Starting phenix.real_space_refine on Sun Aug 9 18:37:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u43_41873/08_2026/8u43_41873_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u43_41873/08_2026/8u43_41873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u43_41873/08_2026/8u43_41873_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u43_41873/08_2026/8u43_41873_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u43_41873/08_2026/8u43_41873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u43_41873/08_2026/8u43_41873.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.094 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 Br 8 7.06 5 P 16 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 12092 2.51 5 N 2924 2.21 5 O 3450 1.98 5 H 18060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36651 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 9019 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 540} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 9019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 9019 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 540} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 9019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 9019 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 540} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 9019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 9019 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 540} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {' NA': 1, 'PCW': 1, 'V5H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'PCW': 1, 'V5H': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'PCW': 1, 'V5H': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'PCW': 1, 'V5H': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 35 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 35 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Time building chain proxies: 6.23, per 1000 atoms: 0.17 Number of scatterers: 36651 At special positions: 0 Unit cell: (136.105, 136.105, 111.89, 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) Br 8 34.99 S 100 16.00 P 16 15.00 Na 1 11.00 O 3450 8.00 N 2924 7.00 C 12092 6.00 H 18060 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: 3.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4200 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 63.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.516A pdb=" N LEU A 365 " --> pdb=" O CYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.778A pdb=" N ASN A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 532 removed outlier: 3.720A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.994A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.928A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.516A pdb=" N LEU B 365 " --> pdb=" O CYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.779A pdb=" N ASN B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.721A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.994A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.928A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 689 Processing helix chain 'B' and resid 689 through 711 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.516A pdb=" N LEU C 365 " --> pdb=" O CYS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.778A pdb=" N ASN C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 removed outlier: 3.720A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 536 through 551 Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.994A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 640 removed outlier: 3.928A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 643 No H-bonds generated for 'chain 'C' and resid 641 through 643' Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 689 through 711 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 362 through 366 removed outlier: 3.516A pdb=" N LEU D 365 " --> pdb=" O CYS D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.778A pdb=" N ASN D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 removed outlier: 3.720A pdb=" N ILE D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.994A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.928A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 689 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 374 removed outlier: 6.699A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 726 through 730 removed outlier: 5.034A pdb=" N GLY A 729 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 374 removed outlier: 6.698A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 726 through 730 removed outlier: 5.035A pdb=" N GLY B 729 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 368 through 374 removed outlier: 6.699A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 726 through 730 removed outlier: 5.034A pdb=" N GLY C 729 