Starting phenix.real_space_refine on Sat Jul 4 04:05:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11cj_75616/07_2026/11cj_75616.cif Found real_map, /net/cci-nas-00/data/ceres_data/11cj_75616/07_2026/11cj_75616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11cj_75616/07_2026/11cj_75616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11cj_75616/07_2026/11cj_75616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11cj_75616/07_2026/11cj_75616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11cj_75616/07_2026/11cj_75616.map" } resolution = 2.52 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= 0.029 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 116 5.16 5 C 11648 2.51 5 N 2776 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s 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: 17684 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "B" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "C" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'8IJ': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'8IJ': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'8IJ': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'8IJ': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.43, per 1000 atoms: 0.19 Number of scatterers: 17684 At special positions: 0 Unit cell: (123.302, 123.302, 112.358, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 8 15.00 O 3136 8.00 N 2776 7.00 C 11648 6.00 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: 1.50 Conformation dependent library (CDL) restraints added in 606.3 milliseconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 64.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 214 through 225 removed outlier: 3.954A pdb=" N VAL A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 299 through 321 Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.519A pdb=" N GLU A 328 " --> pdb=" O LYS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 430 through 455 removed outlier: 3.716A pdb=" N ILE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 500 removed outlier: 3.715A pdb=" N PHE A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.724A pdb=" N MET A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 533 No H-bonds generated for 'chain 'A' and resid 532 through 533' Processing helix chain 'A' and resid 534 through 535 No H-bonds generated for 'chain 'A' and resid 534 through 535' Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.642A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.560A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.966A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 640 Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'A' and resid 674 through 690 Processing helix chain 'A' and resid 690 through 713 removed outlier: 4.077A pdb=" N LYS A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 214 through 225 removed outlier: 3.956A pdb=" N VAL B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 299 through 321 Processing helix chain 'B' and resid 325 through 329 removed outlier: 3.520A pdb=" N GLU B 328 " --> pdb=" O LYS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 416 through 430 Processing helix chain 'B' and resid 430 through 455 removed outlier: 3.717A pdb=" N ILE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 500 removed outlier: 3.714A pdb=" N PHE B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.723A pdb=" N MET B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 533 No H-bonds generated for 'chain 'B' and resid 532 through 533' Processing helix chain 'B' and resid 534 through 535 No H-bonds generated for 'chain 'B' and resid 534 through 535' Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.642A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.560A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.967A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 640 Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 674 through 690 Processing helix chain 'B' and resid 690 through 713 removed outlier: 4.077A pdb=" N LYS B 695 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 214 through 225 removed outlier: 3.955A pdb=" N VAL C 218 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 299 through 321 Processing helix chain 'C' and resid 325 through 329 removed outlier: 3.520A pdb=" N GLU C 328 " --> pdb=" O LYS C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 416 through 430 Processing helix chain 'C' and resid 430 through 455 removed outlier: 3.717A pdb=" N ILE C 434 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 500 removed outlier: 3.715A pdb=" N PHE C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.723A pdb=" N MET C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 