Starting phenix.real_space_refine on Mon Jul 6 17:05:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u43_41873/07_2026/8u43_41873_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u43_41873/07_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_41873/07_2026/8u43_41873_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u43_41873/07_2026/8u43_41873_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u43_41873/07_2026/8u43_41873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u43_41873/07_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-dev-6108/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, 110 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'PCW': 1, 'V5H': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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: 6.42, per 1000 atoms: 0.18 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: 3.07 Conformation dependent library (CDL) restraints added in 786.3 milliseconds 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: 0.54 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: 7.35 Time building geometry restraints manager: 4.14 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: 5.220 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: 0.270 Extract box with map and model: 0.430 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 30.200 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- 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 : 0.825 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: 1.4054 time to fit residues: 418.0833 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 : 0.982 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.189667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133141 restraints weight = 37559.988| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.69 r_work: 0.3199 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1228 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= 0.137 Angle : 0.648 25.917 25540 Z= 0.327 Chirality : 0.037 0.183 2852 Planarity : 0.004 0.040 3132 Dihedral : 16.925 154.703 2992 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.44 % Allowed : 17.87 % Favored : 79.68 % 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: 1.36 (0.18), residues: 2216 helix: 2.24 (0.14), residues: 1352 sheet: 0.58 (0.60), residues: 92 loop : -1.62 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 500 TYR 0.013 0.001 TYR A 584 PHE 0.016 0.001 PHE C 304 TRP 0.012 0.002 TRP A 697 HIS 0.006 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (18888) covalent geometry : angle 0.64803 / 0.33 (25540) hydrogen bonds : bond 0.06532 / 4.38 ( 1040) hydrogen bonds : angle 3.99595 / 2.88 ( 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: 48 poor density : 186 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7568 (t80) REVERT: A 458 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6696 (mt-10) REVERT: A 500 ARG cc_start: 0.7435 (mmm160) cc_final: 0.7181 (mmt180) REVERT: A 727 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.6181 (pp30) REVERT: B 304 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7567 (t80) REVERT: B 458 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: B 500 ARG cc_start: 0.7434 (mmm160) cc_final: 0.7182 (mmt180) REVERT: B 727 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.6128 (pp30) REVERT: C 304 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7519 (t80) REVERT: C 458 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: C 500 ARG cc_start: 0.7409 (mmm160) cc_final: 0.7172 (mmt180) REVERT: C 711 SER cc_start: 0.6704 (t) cc_final: 0.6498 (t) REVERT: C 727 GLN cc_start: 0.6399 (OUTLIER) cc_final: 0.6130 (pp30) REVERT: D 304 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7569 (t80) REVERT: D 458 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6701 (mt-10) REVERT: D 500 ARG cc_start: 0.7387 (mmm160) cc_final: 0.7163 (mmt180) REVERT: D 710 LYS cc_start: 0.7484 (ttmm) cc_final: 0.7282 (mttp) REVERT: D 727 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.6137 (pp30) outliers start: 48 outliers final: 20 residues processed: 233 average time/residue: 1.4553 time to fit residues: 381.8912 Evaluate side-chains 199 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 654 ASP Chi-restraints excluded: chain A residue 721 ARG 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 654 ASP Chi-restraints excluded: chain B residue 721 ARG 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 654 ASP Chi-restraints excluded: chain C residue 721 ARG 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 654 ASP Chi-restraints excluded: chain D residue 721 ARG 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: 5.9990 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 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: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN A 467 ASN B 228 GLN B 467 ASN C 228 GLN C 467 ASN D 228 GLN D 467 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147805 restraints weight = 38267.046| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 0.72 r_work: 0.3304 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.2989 rms_B_bonded: 3.41 restraints_weight: 0.1250 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18888 Z= 0.243 Angle : 0.796 25.576 25540 Z= 0.402 Chirality : 0.044 0.233 2852 Planarity : 0.005 