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 368 through 374 removed outlier: 6.699A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 726 through 730 removed outlier: 5.034A pdb=" N GLY D 729 " --> pdb=" O ASP D 737 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 3012 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.31 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 18024 1.06 - 1.28: 2868 1.28 - 1.50: 8118 1.50 - 1.72: 7766 1.72 - 1.94: 172 Bond restraints: 36948 Sorted by residual: bond pdb=" O28 V5H B 801 " pdb=" P27 V5H B 801 " ideal model delta sigma weight residual 1.506 1.355 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" O28 V5H C 801 " pdb=" P27 V5H C 801 " ideal model delta sigma weight residual 1.506 1.355 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" O28 V5H D 801 " pdb=" P27 V5H D 801 " ideal model delta sigma weight residual 1.506 1.355 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O28 V5H A 801 " pdb=" P27 V5H A 801 " ideal model delta sigma weight residual 1.506 1.355 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CA SER D 722 " pdb=" CB SER D 722 " ideal model delta sigma weight residual 1.539 1.443 0.096 1.36e-02 5.41e+03 4.97e+01 ... (remaining 36943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.12: 66250 9.12 - 18.24: 84 18.24 - 27.36: 20 27.36 - 36.49: 4 36.49 - 45.61: 8 Bond angle restraints: 66366 Sorted by residual: angle pdb=" C GLU D 761 " pdb=" N ASP D 762 " pdb=" H ASP D 762 " ideal model delta sigma weight residual 124.25 78.64 45.61 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C GLU A 761 " pdb=" N ASP A 762 " pdb=" H ASP A 762 " ideal model delta sigma weight residual 124.25 78.68 45.57 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C GLU B 761 " pdb=" N ASP B 762 " pdb=" H ASP B 762 " ideal model delta sigma weight residual 124.25 78.68 45.57 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C GLU C 761 " pdb=" N ASP C 762 " pdb=" H ASP C 762 " ideal model delta sigma weight residual 124.25 78.74 45.51 3.00e+00 1.11e-01 2.30e+02 angle pdb=" CA ASP C 762 " pdb=" N ASP C 762 " pdb=" H ASP C 762 " ideal model delta sigma weight residual 113.95 68.72 45.23 3.00e+00 1.11e-01 2.27e+02 ... (remaining 66361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.28: 16431 29.28 - 58.56: 1048 58.56 - 87.85: 193 87.85 - 117.13: 4 117.13 - 146.41: 16 Dihedral angle restraints: 17692 sinusoidal: 9576 harmonic: 8116 Sorted by residual: dihedral pdb=" C ARG B 721 " pdb=" N ARG B 721 " pdb=" CA ARG B 721 " pdb=" CB ARG B 721 " ideal model delta harmonic sigma weight residual -122.60 -109.50 -13.10 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" C ARG A 721 " pdb=" N ARG A 721 " pdb=" CA ARG A 721 " pdb=" CB ARG A 721 " ideal model delta harmonic sigma weight residual -122.60 -109.54 -13.06 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" C ARG C 721 " pdb=" N ARG C 721 " pdb=" CA ARG C 721 " pdb=" CB ARG C 721 " ideal model delta harmonic sigma weight residual -122.60 -109.54 -13.06 0 2.50e+00 1.60e-01 2.73e+01 ... (remaining 17689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 2808 0.188 - 0.376: 38 0.376 - 0.565: 2 0.565 - 0.753: 0 0.753 - 0.941: 4 Chirality restraints: 2852 Sorted by residual: chirality pdb=" C31 V5H A 801 " pdb=" C32 V5H A 801 " pdb=" C48 V5H A 801 " pdb=" O30 V5H A 801 " both_signs ideal model delta sigma weight residual False 2.44 1.50 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" C31 V5H D 801 " pdb=" C32 V5H D 801 " pdb=" C48 V5H D 801 " pdb=" O30 V5H D 801 " both_signs ideal model delta sigma weight residual False 2.44 1.51 0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C31 V5H B 801 " pdb=" C32 V5H B 801 " pdb=" C48 V5H B 801 " pdb=" O30 V5H B 801 " both_signs ideal model delta sigma weight residual False 2.44 1.51 0.94 2.00e-01 2.50e+01 2.20e+01 ... (remaining 2849 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 509 " 0.066 2.00e-02 2.50e+03 1.16e-01 1.35e+02 pdb=" N SER B 510 " -0.200 2.00e-02 2.50e+03 pdb=" CA SER B 510 " 0.052 2.00e-02 2.50e+03 pdb=" H SER B 510 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 509 " -0.066 2.00e-02 2.50e+03 1.16e-01 1.35e+02 pdb=" N SER C 510 " 0.200 2.00e-02 2.50e+03 pdb=" CA SER C 510 " -0.052 2.00e-02 2.50e+03 pdb=" H SER C 510 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 509 " 0.066 2.00e-02 2.50e+03 1.16e-01 1.35e+02 pdb=" N SER A 510 " -0.200 2.00e-02 2.50e+03 pdb=" CA SER A 510 " 0.052 2.00e-02 2.50e+03 pdb=" H SER A 510 " 0.083 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.31: 8567 2.31 - 2.91: 82538 2.91 - 3.51: 101787 3.51 - 4.10: 141914 4.10 - 4.70: 219196 Nonbonded interactions: 554002 Sorted by model distance: nonbonded pdb=" O ALA D 295 " pdb=" HZ2 LYS D 345 " model vdw 1.713 2.450 nonbonded pdb=" O ALA C 295 " pdb=" HZ2 LYS C 345 " model vdw 1.713 2.450 nonbonded pdb=" O ALA A 295 " pdb=" HZ2 LYS A 345 " model vdw 1.713 