533 No H-bonds generated for 'chain 'C' and resid 532 through 533' Processing helix chain 'C' and resid 534 through 535 No H-bonds generated for 'chain 'C' and resid 534 through 535' Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.643A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.561A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.966A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 640 Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'C' and resid 674 through 690 Processing helix chain 'C' and resid 690 through 713 removed outlier: 4.077A pdb=" N LYS C 695 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 696 " --> pdb=" O GLN C 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 214 through 225 removed outlier: 3.955A pdb=" N VAL D 218 " --> pdb=" O ASN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 259 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 299 through 321 Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.520A pdb=" N GLU D 328 " --> pdb=" O LYS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 345 Processing helix chain 'D' and resid 346 through 355 Processing helix chain 'D' and resid 363 through 367 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 416 through 430 Processing helix chain 'D' and resid 430 through 455 removed outlier: 3.716A pdb=" N ILE D 434 " --> pdb=" O PHE D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 500 removed outlier: 3.715A pdb=" N PHE D 473 " --> pdb=" O THR D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 removed outlier: 3.723A pdb=" N MET D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 533 No H-bonds generated for 'chain 'D' and resid 532 through 533' Processing helix chain 'D' and resid 534 through 535 No H-bonds generated for 'chain 'D' and resid 534 through 535' Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.642A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.561A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.966A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 640 Processing helix chain 'D' and resid 656 through 672 Processing helix chain 'D' and resid 674 through 690 Processing helix chain 'D' and resid 690 through 713 removed outlier: 4.077A pdb=" N LYS D 695 " --> pdb=" O ALA D 691 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN D 696 " --> pdb=" O GLN D 692 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 374 removed outlier: 6.749A pdb=" N SER A 380 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 374 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP A 738 " --> pdb=" O VAL A 729 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 369 through 374 removed outlier: 6.748A pdb=" N SER B 380 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA B 374 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP B 738 " --> pdb=" O VAL B 729 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 369 through 374 removed outlier: 6.748A pdb=" N SER C 380 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 374 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP C 738 " --> pdb=" O VAL C 729 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 369 through 374 removed outlier: 6.749A pdb=" N SER D 380 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA D 374 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP D 738 " --> pdb=" O VAL D 729 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2976 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: 2.90 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2692 1.31 - 1.43: 5047 1.43 - 1.56: 10128 1.56 - 1.68: 29 1.68 - 1.81: 196 Bond restraints: 18092 Sorted by residual: bond pdb=" C29 POV A1202 " pdb="C210 POV A1202 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C29 POV D1202 " pdb="C210 POV D1202 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C29 POV C1202 " pdb="C210 POV C1202 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C29 POV B1202 " pdb="C210 POV B1202 " ideal model delta sigma weight residual 1.333 1.557 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C21 POV A1202 " pdb=" O21 POV A1202 " ideal model delta sigma weight residual 1.330 1.424 -0.094 2.00e-02 2.50e+03 2.20e+01 ... (remaining 18087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 24184 4.09 - 8.19: 180 8.19 - 12.28: 20 12.28 - 16.38: 16 16.38 - 20.47: 4 Bond angle restraints: 24404 Sorted by residual: angle pdb=" O1 8IJ A1201 " pdb=" P2 8IJ A1201 " pdb=" O3 8IJ A1201 " ideal model delta sigma weight residual 121.24 100.77 20.47 3.00e+00 1.11e-01 4.66e+01 angle pdb=" O1 8IJ C1201 " pdb=" P2 8IJ C1201 " pdb=" O3 8IJ C1201 " ideal model delta sigma weight residual 121.24 100.80 20.44 3.00e+00 1.11e-01 4.64e+01 angle pdb=" O1 8IJ D1201 " pdb=" P2 