT: C 264 LYS cc_start: 0.7358 (mttt) cc_final: 0.6992 (mtpt) REVERT: C 267 GLN cc_start: 0.7408 (tt0) cc_final: 0.7119 (mt0) REVERT: C 418 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7501 (mt-10) REVERT: C 497 MET cc_start: 0.6617 (tmt) cc_final: 0.6210 (tmt) REVERT: C 534 LYS cc_start: 0.7600 (mttt) cc_final: 0.7319 (mtpp) outliers start: 6 outliers final: 2 residues processed: 261 average time/residue: 2.3421 time to fit residues: 679.4037 Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain C residue 526 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN A 423 ASN B 423 ASN C 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107503 restraints weight = 37460.807| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.55 r_work: 0.3127 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13005 Z= 0.115 Angle : 0.472 4.419 17634 Z= 0.246 Chirality : 0.036 0.116 2007 Planarity : 0.003 0.042 2118 Dihedral : 14.693 156.669 2084 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.71 % Allowed : 9.03 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.34 (0.21), residues: 1593 helix: 2.76 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 261 HIS 0.003 0.001 HIS C 288 PHE 0.012 0.001 PHE B 146 TYR 0.011 0.001 TYR B 231 ARG 0.003 0.001 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 979) hydrogen bonds : angle 3.87110 ( 2883) covalent geometry : bond 0.00242 (13005) covalent geometry : angle 0.47156 (17634) *********************** 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 200 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8041 (mt0) cc_final: 0.7827 (mt0) REVERT: A 305 MET cc_start: 0.8246 (mmm) cc_final: 0.8040 (mmm) REVERT: A 327 VAL cc_start: 0.7534 (t) cc_final: 0.7321 (p) REVERT: A 444 GLN cc_start: 0.7327 (mt0) cc_final: 0.7117 (mt0) REVERT: B 262 LEU cc_start: 0.7712 (mt) cc_final: 0.7422 (mt) REVERT: B 264 LYS cc_start: 0.6871 (mttt) cc_final: 0.6423 (mtpt) REVERT: B 497 MET cc_start: 0.6427 (tmt) cc_final: 0.5896 (tmt) REVERT: B 534 LYS cc_start: 0.7349 (mttt) cc_final: 0.7088 (mttt) REVERT: C 264 LYS cc_start: 0.7021 (mttt) cc_final: 0.6400 (mtpt) REVERT: C 349 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: C 418 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6591 (mt-10) REVERT: C 534 LYS cc_start: 0.7346 (mttt) cc_final: 0.7007 (mtpp) outliers start: 9 outliers final: 2 residues processed: 196 average time/residue: 2.7713 time to fit residues: 613.0576 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 349 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN B 423 ASN C 508 GLN C 620 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097722 restraints weight = 38433.285| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.55 r_work: 0.2977 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13005 Z= 0.206 Angle : 0.546 6.248 17634 Z= 0.289 Chirality : 0.039 0.133 2007 Planarity : 0.004 0.047 2118 Dihedral : 14.962 151.454 2076 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.35 % Allowed : 10.21 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.68 (0.21), residues: 1593 helix: 2.42 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.54 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 194 HIS 0.005 0.001 HIS C 288 PHE 0.016 0.002 PHE C 146 TYR 0.011 0.002 TYR B 231 ARG 0.003 0.001 ARG C 589 Details of bonding type rmsd hydrogen bonds : bond 0.06447 ( 979) hydrogen bonds : angle 4.11497 ( 2883) covalent geometry : bond 0.00496 (13005) covalent geometry : angle 0.54607 (17634) *********************** 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 207 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 TYR cc_start: 0.7411 (t80) cc_final: 0.7183 (t80) REVERT: A 305 MET cc_start: 0.8227 (mmm) cc_final: 0.8020 (mmm) REVERT: A 313 LEU cc_start: 0.7887 (mt) cc_final: 0.7648 (mt) REVERT: A 508 GLN cc_start: 0.8020 (mt0) cc_final: 0.7214 (mm-40) REVERT: B 231 TYR cc_start: 0.7236 (t80) cc_final: 0.7002 (t80) REVERT: B 242 GLN cc_start: 0.8243 (mt0) cc_final: 0.7964 (mt0) REVERT: B 260 ASP cc_start: 0.7695 (t0) cc_final: 0.7329 (t0) REVERT: B 262 LEU cc_start: 0.7814 (mt) cc_final: 0.7516 (mt) REVERT: B 264 LYS cc_start: 0.6764 (mttt) cc_final: 0.6366 (mtpt) REVERT: C 231 TYR cc_start: 0.6730 (t80) cc_final: 0.6443 (t80) REVERT: C 264 LYS cc_start: 0.6872 (mttt) cc_final: 