2.450 nonbonded pdb=" O ALA B 295 " pdb=" HZ2 LYS B 345 " model vdw 1.713 2.450 nonbonded pdb=" H LYS C 466 " pdb=" OD2 ASP C 471 " model vdw 1.732 2.450 ... (remaining 553997 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 186 through 802) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 5.130 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: 0.230 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 33.610 Find NCS groups from input model: 0.690 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 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 : 0.008 0.151 18888 Z= 0.439 Angle : 1.377 32.525 25540 Z= 0.624 Chirality : 0.061 0.941 2852 Planarity : 0.006 0.100 3132 Dihedral : 21.563 146.410 7164 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.65 % Allowed : 18.08 % Favored : 79.28 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2216 helix: 1.87 (0.14), residues: 1348 sheet: 1.40 (0.60), residues: 84 loop : -1.73 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 500 TYR 0.020 0.002 TYR C 511 PHE 0.009 0.001 PHE D 649 TRP 0.010 0.002 TRP C 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.44 (18888) covalent geometry : angle 1.37700 / 0.62 (25540) hydrogen bonds : bond 0.15064 / 9.78 ( 1040) hydrogen bonds : angle 4.81132 / 3.47 ( 3012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.6690 (t0) cc_final: 0.6464 (t0) REVERT: A 304 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.5823 (t80) REVERT: A 311 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6534 (mm-30) REVERT: A 478 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6627 (mt-10) REVERT: A 500 ARG cc_start: 0.7400 (mmm160) cc_final: 0.7061 (mmt180) REVERT: A 579 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6654 (mtm180) REVERT: A 582 PHE cc_start: 0.7039 (t80) cc_final: 0.6717 (t80) REVERT: A 710 LYS cc_start: 0.7227 (ttmm) cc_final: 0.6826 (mttp) REVERT: B 213 ASN cc_start: 0.6691 (t0) cc_final: 0.6466 (t0) REVERT: B 304 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.5799 (t80) REVERT: B 311 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6421 (mm-30) REVERT: B 478 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6643 (mt-10) REVERT: B 500 ARG cc_start: 0.7401 (mmm160) cc_final: 0.7062 (mmt180) REVERT: B 579 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6652 (mtm180) REVERT: B 582 PHE cc_start: 0.6949 (t80) cc_final: 0.6624 (t80) REVERT: B 710 LYS cc_start: 0.7233 (ttmm) cc_final: 0.6834 (mttp) REVERT: C 213 ASN cc_start: 0.6697 (t0) cc_final: 0.6471 (t0) REVERT: C 304 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.5801 (t80) REVERT: C 311 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6419 (mm-30) REVERT: C 478 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6593 (mt-10) REVERT: C 500 ARG cc_start: 0.7355 (mmm160) cc_final: 0.7018 (mmt180) REVERT: C 579 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6646 (mtm180) REVERT: C 582 PHE cc_start: 0.6952 (t80) cc_final: 0.6623 (t80) REVERT: C 710 LYS cc_start: 0.7224 (ttmm) cc_final: 0.6824 (mttp) REVERT: D 304 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.5776 (t80) REVERT: D 311 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6444 (mm-30) REVERT: D 478 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6575 (mt-10) REVERT: D 500 ARG cc_start: 0.7316 (mmm160) cc_final: 0.7018 (mmt180) REVERT: D 579 ARG cc_start: 0.6951 (mtm-85) cc_final: 0.6652 (mtm180) REVERT: D 582 PHE cc_start: 0.6955 (t80) cc_final: 0.6630 (t80) REVERT: D 710 LYS cc_start: 0.7241 (ttmm) cc_final: 0.6841 (mttp) outliers start: 52 outliers final: 16 residues processed: 265 average time/residue: 1.3473 time to fit residues: 401.0403 Evaluate side-chains 212 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.0370 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN A 755 ASN B 393 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN C 393 ASN C 755 ASN D 393 ASN D 755 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.190583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133469 restraints weight = 37644.408| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.64 r_work: 0.3213 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work: 0.2940 rms_B_bonded: 4.80 restraints_weight: 0.1250 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18888 Z= 0.126 Angle : 0.636 25.929 25540 Z= 0.320 Chirality : 0.036 0.157 2852 Planarity : 0.004 0.041 3132 Dihedral : 16.757 154.185 2992 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.65 % Allowed : 17.92 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.18), residues: 2216 helix: 2.31 (0.14), residues: 1352 sheet: 1.31 (0.60), residues: 84 loop : -1.62 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 500 TYR 0.012 0.001 TYR D 584 PHE 0.015 0.001 PHE D 304 TRP 0.011 0.001 TRP D 697 HIS 0.006 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (18888) covalent geometry : angle 0.63634 / 0.32 (25540) hydrogen bonds : bond 0.06203 / 4.16 ( 1040) hydrogen bonds : angle 3.97511 / 2.86 ( 3012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7616 (t80) REVERT: A 458 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6729 (mt-10) REVERT: A 500 ARG cc_start: 0.7406 (mmm160) cc_final: 0.7122 (mmt180) REVERT: A 710 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7356 (mttp) REVERT: A 727 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.6300 (pp30) REVERT: B 304 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7624 (t80) REVERT: B 458 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6744 (mt-10) REVERT: B 500 ARG cc_start: 0.7404 (mmm160) cc_final: 0.7122 (mmt180) REVERT: B 710 LYS cc_start: 0.7547 (ttmm) cc_final: 0.7345 (mttp) REVERT: B 727 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.6222 (pp30) REVERT: C 304 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7565 (t80) REVERT: C 458 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6739 (mt-10) REVERT: C 500 ARG cc_start: 0.7396 (mmm160) cc_final: 0.7118 (mmt180) REVERT: C 710 LYS cc_start: 0.7571 (ttmm) cc_final: 0.7354 (mttp) REVERT: C 727 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.6286 (pp30) REVERT: D 304 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7561 (t80) REVERT: D 458 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6749 (mt-10) REVERT: D 500 ARG cc_start: 0.7359 (mmm160) cc_final: 0.7105 (mmt180) REVERT: D 710 LYS cc_start: 0.7571 (ttmm) cc_final: 0.7351 (mttp) REVERT: D 727 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.6304 (pp30) outliers start: 52 outliers final: 28 residues processed: 233 average time/residue: 1.4294 time to fit residues: 375.2909 Evaluate side-chains 206 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 458 GLU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 14 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN A 393 ASN A 467 ASN B 228 GLN B 393 ASN B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 393 ASN C 467 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN D 228 GLN D 393 ASN D 467 ASN D 748 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150392 restraints weight = 38195.190| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 0.72 r_work: 0.3310 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work: 0.3009 rms_B_bonded: 3.25 restraints_weight: 0.1250 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 18888 Z= 0.211 Angle : 0.753 25.653 25540 Z= 0.378 Chirality : 0.042 0.227 2852 Planarity : 0.005 0.041 3132 Dihedral : 18.398 157.793 2988 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.00 % Allowed : 16.96 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.18), residues: 2216 helix: 1.96 (0.13), residues: 1332 sheet: 0.44 (0.58), residues: 92 loop : -1.83 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 500 TYR 0.020 0.002 TYR A 584 PHE 0.020 0.002 PHE C 649 TRP 0.020 0.003 TRP B 697 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (18888) covalent geometry : angle 0.75341 / 0.38 (25540) hydrogen bonds : bond 0.08634 / 5.78 ( 1040) hydrogen bonds : angle 4.10172 / 2.96 ( 3012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.990 Fit side-chains REVERT: A 304 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7611 (t80) REVERT: A 458 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: A 709 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 721 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.5427 (pmt170) REVERT: A 727 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5928 (pp30) REVERT: B 304 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7616 (t80) REVERT: B 458 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6799 (mt-10) REVERT: B 709 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7409 (mt-10) REVERT: B 721 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5430 (pmt170) REVERT: B 727 GLN cc_start: 0.6465 (OUTLIER) cc_final: 0.5923 (pp30) REVERT: C 304 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7529 (t80) REVERT: C 458 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: C 709 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 721 ARG cc_start: 0.6003 (OUTLIER) cc_final: 0.5404 (pmt170) REVERT: C 727 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.5926 (pp30) REVERT: D 304 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7605 (t80) REVERT: D 458 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6817 (mt-10) REVERT: D 709 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7497 (mt-10) REVERT: D 721 ARG cc_start: 0.6010 (OUTLIER) cc_final: 0.5414 (pmt170) REVERT: D 727 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.6163 (pp30) outliers start: 59 outliers final: 20 residues processed: 234 average time/residue: 1.2692 time to fit residues: 339.4099 Evaluate side-chains 218 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 