8IJ D1201 " pdb=" O3 8IJ D1201 " ideal model delta sigma weight residual 121.24 100.80 20.44 3.00e+00 1.11e-01 4.64e+01 angle pdb=" O1 8IJ B1201 " pdb=" P2 8IJ B1201 " pdb=" O3 8IJ B1201 " ideal model delta sigma weight residual 121.24 100.83 20.41 3.00e+00 1.11e-01 4.63e+01 angle pdb=" C29 POV C1202 " pdb="C210 POV C1202 " pdb="C211 POV C1202 " ideal model delta sigma weight residual 127.67 112.41 15.26 3.00e+00 1.11e-01 2.59e+01 ... (remaining 24399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 10288 34.99 - 69.98: 528 69.98 - 104.98: 28 104.98 - 139.97: 8 139.97 - 174.96: 12 Dihedral angle restraints: 10864 sinusoidal: 4620 harmonic: 6244 Sorted by residual: dihedral pdb=" C52 8IJ C1201 " pdb=" C53 8IJ C1201 " pdb=" C54 8IJ C1201 " pdb=" C55 8IJ C1201 " ideal model delta sinusoidal sigma weight residual 298.77 123.81 174.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C52 8IJ A1201 " pdb=" C53 8IJ A1201 " pdb=" C54 8IJ A1201 " pdb=" C55 8IJ A1201 " ideal model delta sinusoidal sigma weight residual 298.77 123.83 174.94 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C52 8IJ D1201 " pdb=" C53 8IJ D1201 " pdb=" C54 8IJ D1201 " pdb=" C55 8IJ D1201 " ideal model delta sinusoidal sigma weight residual 298.77 123.84 174.93 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1724 0.031 - 0.061: 692 0.061 - 0.092: 217 0.092 - 0.123: 83 0.123 - 0.153: 4 Chirality restraints: 2720 Sorted by residual: chirality pdb=" C14 8IJ A1201 " pdb=" C12 8IJ A1201 " pdb=" C5 8IJ A1201 " pdb=" O15 8IJ A1201 " both_signs ideal model delta sigma weight residual False 2.49 2.34 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" C14 8IJ C1201 " pdb=" C12 8IJ C1201 " pdb=" C5 8IJ C1201 " pdb=" O15 8IJ C1201 " both_signs ideal model delta sigma weight residual False 2.49 2.34 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" C14 8IJ D1201 " pdb=" C12 8IJ D1201 " pdb=" C5 8IJ D1201 " pdb=" O15 8IJ D1201 " both_signs ideal model delta sigma weight residual False 2.49 2.34 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 2717 not shown) Planarity restraints: 2968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1202 " -0.162 2.00e-02 2.50e+03 3.43e-01 1.17e+03 pdb=" C29 POV A1202 " 0.460 2.00e-02 2.50e+03 pdb="C210 POV A1202 " -0.455 2.00e-02 2.50e+03 pdb="C211 POV A1202 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D1202 " -0.162 2.00e-02 2.50e+03 3.43e-01 1.17e+03 pdb=" C29 POV D1202 " 0.461 2.00e-02 2.50e+03 pdb="C210 POV D1202 " -0.455 2.00e-02 2.50e+03 pdb="C211 POV D1202 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C1202 " -0.162 2.00e-02 2.50e+03 3.43e-01 1.17e+03 pdb=" C29 POV C1202 " 0.461 2.00e-02 2.50e+03 pdb="C210 POV C1202 " -0.455 2.00e-02 2.50e+03 pdb="C211 POV C1202 " 0.156 2.00e-02 2.50e+03 ... (remaining 2965 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 7186 2.93 - 3.42: 17565 3.42 - 3.92: 30213 3.92 - 4.41: 34247 4.41 - 4.90: 56356 Nonbonded interactions: 145567 Sorted by model distance: nonbonded pdb=" O LEU A 220 " pdb=" ND2 ASN A 224 " model vdw 2.439 3.120 nonbonded pdb=" O LEU B 220 " pdb=" ND2 ASN B 224 " model vdw 2.439 3.120 nonbonded pdb=" O LEU D 220 " pdb=" ND2 ASN D 224 " model vdw 2.440 3.120 nonbonded pdb=" O LEU C 220 " pdb=" ND2 ASN C 224 " model vdw 2.440 3.120 nonbonded pdb=" N ASP A 301 " pdb=" OD1 ASP A 301 " model vdw 2.573 3.120 ... (remaining 145562 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.006 0.225 18092 Z= 0.306 Angle : 0.919 20.475 24404 Z= 0.408 Chirality : 0.038 0.153 2720 Planarity : 0.013 0.343 2968 Dihedral : 20.372 174.959 6856 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.70 % Allowed : 24.14 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.32 (0.18), residues: 2108 helix: 2.22 (0.15), residues: 1220 sheet: 0.92 (0.65), residues: 76 loop : -1.31 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 429 TYR 0.019 0.002 TYR B 199 PHE 0.011 0.002 PHE D 267 TRP 0.012 0.001 TRP A 698 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.31 (18092) covalent geometry : angle 0.91894 / 0.41 (24404) hydrogen bonds : bond 0.13284 / 8.79 ( 1016) hydrogen bonds : angle 4.94229 / 3.60 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 246 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7527 (t80) REVERT: A 429 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7381 (mtp-110) REVERT: A 433 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7150 (tmt-80) REVERT: A 451 MET cc_start: 0.8560 (mtp) cc_final: 0.8269 (mtm) REVERT: A 711 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7525 (mttp) REVERT: A 748 VAL cc_start: 0.8659 (t) cc_final: 0.8263 (p) REVERT: B 305 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7542 (t80) REVERT: B 429 