0.045 3132 Dihedral : 19.037 159.342 2988 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.90 % Allowed : 17.21 % Favored : 79.89 % 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: 0.72 (0.18), residues: 2216 helix: 1.79 (0.13), residues: 1332 sheet: 0.53 (0.57), residues: 92 loop : -1.93 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 557 TYR 0.023 0.003 TYR A 584 PHE 0.022 0.003 PHE A 649 TRP 0.022 0.003 TRP D 697 HIS 0.005 0.002 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (18888) covalent geometry : angle 0.79605 / 0.40 (25540) hydrogen bonds : bond 0.09282 / 6.20 ( 1040) hydrogen bonds : angle 4.16477 / 3.01 ( 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 248 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7553 (t80) REVERT: A 709 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7560 (mt-10) REVERT: A 727 GLN cc_start: 0.6502 (OUTLIER) cc_final: 0.6221 (pp30) REVERT: B 304 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7574 (t80) REVERT: B 709 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 727 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.6200 (pp30) REVERT: C 304 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7579 (t80) REVERT: C 709 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7563 (mt-10) REVERT: C 727 GLN cc_start: 0.6488 (OUTLIER) cc_final: 0.6209 (pp30) REVERT: D 304 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7554 (t80) REVERT: D 709 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7556 (mt-10) REVERT: D 727 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6223 (pp30) outliers start: 57 outliers final: 24 residues processed: 240 average time/residue: 1.2314 time to fit residues: 339.1523 Evaluate side-chains 219 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 596 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 ARG 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 596 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 721 ARG 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 596 VAL Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 721 ARG 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 596 VAL Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 721 ARG 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: 10.0000 chunk 103 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 215 optimal weight: 0.0970 chunk 56 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 72 optimal weight: 4.9990 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN A 467 ASN B 393 ASN B 467 ASN C 393 ASN D 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.190749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135244 restraints weight = 39721.369| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.65 r_work: 0.3236 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18888 Z= 0.111 Angle : 0.600 26.060 25540 Z= 0.303 Chirality : 0.034 0.122 2852 Planarity : 0.004 0.042 3132 Dihedral : 15.543 150.197 2988 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.34 % Allowed : 17.57 % Favored : 80.09 % 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: 1.54 (0.18), residues: 2216 helix: 2.48 (0.14), residues: 1352 sheet: 1.44 (0.55), residues: 84 loop : -1.82 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 500 TYR 0.007 0.001 TYR C 738 PHE 0.009 0.001 PHE B 304 TRP 0.011 0.001 TRP D 697 HIS 0.005 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (18888) covalent geometry : angle 0.59973 / 0.30 (25540) hydrogen bonds : bond 0.05262 / 3.52 ( 1040) hydrogen bonds : angle 3.83183 / 2.75 ( 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 240 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 1.039 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: A 304 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7144 (t80) REVERT: A 500 ARG cc_start: 0.7380 (mmm160) cc_final: 0.7110 (mmt180) REVERT: A 600 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: A 721 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.5302 (pmt170) REVERT: A 727 GLN cc_start: 0.6282 (OUTLIER) cc_final: 0.5897 (pp30) REVERT: B 304 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7147 (t80) REVERT: B 458 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: B 500 ARG cc_start: 0.7381 (mmm160) cc_final: 0.7105 (mmt180) REVERT: B 600 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: B 721 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.5312 (pmt170) REVERT: B 727 GLN cc_start: 0.6271 (OUTLIER) cc_final: 0.5977 (pp30) REVERT: C 304 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7157 (t80) REVERT: C 458 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6615 (mt-10) REVERT: C 500 ARG cc_start: 0.7385 (mmm160) cc_final: 0.7118 (mmt180) REVERT: C 600 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: C 721 ARG cc_start: 0.5765 (OUTLIER) cc_final: 0.5189 (pmt170) REVERT: C 727 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5897 (pp30) REVERT: D 304 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7157 (t80) REVERT: D 500 ARG cc_start: 0.7374 (mmm160) cc_final: 0.7108 (mmt180) REVERT: D 600 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7862 (mm-30) REVERT: D 710 LYS cc_start: 0.7381 (ttmm) cc_final: 0.7169 (mttp) REVERT: D 721 ARG cc_start: 0.5784 (OUTLIER) cc_final: 0.5321 (pmt170) REVERT: D 727 