458 GLU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 50 optimal weight: 0.0170 chunk 59 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN A 467 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN B 393 ASN B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN C 393 ASN C 467 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN D 393 ASN D 467 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.186191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153338 restraints weight = 38789.137| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 0.70 r_work: 0.3356 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work: 0.3031 rms_B_bonded: 3.70 restraints_weight: 0.1250 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18888 Z= 0.146 Angle : 0.655 25.803 25540 Z= 0.331 Chirality : 0.037 0.149 2852 Planarity : 0.005 0.062 3132 Dihedral : 16.960 154.311 2988 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.55 % Allowed : 17.11 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2216 helix: 2.21 (0.14), residues: 1332 sheet: 0.44 (0.58), residues: 92 loop : -1.88 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 500 TYR 0.013 0.002 TYR C 584 PHE 0.013 0.002 PHE D 304 TRP 0.014 0.002 TRP B 697 HIS 0.004 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (18888) covalent geometry : angle 0.65464 / 0.33 (25540) hydrogen bonds : bond 0.07046 / 4.72 ( 1040) hydrogen bonds : angle 3.96697 / 2.86 ( 3012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7522 (t80) REVERT: A 458 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6812 (mt-10) REVERT: A 500 ARG cc_start: 0.7558 (mmm160) cc_final: 0.7256 (mmt180) REVERT: A 711 SER cc_start: 0.6797 (t) cc_final: 0.6593 (t) REVERT: A 721 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5421 (pmt170) REVERT: A 727 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.6121 (pp30) REVERT: B 304 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7520 (t80) REVERT: B 458 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6818 (mt-10) REVERT: B 500 ARG cc_start: 0.7561 (mmm160) cc_final: 0.7256 (mmt180) REVERT: B 711 SER cc_start: 0.6754 (t) cc_final: 0.6549 (t) REVERT: B 721 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.5423 (pmt170) REVERT: B 727 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.6105 (pp30) REVERT: C 304 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7517 (t80) REVERT: C 458 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: C 500 ARG cc_start: 0.7556 (mmm160) cc_final: 0.7258 (mmt180) REVERT: C 711 SER cc_start: 0.6820 (t) cc_final: 0.6617 (t) REVERT: C 721 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.5430 (pmt170) REVERT: C 727 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.6115 (pp30) REVERT: D 304 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7516 (t80) REVERT: D 458 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: D 500 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7254 (mmt180) REVERT: D 721 ARG cc_start: 0.5891 (OUTLIER) cc_final: 0.5429 (pmt170) REVERT: D 727 GLN cc_start: 0.6423 (OUTLIER) cc_final: 0.6123 (pp30) outliers start: 50 outliers final: 22 residues processed: 228 average time/residue: 1.2932 time to fit residues: 336.2970 Evaluate side-chains 214 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 458 GLU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN B 393 ASN B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN C 393 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN D 393 ASN D 467 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.186883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145620 restraints weight = 38968.903| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 0.87 r_work: 0.3395 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work: 0.3145 rms_B_bonded: 4.72 restraints_weight: 0.1250 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18888 Z= 0.132 Angle : 0.638 25.931 25540 Z= 0.322 Chirality : 0.036 0.136 2852 Planarity : 0.004 0.042 3132 Dihedral : 16.215 152.751 2988 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.24 % Allowed : 16.80 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2216 helix: 2.31 (0.14), residues: 1332 sheet: 0.37 (0.57), residues: 92 loop : -1.89 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 500 TYR 0.012 0.001 TYR C 584 PHE 0.012 0.001 PHE D 304 TRP 0.012 0.002 TRP A 697 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (18888) covalent geometry : angle 0.63831 / 0.32 (25540) hydrogen bonds : bond 0.06666 / 4.47 ( 1040) hydrogen bonds : angle 3.90884 / 2.82 ( 3012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7651 (t80) REVERT: A 499 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7141 (mmm160) REVERT: A 711 SER cc_start: 0.6779 (t) cc_final: 0.6564 (t) REVERT: A 721 ARG cc_start: 0.5834 (OUTLIER) cc_final: 0.5248 (pmt170) REVERT: A 727 