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7328 (mtp-110) REVERT: B 433 ARG cc_start: 0.7754 (mtt90) cc_final: 0.7362 (mmt180) REVERT: B 451 MET cc_start: 0.8590 (mtp) cc_final: 0.8300 (mtm) REVERT: B 711 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7541 (mttp) REVERT: B 748 VAL cc_start: 0.8677 (t) cc_final: 0.8282 (p) REVERT: C 305 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7537 (t80) REVERT: C 429 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7355 (mtp-110) REVERT: C 433 ARG cc_start: 0.7754 (mtt90) cc_final: 0.7349 (mmt180) REVERT: C 451 MET cc_start: 0.8591 (mtp) cc_final: 0.8301 (mtm) REVERT: C 711 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7529 (mttp) REVERT: C 748 VAL cc_start: 0.8683 (t) cc_final: 0.8287 (p) REVERT: D 305 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7532 (t80) REVERT: D 429 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7357 (mtp-110) REVERT: D 433 ARG cc_start: 0.7763 (mtt90) cc_final: 0.7144 (tmt-80) REVERT: D 451 MET cc_start: 0.8575 (mtp) cc_final: 0.8283 (mtm) REVERT: D 711 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7519 (mttp) REVERT: D 748 VAL cc_start: 0.8668 (t) cc_final: 0.8265 (p) outliers start: 13 outliers final: 0 residues processed: 254 average time/residue: 0.6508 time to fit residues: 183.8486 Evaluate side-chains 225 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain D residue 305 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 224 ASN A 261 GLN A 274 GLN B 214 ASN B 224 ASN B 261 GLN B 274 GLN C 214 ASN C 224 ASN C 261 GLN C 274 GLN D 214 ASN D 224 ASN D 261 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.159722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125883 restraints weight = 16107.664| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.64 r_work: 0.3218 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18092 Z= 0.128 Angle : 0.514 6.168 24404 Z= 0.280 Chirality : 0.038 0.136 2720 Planarity : 0.003 0.033 2968 Dihedral : 17.196 149.314 2824 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.05 % Allowed : 21.47 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.58 (0.18), residues: 2108 helix: 2.31 (0.14), residues: 1236 sheet: 1.18 (0.63), residues: 76 loop : -1.09 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 429 TYR 0.017 0.002 TYR C 199 PHE 0.015 0.001 PHE D 305 TRP 0.011 0.001 TRP A 698 HIS 0.004 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (18092) covalent geometry : angle 0.51449 / 0.28 (24404) hydrogen bonds : bond 0.04476 / 3.05 ( 1016) hydrogen bonds : angle 4.12146 / 3.01 ( 2976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: A 429 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7121 (mtp-110) REVERT: A 433 ARG cc_start: 0.7605 (mtt90) cc_final: 0.6786 (tmt-80) REVERT: A 553 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8072 (mm) REVERT: A 711 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7451 (mttp) REVERT: A 738 ASP cc_start: 0.7757 (p0) cc_final: 0.7442 (p0) REVERT: A 748 VAL cc_start: 0.8598 (t) cc_final: 0.8116 (p) REVERT: B 261 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: B 429 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7099 (mtp-110) REVERT: B 433 ARG cc_start: 0.7599 (mtt90) cc_final: 0.6799 (tmt-80) REVERT: B 553 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 711 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7471 (mttp) REVERT: B 738 ASP cc_start: 0.7761 (p0) cc_final: 0.7445 (p0) REVERT: B 748 VAL cc_start: 0.8594 (t) cc_final: 0.8118 (p) REVERT: C 429 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7125 (mtp-110) REVERT: C 433 ARG cc_start: 0.7585 (mtt90) cc_final: 0.6795 (tmt-80) REVERT: C 553 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8071 (mm) REVERT: C 711 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7465 (mttp) REVERT: C 738 ASP cc_start: 0.7744 (p0) cc_final: 0.7414 (p0) REVERT: C 748 VAL cc_start: 0.8611 (t) cc_final: 0.8129 (p) REVERT: D 261 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8035 (mt0) REVERT: D 429 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7115 (mtp-110) REVERT: D 433 ARG cc_start: 0.7594 (mtt90) cc_final: 0.6794 (tmt-80) REVERT: D 553 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8072 (mm) REVERT: D 711 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7469 (mttp) REVERT: D 738 ASP cc_start: 0.7757 (p0) cc_final: 0.7450 (p0) REVERT: D 748 VAL cc_start: 0.8605 (t) cc_final: 0.8126 (p) outliers start: 57 outliers final: 16 residues processed: 264 average time/residue: 0.5363 time to fit residues: 159.3981 Evaluate side-chains 250 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 751 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 168 