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.5992 (pp30) outliers start: 46 outliers final: 12 residues processed: 236 average time/residue: 1.2655 time to fit residues: 341.7274 Evaluate side-chains 222 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 596 VAL Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 721 ARG 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 600 GLU Chi-restraints excluded: chain B residue 721 ARG 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 600 GLU Chi-restraints excluded: chain C residue 721 ARG 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 596 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 721 ARG 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: 4.9990 chunk 203 optimal weight: 1.9990 chunk 171 optimal weight: 0.0050 chunk 24 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN A 467 ASN B 393 ASN B 467 ASN C 393 ASN C 467 ASN D 393 ASN D 467 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.187514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.151181 restraints weight = 39427.623| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 0.75 r_work: 0.3335 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work: 0.3037 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 18888 Z= 0.130 Angle : 0.636 25.986 25540 Z= 0.319 Chirality : 0.036 0.122 2852 Planarity : 0.004 0.037 3132 Dihedral : 15.079 150.531 2988 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.39 % Allowed : 17.46 % Favored : 80.14 % 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: 1.45 (0.18), residues: 2216 helix: 2.48 (0.14), residues: 1332 sheet: 0.64 (0.58), residues: 92 loop : -1.81 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 500 TYR 0.011 0.001 TYR D 584 PHE 0.013 0.001 PHE C 649 TRP 0.011 0.002 TRP D 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (18888) covalent geometry : angle 0.63594 / 0.32 (25540) hydrogen bonds : bond 0.06421 / 4.31 ( 1040) hydrogen bonds : angle 3.82048 / 2.75 ( 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 223 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7492 (t80) REVERT: A 499 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6996 (mmm160) REVERT: A 727 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.6025 (pp30) REVERT: B 304 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7478 (t80) REVERT: B 499 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7000 (mmm160) REVERT: B 721 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5248 (pmt170) REVERT: B 727 GLN cc_start: 0.6262 (OUTLIER) cc_final: 0.6017 (pp30) REVERT: C 304 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7483 (t80) REVERT: C 499 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7020 (mmm160) REVERT: C 727 GLN cc_start: 0.6288 (OUTLIER) cc_final: 0.6034 (pp30) REVERT: D 304 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7484 (t80) REVERT: D 499 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7010 (mmm160) REVERT: D 727 GLN cc_start: 0.6283 (OUTLIER) cc_final: 0.6011 (pp30) outliers start: 47 outliers final: 20 residues processed: 220 average time/residue: 1.3189 time to fit residues: 330.4942 Evaluate side-chains 211 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 499 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 721 ARG 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 499 ARG Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 726 LEU 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 499 ARG Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 721 ARG 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 499 ARG Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 721 ARG 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: 3.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 748 ASN B 748 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN D 748 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.183849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148582 restraints weight = 38940.809| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 0.72 r_work: 0.3312 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3047 rms_B_bonded: 3.09 restraints_weight: 0.1250 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 18888 Z= 0.210 Angle : 0.740 25.786 25540 Z= 0.373 Chirality : 0.041 0.194 2852 Planarity : 0.005 0.087 3132 Dihedral : 16.331 153.204 2988 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.49 % Allowed : 17.62 % Favored : 79.89 % 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: 0.91 (0.18), residues: 2216 helix: 2.05 (0.13), residues: 1328 sheet: 0.40 (0.57), residues: 92 loop : -2.01 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 500 TYR 0.019 0.002 TYR A 584 PHE 0.020 0.002 PHE C 649 TRP 0.019 0.003 TRP A 697 HIS 0.003 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (18888) covalent geometry : angle 0.74043 / 0.37 (25540) hydrogen bonds : bond 0.08393 / 5.62 ( 1040) hydrogen bonds : angle 4.00976 / 2.89 ( 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 236 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 1.023 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 304 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7521 (t80) REVERT: A 499 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6939 (mmm160) REVERT: A 500 ARG cc_start: 0.7576 (mmm160) cc_final: 0.7297 (mmt180) REVERT: A 709 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 727 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.6113 (pp30) REVERT: B 304 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7525 (t80) REVERT: B 499 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6945 (mmm160) REVERT: B 500 ARG cc_start: 0.7583 (mmm160) cc_final: 0.7296 (mmt180) REVERT: B 709 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7427 (mt-10) REVERT: B 727 GLN cc_start: 0.6365 (OUTLIER) cc_final: 0.6096 (pp30) REVERT: C 304 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7414 (t80) REVERT: C 393 ASN cc_start: 0.6955 (OUTLIER) cc_final: 0.6753 (m-40) REVERT: C 458 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6716 (mt-10) REVERT: C 499 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6945 (mmm160) REVERT: C 500 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7301 (mmt180) REVERT: C 709 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7428 (mt-10) REVERT: C 727 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.6105 (pp30) REVERT: D 304 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7406 (t80) REVERT: D 499 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6933 (mmm160) REVERT: D 500 ARG cc_start: 0.7601 (mmm160) cc_final: 0.7277 (mmt180) REVERT: D 709 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7401 (mt-10) REVERT: D 727 GLN cc_start: 0.6382 (OUTLIER) cc_final: 0.6112 (pp30) outliers start: 49 outliers final: 17 residues processed: 229 average time/residue: 1.2736 time to fit residues: 333.2219 Evaluate side-chains 212 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 721 ARG 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 721 ARG 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 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 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 721 ARG 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: 3.9990 chunk 172 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 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: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 748 ASN B 467 ASN B 748 ASN C 393 ASN C 467 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN D 467 ASN D 748 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.185013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.152158 restraints weight = 38878.103| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 0.69 r_work: 0.3335 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3013 rms_B_bonded: 3.70 restraints_weight: 0.1250 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 18888 Z= 0.167 Angle : 0.689 26.255 25540 Z= 0.349 Chirality : 0.038 0.135 2852 Planarity : 0.005 0.059 3132 Dihedral : 15.653 152.664 2988 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.49 % Allowed : 17.11 % 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: 0.95 (0.18), residues: 2216 helix: 2.11 (0.13), residues: 1332 sheet: 0.19 (0.57), residues: 92 loop : -2.05 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 500 TYR 0.014 0.002 TYR D 584 PHE 0.015 0.002 PHE C 649 TRP 0.016 0.002 TRP D 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (18888) covalent geometry : angle 0.68901 / 0.35 (25540) hydrogen bonds : bond 0.07557 / 5.07 ( 1040) hydrogen bonds : angle 3.95580 / 2.85 ( 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 240 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7367 (t80) REVERT: A 499 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6873 (mmm160) REVERT: A 709 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 727 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.6095 (pp30) REVERT: B 304 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7371 (t80) REVERT: B 499 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6885 (mmm160) REVERT: B 709 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 727 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.6060 (pp30) REVERT: C 304 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7389 (t80) REVERT: C 458 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: C 499 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6887 (mmm160) REVERT: C 709 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 727 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.6095 (pp30) REVERT: D 304 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7379 (t80) REVERT: D 499 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6871 (mmm160) REVERT: D 500 ARG cc_start: 0.7665 (mmm160) cc_final: 0.7300 (mmt180) REVERT: D 709 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7502 (mt-10) REVERT: D 727 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.6087 (pp30) outliers start: 49 outliers final: 28 residues processed: 238 average time/residue: 1.2321 time to fit residues: 336.1519 Evaluate side-chains 232 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 471 ASP 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 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 471 ASP 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 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 471 ASP 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 721 ARG 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 727 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 0.5980 chunk 199 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN C 467 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.186394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155299 restraints weight = 38609.142| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 0.67 r_work: 0.3361 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work: 0.3053 rms_B_bonded: 3.61 restraints_weight: 0.1250 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18888 Z= 0.139 Angle : 0.655 26.344 25540 Z= 0.331 Chirality : 0.036 0.122 2852 Planarity : 0.005 0.096 3132 Dihedral : 15.174 151.423 2988 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.29 % Allowed : 17.87 % Favored : 79.84 % 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: 1.11 (0.18), residues: 2216 helix: 2.27 (0.14), residues: 1332 sheet: 0.27 (0.56), residues: 92 loop : -2.06 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 500 TYR 0.012 0.002 TYR B 738 PHE 0.013 0.001 PHE A 304 TRP 0.013 0.002 TRP D 697 HIS 0.003 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (18888) covalent geometry : angle 0.65520 / 0.33 (25540) hydrogen bonds : bond 0.06845 / 4.59 ( 1040) hydrogen bonds : angle 3.93337 / 2.83 ( 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 230 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 499 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6881 (mmm160) REVERT: A 500 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7365 (mmt180) REVERT: A 727 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.6026 (pp30) REVERT: B 304 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7475 (t80) REVERT: B 499 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6889 (mmm160) REVERT: B 500 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7362 (mmt180) REVERT: B 727 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.5978 (pp30) REVERT: C 304 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7385 (t80) REVERT: C 458 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6715 (mt-10) REVERT: C 499 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6892 (mmm160) REVERT: C 500 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7371 (mmt180) REVERT: C 727 GLN cc_start: 0.6299 (OUTLIER) cc_final: 0.6026 (pp30) REVERT: D 304 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7387 (t80) REVERT: D 499 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6853 (mmm160) REVERT: D 727 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.6025 (pp30) outliers start: 45 outliers final: 28 residues processed: 228 average time/residue: 1.2266 time to fit residues: 321.4552 Evaluate side-chains 225 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 471 ASP 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 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 471 ASP 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 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 471 ASP 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 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 727 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 2.9990 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: 0.8980 chunk 20 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 106 optimal weight: 0.0370 chunk 194 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 748 ASN B 467 ASN B 748 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN C 748 ASN D 467 ASN D 748 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.186922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149362 restraints weight = 37803.706| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 0.68 r_work: 0.3362 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3047 rms_B_bonded: 3.38 restraints_weight: 0.1250 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18888 Z= 0.137 Angle : 0.653 26.386 25540 Z= 0.330 Chirality : 0.036 0.124 2852 Planarity : 0.005 0.092 3132 Dihedral : 15.030 149.791 2988 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.14 % Allowed : 18.38 % Favored : 79.48 % 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: 1.17 (0.18), residues: 2216 helix: 2.33 (0.14), residues: 1332 sheet: 0.23 (0.56), residues: 92 loop : -2.05 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 500 TYR 0.011 0.001 TYR D 584 PHE 0.013 0.001 PHE C 304 TRP 0.012 0.002 TRP C 697 HIS 0.003 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (18888) covalent geometry : angle 0.65288 / 0.33 (25540) hydrogen bonds : bond 0.06664 / 4.48 ( 1040) hydrogen bonds : angle 3.90857 / 2.82 ( 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 231 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6805 (mmm160) REVERT: A 500 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7283 (mmt180) REVERT: A 727 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5967 (pp30) REVERT: B 304 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7317 (t80) REVERT: B 499 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6812 (mmm160) REVERT: B 500 ARG cc_start: 0.7637 (mmm160) cc_final: 0.7289 (mmt180) REVERT: B 727 GLN cc_start: 0.6240 (OUTLIER) cc_final: 0.5982 (pp30) REVERT: C 304 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7325 (t80) REVERT: C 458 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6706 (mt-10) REVERT: C 499 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6816 (mmm160) REVERT: C 500 ARG cc_start: 0.7641 (mmm160) cc_final: 