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.6110 (pp30) REVERT: B 304 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7653 (t80) REVERT: B 499 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7096 (mmm160) REVERT: B 711 SER cc_start: 0.6780 (t) cc_final: 0.6564 (t) REVERT: B 721 ARG cc_start: 0.5833 (OUTLIER) cc_final: 0.5347 (pmt170) REVERT: B 727 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.6110 (pp30) REVERT: C 304 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7657 (t80) REVERT: C 499 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7102 (mmm160) REVERT: C 711 SER cc_start: 0.6801 (t) cc_final: 0.6589 (t) REVERT: C 721 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.5229 (pmt170) REVERT: C 727 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.6119 (pp30) REVERT: D 304 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7648 (t80) REVERT: D 499 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7095 (mmm160) REVERT: D 721 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.5210 (pmt170) REVERT: D 727 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.6120 (pp30) outliers start: 44 outliers final: 20 residues processed: 219 average time/residue: 1.2537 time to fit residues: 314.2821 Evaluate side-chains 216 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 499 ARG Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145843 restraints weight = 38670.099| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 0.78 r_work: 0.3281 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work: 0.2980 rms_B_bonded: 3.53 restraints_weight: 0.1250 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 18888 Z= 0.210 Angle : 0.752 25.786 25540 Z= 0.380 Chirality : 0.042 0.213 2852 Planarity : 0.006 0.076 3132 Dihedral : 17.741 153.855 2988 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.55 % Allowed : 17.26 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 2216 helix: 1.88 (0.13), residues: 1332 sheet: 0.35 (0.56), residues: 92 loop : -2.07 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 500 TYR 0.020 0.002 TYR B 584 PHE 0.019 0.002 PHE C 649 TRP 0.019 0.003 TRP A 697 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (18888) covalent geometry : angle 0.75155 / 0.38 (25540) hydrogen bonds : bond 0.08636 / 5.78 ( 1040) hydrogen bonds : angle 4.09238 / 2.96 ( 3012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7408 (t80) REVERT: A 499 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6984 (mmm160) REVERT: A 500 ARG cc_start: 0.7637 (mmm160) cc_final: 0.7263 (mmt180) REVERT: A 709 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7497 (mt-10) REVERT: B 304 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7406 (t80) REVERT: B 499 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6883 (mmm160) REVERT: B 500 ARG cc_start: 0.7634 (mmm160) cc_final: 0.7256 (mmt180) REVERT: B 709 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7489 (mt-10) REVERT: C 304 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7410 (t80) REVERT: C 499 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6897 (mmm160) REVERT: C 500 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7256 (mmt180) REVERT: C 709 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7489 (mt-10) REVERT: D 304 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7410 (t80) REVERT: D 499 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6893 (mmm160) REVERT: D 500 ARG cc_start: 0.7635 (mmm160) cc_final: 0.7255 (mmt180) outliers start: 50 outliers final: 32 residues processed: 220 average time/residue: 1.2777 time to fit residues: 321.3398 Evaluate side-chains 210 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 499 ARG Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 83 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.185247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152875 restraints weight = 39150.735| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 0.67 r_work: 0.3335 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work: 0.3019 rms_B_bonded: 3.54 restraints_weight: 0.1250 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18888 Z= 0.155 Angle : 0.672 26.247 25540 Z= 0.341 Chirality : 0.037 0.124 2852 Planarity : 0.005 0.059 3132 Dihedral : 16.507 153.154 2988 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.24 % Allowed : 17.26 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2216 helix: 2.12 (0.14), residues: 1332 sheet: 0.22 (0.56), residues: 92 loop : -2.06 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 500 TYR 0.014 0.002 TYR D 584 PHE 0.016 0.002 PHE B 582 TRP 0.015 0.002 TRP D 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (18888) covalent geometry : angle 0.67168 / 0.34 (25540) hydrogen bonds : bond 0.07316 / 4.90 ( 1040) hydrogen bonds : angle 3.97615 / 2.87 ( 3012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 1.029 Fit side-chains REVERT: A 304 