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 224 ASN A 261 GLN A 498 GLN B 214 ASN B 224 ASN B 261 GLN C 214 ASN C 224 ASN D 214 ASN D 224 ASN D 261 GLN D 274 GLN D 498 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.155173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121087 restraints weight = 16126.887| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.58 r_work: 0.3153 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18092 Z= 0.210 Angle : 0.625 5.777 24404 Z= 0.335 Chirality : 0.043 0.154 2720 Planarity : 0.004 0.038 2968 Dihedral : 17.389 171.822 2824 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.50 % Allowed : 18.52 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2108 helix: 1.79 (0.14), residues: 1264 sheet: 1.08 (0.58), residues: 76 loop : -1.15 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 429 TYR 0.023 0.003 TYR C 199 PHE 0.026 0.002 PHE B 267 TRP 0.016 0.002 TRP C 698 HIS 0.005 0.002 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (18092) covalent geometry : angle 0.62463 / 0.34 (24404) hydrogen bonds : bond 0.05642 / 3.82 ( 1016) hydrogen bonds : angle 4.20199 / 3.05 ( 2976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 222 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.5700 (mp0) REVERT: A 429 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7202 (mtm110) REVERT: A 433 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7021 (mmt180) REVERT: A 553 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8211 (mm) REVERT: A 711 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7501 (mttp) REVERT: A 737 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8040 (p0) REVERT: A 738 ASP cc_start: 0.7962 (p0) cc_final: 0.7359 (p0) REVERT: A 748 VAL cc_start: 0.8635 (t) cc_final: 0.8197 (p) REVERT: B 360 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: B 429 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7213 (mtm110) REVERT: B 433 ARG cc_start: 0.7650 (mtt90) cc_final: 0.7051 (mmt180) REVERT: B 553 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8213 (mm) REVERT: B 711 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7511 (mttp) REVERT: B 737 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8027 (p0) REVERT: B 738 ASP cc_start: 0.7965 (p0) cc_final: 0.7365 (p0) REVERT: B 748 VAL cc_start: 0.8633 (t) cc_final: 0.8187 (p) REVERT: C 360 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.5682 (mp0) REVERT: C 429 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7227 (mtm110) REVERT: C 433 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7028 (mmt180) REVERT: C 553 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8220 (mm) REVERT: C 711 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7517 (mttp) REVERT: C 737 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8022 (p0) REVERT: C 738 ASP cc_start: 0.7956 (p0) cc_final: 0.7354 (p0) REVERT: C 748 VAL cc_start: 0.8642 (t) cc_final: 0.8202 (p) REVERT: D 360 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.5709 (mp0) REVERT: D 429 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7227 (mtm110) REVERT: D 433 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7025 (mmt180) REVERT: D 553 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8219 (mm) REVERT: D 711 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7494 (mttp) REVERT: D 737 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8036 (p0) REVERT: D 738 ASP cc_start: 0.7959 (p0) cc_final: 0.7357 (p0) REVERT: D 748 VAL cc_start: 0.8637 (t) cc_final: 0.8199 (p) outliers start: 84 outliers final: 36 residues processed: 288 average time/residue: 0.5627 time to fit residues: 181.3319 Evaluate side-chains 267 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 751 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 224 ASN A 261 GLN A 498 GLN B 214 ASN B 224 ASN B 261 GLN B 498 GLN C 214 ASN C 224 ASN C 498 GLN D 214 ASN D 224 ASN D 261 GLN D 498 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.158011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124113 restraints weight = 16160.250| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.60 r_work: 0.3191 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18092 Z= 0.131 Angle : 0.504 5.178 24404 Z= 0.278 Chirality : 0.038 0.140 2720 Planarity : 0.003 0.035 2968 Dihedral : 15.462 173.125 2824 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.85 % Allowed : 18.47 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.37 (0.18), residues: 2108 helix: 2.05 (0.14), residues: 1264 sheet: 1.07 (0.60), residues: 76 loop : -1.12 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.017 0.002 TYR A 199 PHE 0.017 0.001 PHE C 305 TRP 0.012 0.001 TRP D 698 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (18092) covalent