0.6442 (mtpt) REVERT: C 313 LEU cc_start: 0.7867 (mt) cc_final: 0.7633 (mt) REVERT: C 335 GLU cc_start: 0.7521 (pt0) cc_final: 0.7246 (pt0) REVERT: C 349 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: C 534 LYS cc_start: 0.7409 (mttt) cc_final: 0.7016 (mttm) outliers start: 17 outliers final: 9 residues processed: 200 average time/residue: 2.0526 time to fit residues: 458.1343 Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 50 optimal weight: 0.0570 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN A 620 ASN B 423 ASN C 423 ASN C 426 ASN C 508 GLN C 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099397 restraints weight = 38556.167| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.55 r_work: 0.3014 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13005 Z= 0.141 Angle : 0.470 4.791 17634 Z= 0.247 Chirality : 0.036 0.117 2007 Planarity : 0.004 0.044 2118 Dihedral : 13.946 144.924 2076 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.19 % Allowed : 11.72 % Favored : 87.09 % 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: 2.91 (0.21), residues: 1593 helix: 2.56 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -1.47 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 323 HIS 0.003 0.001 HIS B 288 PHE 0.015 0.001 PHE A 146 TYR 0.009 0.001 TYR C 553 ARG 0.003 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 979) hydrogen bonds : angle 3.87878 ( 2883) covalent geometry : bond 0.00326 (13005) covalent geometry : angle 0.47004 (17634) *********************** 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 201 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8086 (mt0) cc_final: 0.7870 (mt0) REVERT: A 313 LEU cc_start: 0.7771 (mt) cc_final: 0.7558 (mt) REVERT: A 335 GLU cc_start: 0.7436 (pt0) cc_final: 0.7201 (pt0) REVERT: A 482 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.6987 (t0) REVERT: A 508 GLN cc_start: 0.8047 (mt0) cc_final: 0.7196 (mm-40) REVERT: A 601 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6753 (tt) REVERT: B 151 ASP cc_start: 0.7173 (m-30) cc_final: 0.6650 (m-30) REVERT: B 242 GLN cc_start: 0.8235 (mt0) cc_final: 0.7970 (mt0) REVERT: B 262 LEU cc_start: 0.7723 (mt) cc_final: 0.7449 (mt) REVERT: B 264 LYS cc_start: 0.6753 (mttt) cc_final: 0.6370 (mtpt) REVERT: B 497 MET cc_start: 0.6958 (tmt) cc_final: 0.6449 (tmt) REVERT: C 264 LYS cc_start: 0.6822 (mttt) cc_final: 0.6383 (mtpt) REVERT: C 335 GLU cc_start: 0.7492 (pt0) cc_final: 0.7147 (pt0) REVERT: C 349 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6977 (mp0) outliers start: 15 outliers final: 5 residues processed: 197 average time/residue: 1.9235 time to fit residues: 427.3520 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 : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 59 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN A 479 ASN B 423 ASN C 423 ASN C 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101287 restraints weight = 39310.838| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.54 r_work: 0.3065 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13005 Z= 0.165 Angle : 0.491 5.561 17634 Z= 0.257 Chirality : 0.037 0.116 2007 Planarity : 0.004 0.046 2118 Dihedral : 13.640 142.257 2076 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.58 % Allowed : 12.35 % Favored : 86.06 % 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: 2.80 (0.21), residues: 1593 helix: 2.48 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.004 0.001 HIS C 288 PHE 0.017 0.001 PHE C 146 TYR 0.010 0.001 TYR C 553 ARG 0.002 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.05482 ( 979) hydrogen bonds : angle 3.94187 ( 2883) covalent geometry : bond 0.00392 (13005) covalent geometry : angle 0.49057 (17634) *********************** 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 195 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 4.