0.7297 (mmt180) REVERT: C 727 GLN cc_start: 0.6277 (OUTLIER) cc_final: 0.6002 (pp30) REVERT: D 304 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7319 (t80) REVERT: D 499 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6800 (mmm160) REVERT: D 500 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7321 (mmt180) REVERT: D 727 GLN cc_start: 0.6282 (OUTLIER) cc_final: 0.6011 (pp30) outliers start: 42 outliers final: 29 residues processed: 230 average time/residue: 1.2108 time to fit residues: 320.6331 Evaluate side-chains 228 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 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 471 ASP 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 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 471 ASP 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 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 471 ASP 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 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 727 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 214 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 193 optimal weight: 0.0570 chunk 6 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 748 ASN B 467 ASN B 748 ASN C 467 ASN C 748 ASN D 467 ASN D 748 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.186235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152740 restraints weight = 37233.931| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 0.63 r_work: 0.3338 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work: 0.3067 rms_B_bonded: 3.43 restraints_weight: 0.1250 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2324 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= 0.148 Angle : 0.668 26.356 25540 Z= 0.337 Chirality : 0.037 0.130 2852 Planarity : 0.005 0.090 3132 Dihedral : 15.202 149.715 2988 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.09 % Allowed : 18.53 % Favored : 79.38 % 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: 1.08 (0.18), residues: 2216 helix: 2.26 (0.14), residues: 1332 sheet: 0.15 (0.56), residues: 92 loop : -2.08 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 500 TYR 0.014 0.002 TYR A 584 PHE 0.014 0.002 PHE D 304 TRP 0.014 0.002 TRP D 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (18888) covalent geometry : angle 0.66847 / 0.34 (25540) hydrogen bonds : bond 0.07065 / 4.74 ( 1040) hydrogen bonds : angle 3.91456 / 2.82 ( 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 225 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6883 (mmm160) REVERT: A 727 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.5961 (pp30) REVERT: B 499 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6887 (mmm160) REVERT: B 727 GLN cc_start: 0.6217 (OUTLIER) cc_final: 0.5952 (pp30) REVERT: C 458 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6719 (mt-10) REVERT: C 499 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6889 (mmm160) REVERT: C 727 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5972 (pp30) REVERT: D 499 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6883 (mmm160) REVERT: D 500 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7380 (mmt180) REVERT: D 727 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.5982 (pp30) outliers start: 41 outliers final: 32 residues processed: 224 average time/residue: 1.2274 time to fit residues: 315.4443 Evaluate side-chains 225 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 471 ASP 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 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 471 ASP 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 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 471 ASP 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 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 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: 6.9990 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 186 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN B 467 ASN C 467 ASN ** C 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 = 0.4078 r_free = 0.4078 target = 0.186408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.152876 restraints weight = 37541.403| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 0.61 r_work: 0.3367 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.3048 rms_B_bonded: 3.36 restraints_weight: 0.1250 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2366 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= 0.149 Angle : 0.671 26.401 25540 Z= 0.338 Chirality : 0.037 0.124 2852 Planarity : 0.006 0.111 3132 Dihedral : 14.743 149.593 2988 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.93 % Allowed : 18.69 % Favored : 79.38 % 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: 1.05 (0.18), residues: 2216 helix: 2.23 (0.14), residues: 1332 sheet: 0.18 (0.56), residues: 92 loop : -2.09 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 500 TYR 0.013 0.002 TYR A 584 PHE 0.014 0.002 PHE D 304 TRP 0.014 0.002 TRP A 697 HIS 0.003 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (18888) covalent geometry : angle 0.67050 / 0.34 (25540) hydrogen bonds : bond 0.07059 / 4.74 ( 1040) hydrogen bonds : angle 3.92904 / 2.83 ( 3012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16060.25 seconds wall clock time: 272 minutes 2.83 seconds (16322.83 seconds total)