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7363 (t80) REVERT: A 499 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6839 (mmm160) REVERT: A 500 ARG cc_start: 0.7634 (mmm160) cc_final: 0.7281 (mmt180) REVERT: A 716 MET cc_start: 0.2695 (mtp) cc_final: 0.2459 (mpp) REVERT: A 727 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.6089 (pp30) REVERT: B 304 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7391 (t80) REVERT: B 499 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6853 (mmm160) REVERT: B 500 ARG cc_start: 0.7643 (mmm160) cc_final: 0.7277 (mmt180) REVERT: B 716 MET cc_start: 0.2640 (mtp) cc_final: 0.2413 (mpp) REVERT: B 727 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.6078 (pp30) REVERT: C 304 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7371 (t80) REVERT: C 499 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6848 (mmm160) REVERT: C 500 ARG cc_start: 0.7637 (mmm160) cc_final: 0.7279 (mmt180) REVERT: C 716 MET cc_start: 0.2643 (mtp) cc_final: 0.2410 (mpp) REVERT: C 727 GLN cc_start: 0.6410 (OUTLIER) cc_final: 0.6086 (pp30) REVERT: D 304 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7385 (t80) REVERT: D 499 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6839 (mmm160) REVERT: D 500 ARG cc_start: 0.7651 (mmm160) cc_final: 0.7278 (mmt180) REVERT: D 716 MET cc_start: 0.2700 (mtp) cc_final: 0.2461 (mpp) REVERT: D 727 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.6090 (pp30) outliers start: 44 outliers final: 29 residues processed: 224 average time/residue: 1.2495 time to fit residues: 320.1860 Evaluate side-chains 220 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 499 ARG Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 75 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.186862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.154074 restraints weight = 39339.645| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 0.68 r_work: 0.3370 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work: 0.3090 rms_B_bonded: 3.20 restraints_weight: 0.1250 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18888 Z= 0.131 Angle : 0.635 26.389 25540 Z= 0.321 Chirality : 0.036 0.124 2852 Planarity : 0.004 0.049 3132 Dihedral : 15.449 150.769 2988 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.29 % Allowed : 17.31 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.18), residues: 2216 helix: 2.31 (0.14), residues: 1332 sheet: 0.18 (0.56), residues: 92 loop : -2.03 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 500 TYR 0.011 0.001 TYR D 584 PHE 0.013 0.001 PHE A 304 TRP 0.012 0.002 TRP B 697 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (18888) covalent geometry : angle 0.63509 / 0.32 (25540) hydrogen bonds : bond 0.06514 / 4.37 ( 1040) hydrogen bonds : angle 3.90644 / 2.81 ( 3012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 1.163 Fit side-chains REVERT: A 304 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7367 (t80) REVERT: A 499 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6855 (mmm160) REVERT: A 727 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.6085 (pp30) REVERT: B 304 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7366 (t80) REVERT: B 499 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6859 (mmm160) REVERT: B 500 ARG cc_start: 0.7556 (mmm160) cc_final: 0.7264 (mmt180) REVERT: B 727 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.5987 (pp30) REVERT: C 304 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7373 (t80) REVERT: C 499 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6854 (mmm160) REVERT: C 500 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7268 (mmt180) REVERT: C 727 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.6081 (pp30) REVERT: D 304 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7379 (t80) REVERT: D 499 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6842 (mmm160) REVERT: D 500 ARG cc_start: 0.7564 (mmm160) cc_final: 0.7267 (mmt180) REVERT: D 727 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.6072 (pp30) outliers start: 45 outliers final: 32 residues processed: 221 average time/residue: 1.2602 time to fit residues: 318.6967 Evaluate side-chains 221 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 499 ARG Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.185856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.150223 restraints weight = 38939.276| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 0.71 r_work: 0.3345 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3069 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18888 Z= 0.150 Angle : 0.678 26.338 25540 Z= 0.340 Chirality : 0.037 0.136 2852 Planarity : 0.005 0.118 3132 Dihedral : 15.439 150.527 2988 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.29 % Allowed : 17.92 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.18), residues: 2216 helix: 2.22 (0.14), residues: 1328 sheet: 0.09 (0.56), residues: 92 loop : -2.09 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 500 TYR 0.014 0.002 TYR C 584 PHE 0.017 0.002 PHE B 582 TRP 0.014 0.002 TRP B 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (18888) covalent geometry : angle 0.67845 / 0.34 (25540) hydrogen bonds : bond 0.07097 / 4.76 ( 1040) hydrogen bonds : angle 3.93984 / 2.84 ( 3012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7355 (t80) REVERT: A 499 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6889 (mmm160) REVERT: A 500 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7276 (mmt180) REVERT: B 304 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7353 (t80) REVERT: B 499 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6896 (mmm160) REVERT: C 304 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7362 (t80) REVERT: C 499 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6896 (mmm160) REVERT: D 304 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7360 (t80) REVERT: D 499 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6892 (mmm160) outliers start: 45 outliers final: 36 residues processed: 229 average time/residue: 1.2452 time to fit residues: 326.6411 Evaluate side-chains 229 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 499 ARG Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 214 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.185720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150294 restraints weight = 38199.477| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 0.68 r_work: 0.3310 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work: 0.2994 rms_B_bonded: 4.01 restraints_weight: 0.1250 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18888 Z= 0.156 Angle : 0.684 26.345 25540 Z= 0.344 Chirality : 0.038 0.136 2852 Planarity : 0.006 0.110 3132 Dihedral : 15.371 150.479 2988 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.44 % Allowed : 17.82 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2216 helix: 2.17 (0.14), residues: 1328 sheet: 0.09 (0.56), residues: 92 loop : -2.12 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 500 TYR 0.014 0.002 TYR C 584 PHE 0.016 0.002 PHE B 582 TRP 0.015 0.002 TRP C 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (18888) covalent geometry : angle 0.68447 / 0.34 (25540) hydrogen bonds : bond 0.07267 / 4.88 ( 1040) hydrogen bonds : angle 3.96046 / 2.85 ( 3012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 499 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6871 (mmm160) REVERT: A 500 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7215 (mmt180) REVERT: B 499 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6871 (mmm160) REVERT: B 500 ARG cc_start: 0.7670 (mmm160) cc_final: 0.7354 (mmt180) REVERT: C 499 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6867 (mmm160) REVERT: C 500 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7353 (mmt180) REVERT: D 499 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6860 (mmm160) REVERT: D 500 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7357 (mmt180) outliers start: 48 outliers final: 40 residues processed: 231 average time/residue: 1.2988 time to fit residues: 342.7592 Evaluate side-chains 228 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 727 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 721 ARG Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 499 ARG Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 727 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 46 optimal weight: 2.9990 chunk 174 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 146 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN C 467 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.188963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.148233 restraints weight = 37712.804| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 0.74 r_work: 0.3389 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work: 0.3123 rms_B_bonded: 4.34 restraints_weight: 0.1250 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18888 Z= 0.119 Angle : 0.629 26.505 25540 Z= 0.316 Chirality : 0.035 0.131 2852 Planarity : 0.005 0.101 3132 Dihedral : 14.514 146.977 2988 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.78 % Allowed : 18.69 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 2216 helix: 2.59 (0.14), residues: 1312 sheet: 0.17 (0.55), residues: 92 loop : -1.97 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 500 TYR 0.007 0.001 TYR B 309 PHE 0.012 0.001 PHE A 304 TRP 0.011 0.001 TRP B 697 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (18888) covalent geometry : angle 0.62870 / 0.32 (25540) hydrogen bonds : bond 0.05830 / 3.92 ( 1040) hydrogen bonds : angle 3.83842 / 2.76 ( 3012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15942.53 seconds wall clock time: 269 minutes 41.52 seconds (16181.52 seconds total)