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8293 (mt0) cc_final: 0.8042 (mt0) REVERT: A 313 LEU cc_start: 0.8085 (mt) cc_final: 0.7866 (mt) REVERT: A 482 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7149 (t0) REVERT: A 508 GLN cc_start: 0.8317 (mt0) cc_final: 0.7605 (mm-40) REVERT: A 601 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7326 (tt) REVERT: B 151 ASP cc_start: 0.7545 (m-30) cc_final: 0.6980 (m-30) REVERT: B 242 GLN cc_start: 0.8406 (mt0) cc_final: 0.8124 (mt0) REVERT: B 260 ASP cc_start: 0.7952 (t0) cc_final: 0.7598 (t0) REVERT: B 262 LEU cc_start: 0.8078 (mt) cc_final: 0.7772 (mt) REVERT: B 264 LYS cc_start: 0.7254 (mttt) cc_final: 0.6853 (mtpt) REVERT: C 264 LYS cc_start: 0.7307 (mttt) cc_final: 0.6920 (mtpt) REVERT: C 335 GLU cc_start: 0.7737 (pt0) cc_final: 0.7380 (pt0) REVERT: C 349 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: C 428 MET cc_start: 0.7885 (mmt) cc_final: 0.7601 (mmt) REVERT: C 534 LYS cc_start: 0.7781 (mttt) cc_final: 0.7461 (mttm) outliers start: 20 outliers final: 10 residues processed: 190 average time/residue: 2.5756 time to fit residues: 554.8299 Evaluate side-chains 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 3 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 423 ASN B 423 ASN C 423 ASN C 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.096614 restraints weight = 38160.652| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.60 r_work: 0.2983 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13005 Z= 0.199 Angle : 0.525 5.968 17634 Z= 0.275 Chirality : 0.038 0.120 2007 Planarity : 0.004 0.047 2118 Dihedral : 13.468 141.359 2076 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.90 % Allowed : 12.43 % Favored : 85.67 % 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: 2.57 (0.21), residues: 1593 helix: 2.37 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -1.56 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 178 HIS 0.005 0.001 HIS C 288 PHE 0.018 0.001 PHE C 146 TYR 0.012 0.001 TYR C 553 ARG 0.002 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.06016 ( 979) hydrogen bonds : angle 4.05026 ( 2883) covalent geometry : bond 0.00480 (13005) covalent geometry : angle 0.52470 (17634) *********************** 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 199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8251 (mt0) cc_final: 0.7990 (mt0) REVERT: A 313 LEU cc_start: 0.8014 (mt) cc_final: 0.7758 (mt) REVERT: A 482 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6999 (t0) REVERT: A 508 GLN cc_start: 0.8159 (mt0) cc_final: 0.7389 (mm-40) REVERT: A 601 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7170 (tt) REVERT: B 151 ASP cc_start: 0.7315 (m-30) cc_final: 0.6837 (m-30) REVERT: B 242 GLN cc_start: 0.8378 (mt0) cc_final: 0.8081 (mt0) REVERT: B 260 ASP cc_start: 0.7858 (t0) cc_final: 0.7483 (t0) REVERT: B 262 LEU cc_start: 0.7993 (mt) cc_final: 0.7697 (mt) REVERT: B 264 LYS cc_start: 0.6993 (mttt) cc_final: 0.6595 (mtpt) REVERT: B 497 MET cc_start: 0.7211 (tmt) cc_final: 0.6706 (tmt) REVERT: C 264 LYS cc_start: 0.7050 (mttt) cc_final: 0.6653 (mtpt) REVERT: C 335 GLU cc_start: 0.7582 (pt0) cc_final: 0.7217 (pt0) REVERT: C 349 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: C 428 MET cc_start: 0.7583 (mmt) cc_final: 0.7321 (mmt) REVERT: C 534 LYS cc_start: 0.7669 (mttt) cc_final: 0.7292 (mttm) outliers start: 24 outliers final: 14 residues processed: 191 average time/residue: 1.9547 time to fit residues: 419.6139 Evaluate side-chains 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN B 423 ASN C 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.100476 restraints weight = 37813.133| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.61 r_work: 0.3029 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13005 Z= 0.102 Angle : 0.432 4.498 17634 Z= 0.226 Chirality : 0.035 0.112 2007 Planarity : 0.003 0.041 2118 Dihedral : 12.289 132.391 2076 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.95 % Allowed : 13.54 % Favored : 85.51 % 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: 3.19 (0.22), residues: 1593 helix: 2.75 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 323 HIS 0.002 0.000 HIS C 288 PHE 0.017 0.001 PHE C 146 TYR 0.006 0.001 TYR C 553 ARG 0.002 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 979) hydrogen bonds : angle 3.72970 ( 2883) covalent geometry : bond 0.00216 (13005) covalent geometry : angle 0.43210 (17634) *********************** 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: 12 poor density : 177 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 LEU cc_start: 0.7743 (mt) cc_final: 0.7540 (mt) REVERT: A 508 GLN cc_start: 0.8025 (mt0) cc_final: 0.7290 (mm-40) REVERT: A 601 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6790 (tt) REVERT: B 151 ASP cc_start: 0.7171 (m-30) cc_final: 0.6732 (m-30) REVERT: B 242 GLN cc_start: 0.8171 (mt0) cc_final: 0.7917 (mt0) REVERT: B 262 LEU cc_start: 0.7870 (mt) cc_final: 0.7601 (mt) REVERT: B 264 LYS cc_start: 0.6773 (mttt) cc_final: 0.6378 (mtpt) REVERT: C 195 LEU cc_start: 0.6317 (mt) cc_final: 0.6017 (mt) REVERT: C 264 LYS cc_start: 0.6888 (mttt) cc_final: 0.6459 (mtpt) REVERT: C 335 GLU cc_start: 0.7518 (pt0) cc_final: 0.7133 (pt0) REVERT: C 349 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: C 428 MET cc_start: 0.7527 (mmt) cc_final: 0.7227 (mmt) REVERT: C 534 LYS cc_start: 0.7501 (mttt) cc_final: 0.7137 (mttm) outliers start: 12 outliers final: 5 residues processed: 187 average time/residue: 2.2139 time to fit residues: 467.5419 Evaluate side-chains 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 136 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN B 423 ASN C 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096871 restraints weight = 37964.843| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.66 r_work: 0.2946 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13005 Z= 0.184 Angle : 0.505 5.727 17634 Z= 0.264 Chirality : 0.037 0.117 2007 Planarity : 0.004 0.045 2118 Dihedral : 12.871 136.053 2076 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.03 % Allowed : 14.17 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.80 (0.22), residues: 1593 helix: 2.48 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -1.44 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 178 HIS 0.005 0.001 HIS C 288 PHE 0.018 0.001 PHE A 146 TYR 0.010 0.001 TYR C 553 ARG 0.002 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.05672 ( 979) hydrogen bonds : angle 3.94302 ( 2883) covalent geometry : bond 0.00444 (13005) covalent geometry : angle 0.50523 (17634) *********************** 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 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 5.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8249 (mt0) cc_final: 0.7988 (mt0) REVERT: A 313 LEU cc_start: 0.7986 (mt) cc_final: 0.7741 (mt) REVERT: A 482 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7136 (t0) REVERT: A 601 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7207 (tt) REVERT: B 151 ASP cc_start: 0.7343 (m-30) cc_final: 0.6783 (m-30) REVERT: B 242 GLN cc_start: 0.8343 (mt0) cc_final: 0.8060 (mt0) REVERT: B 260 ASP cc_start: 0.7899 (t0) cc_final: 0.7526 (t0) REVERT: B 262 LEU cc_start: 0.8044 (mt) cc_final: 0.7756 (mt) REVERT: B 264 LYS cc_start: 0.7033 (mttt) cc_final: 0.6633 (mtpt) REVERT: B 497 MET cc_start: 0.7325 (tmt) cc_final: 0.6811 (tmt) REVERT: C 195 LEU cc_start: 0.6497 (mt) cc_final: 0.6190 (mt) REVERT: C 264 LYS cc_start: 0.7128 (mttt) cc_final: 0.6702 (mtpt) REVERT: C 335 GLU cc_start: 0.7632 (pt0) cc_final: 0.7260 (pt0) REVERT: C 349 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: C 428 MET cc_start: 0.7683 (mmt) cc_final: 0.7400 (mmt) REVERT: C 534 LYS cc_start: 0.7703 (mttt) cc_final: 0.7335 (mttm) outliers start: 13 outliers final: 7 residues processed: 187 average time/residue: 2.7709 time to fit residues: 595.5228 Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 7 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN B 423 ASN C 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.098271 restraints weight = 37837.283| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.55 r_work: 0.2996 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13005 Z= 0.161 Angle : 0.485 5.439 17634 Z= 0.253 Chirality : 0.036 0.114 2007 Planarity : 0.004 0.043 2118 Dihedral : 12.747 134.351 2076 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.11 % Allowed : 14.33 % Favored : 84.56 % 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: 2.81 (0.22), residues: 1593 helix: 2.48 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 178 HIS 0.004 0.001 HIS B 288 PHE 0.018 0.001 PHE A 146 TYR 0.010 0.001 TYR C 553 ARG 0.002 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.05277 ( 979) hydrogen bonds : angle 3.90207 ( 2883) covalent geometry : bond 0.00380 (13005) covalent geometry : angle 0.48459 (17634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 1.920 Fit side-chains revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8185 (mt0) cc_final: 0.7953 (mt0) REVERT: A 313 LEU cc_start: 0.7814 (mt) cc_final: 0.7567 (mt) REVERT: A 482 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7047 (t0) REVERT: A 601 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6791 (tt) REVERT: B 151 ASP cc_start: 0.7128 (m-30) cc_final: 0.6651 (m-30) REVERT: B 242 GLN cc_start: 0.8217 (mt0) cc_final: 0.7931 (mt0) REVERT: B 260 ASP cc_start: 0.7673 (t0) cc_final: 0.7305 (t0) REVERT: B 262 LEU cc_start: 0.7831 (mt) cc_final: 0.7572 (mt) REVERT: B 264 LYS cc_start: 0.6727 (mttt) cc_final: 0.6329 (mtpt) REVERT: B 497 MET cc_start: 0.7260 (tmt) cc_final: 0.6748 (tmt) REVERT: C 195 LEU cc_start: 0.6289 (mt) cc_final: 0.5994 (mt) REVERT: C 264 LYS cc_start: 0.6915 (mttt) cc_final: 0.6440 (mtpt) REVERT: C 335 GLU cc_start: 0.7489 (pt0) cc_final: 0.7096 (pt0) REVERT: C 349 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: C 428 MET cc_start: 0.7475 (mmt) cc_final: 0.7145 (mmt) REVERT: C 526 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7174 (t80) REVERT: C 534 LYS cc_start: 0.7449 (mttt) cc_final: 0.7059 (mttm) outliers start: 14 outliers final: 8 residues processed: 187 average time/residue: 1.9495 time to fit residues: 414.6089 Evaluate side-chains 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN B 423 ASN C 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100771 restraints weight = 37691.849| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.55 r_work: 0.3043 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13005 Z= 0.109 Angle : 0.438 4.671 17634 Z= 0.228 Chirality : 0.035 0.111 2007 Planarity : 0.003 0.040 2118 Dihedral : 12.034 128.955 2076 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.95 % Allowed : 14.49 % Favored : 84.56 % 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: 3.25 (0.22), residues: 1593 helix: 2.79 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -1.32 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 323 HIS 0.002 0.000 HIS C 288 PHE 0.021 0.001 PHE A 146 TYR 0.006 0.001 TYR C 553 ARG 0.002 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 979) hydrogen bonds : angle 3.70997 ( 2883) covalent geometry : bond 0.00241 (13005) covalent geometry : angle 0.43809 (17634) ********************** 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 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7071 (t0) REVERT: A 601 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6802 (tt) REVERT: B 151 ASP cc_start: 0.7138 (m-30) cc_final: 0.6640 (m-30) REVERT: B 242 GLN cc_start: 0.8188 (mt0) cc_final: 0.7933 (mt0) REVERT: B 262 LEU cc_start: 0.7861 (mt) cc_final: 0.7591 (mt) REVERT: B 264 LYS cc_start: 0.6754 (mttt) cc_final: 0.6371 (mtpt) REVERT: C 195 LEU cc_start: 0.6414 (mt) cc_final: 0.6148 (mt) REVERT: C 264 LYS cc_start: 0.6909 (mttt) cc_final: 0.6480 (mtpt) REVERT: C 335 GLU cc_start: 0.7531 (pt0) cc_final: 0.7160 (pt0) REVERT: C 349 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: C 428 MET cc_start: 0.7491 (mmt) cc_final: 0.7202 (mmt) REVERT: C 534 LYS cc_start: 0.7494 (mttt) cc_final: 0.7140 (mttm) outliers start: 12 outliers final: 6 residues processed: 187 average time/residue: 1.8701 time to fit residues: 394.1144 Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 1 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN A 620 ASN B 423 ASN C 423 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097959 restraints weight = 37732.794| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.53 r_work: 0.3003 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3986 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= 0.181 Angle : 0.504 5.738 17634 Z= 0.264 Chirality : 0.037 0.115 2007 Planarity : 0.004 0.044 2118 Dihedral : 12.669 134.533 2076 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.71 % Allowed : 14.89 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.84 (0.22), residues: 1593 helix: 2.51 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 178 HIS 0.005 0.001 HIS C 288 PHE 0.017 0.001 PHE C 413 TYR 0.011 0.001 TYR C 553 ARG 0.002 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.05616 ( 979) hydrogen bonds : angle 3.93574 ( 2883) covalent geometry : bond 0.00433 (13005) covalent geometry : angle 0.50427 (17634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18486.36 seconds wall clock time: 327 minutes 31.91 seconds (19651.91 seconds total)