geometry : angle 0.50391 / 0.28 (24404) hydrogen bonds : bond 0.04470 / 3.04 ( 1016) hydrogen bonds : angle 3.96328 / 2.88 ( 2976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 227 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7116 (mtm110) REVERT: A 433 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7047 (mmt180) REVERT: A 553 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 661 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8054 (mm) REVERT: A 710 GLU cc_start: 0.7569 (tt0) cc_final: 0.7349 (mt-10) REVERT: A 711 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7508 (mttp) REVERT: A 725 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7490 (ptmt) REVERT: A 738 ASP cc_start: 0.7910 (p0) cc_final: 0.7643 (p0) REVERT: A 748 VAL cc_start: 0.8592 (t) cc_final: 0.8112 (p) REVERT: B 429 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7122 (mtm110) REVERT: B 433 ARG cc_start: 0.7672 (mtt90) cc_final: 0.7082 (mmt180) REVERT: B 553 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 661 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8054 (mm) REVERT: B 711 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7494 (mttp) REVERT: B 725 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7493 (ptmt) REVERT: B 738 ASP cc_start: 0.7931 (p0) cc_final: 0.7667 (p0) REVERT: B 748 VAL cc_start: 0.8595 (t) cc_final: 0.8112 (p) REVERT: C 429 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7124 (mtm110) REVERT: C 433 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7054 (mmt180) REVERT: C 461 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6753 (mm) REVERT: C 553 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8224 (mm) REVERT: C 661 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8056 (mm) REVERT: C 711 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7497 (mttp) REVERT: C 725 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7488 (ptmt) REVERT: C 738 ASP cc_start: 0.7934 (p0) cc_final: 0.7670 (p0) REVERT: C 748 VAL cc_start: 0.8597 (t) cc_final: 0.8114 (p) REVERT: D 429 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7124 (mtm110) REVERT: D 433 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7045 (mmt180) REVERT: D 461 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6746 (mm) REVERT: D 553 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8224 (mm) REVERT: D 711 LYS cc_start: 0.7899 (ttpt) cc_final: 0.7498 (mttp) REVERT: D 725 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7492 (ptmt) REVERT: D 738 ASP cc_start: 0.7922 (p0) cc_final: 0.7669 (p0) REVERT: D 748 VAL cc_start: 0.8593 (t) cc_final: 0.8116 (p) outliers start: 72 outliers final: 31 residues processed: 282 average time/residue: 0.5348 time to fit residues: 169.8539 Evaluate side-chains 272 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 751 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 224 ASN A 498 GLN B 214 ASN B 224 ASN B 498 GLN C 214 ASN C 224 ASN C 498 GLN D 214 ASN D 224 ASN D 498 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121207 restraints weight = 16094.785| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.62 r_work: 0.3153 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18092 Z= 0.168 Angle : 0.561 5.365 24404 Z= 0.304 Chirality : 0.040 0.146 2720 Planarity : 0.004 0.038 2968 Dihedral : 14.607 163.057 2824 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.01 % Allowed : 19.22 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.21 (0.18), residues: 2108 helix: 1.89 (0.14), residues: 1268 sheet: 0.95 (0.58), residues: 76 loop : -1.13 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 429 TYR 0.020 0.002 TYR A 199 PHE 0.018 0.002 PHE A 267 TRP 0.013 0.002 TRP D 698 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (18092) covalent geometry : angle 0.56091 / 0.30 (24404) hydrogen bonds : bond 0.05089 / 3.46 ( 1016) hydrogen bonds : angle 4.04636 / 2.93 ( 2976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 223 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7162 (mtm110) REVERT: A 433 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7024 (mmt180) REVERT: A 553 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8208 (mm) REVERT: A 661 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.8014 (mm) REVERT: A 710 GLU cc_start: 0.7605 (tt0) cc_final: 0.7359 (mt-10) REVERT: A 711 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7478 (mttp) REVERT: A 725 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7460 (ptmt) REVERT: A 748 VAL cc_start: 0.8591 (t) cc_final: 0.8125 (p) REVERT: B 429 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7163 (mtm110) REVERT: B 433 ARG cc_start: 0.7639 (mtt90) cc_final: 0.7018 (mmt180) REVERT: B 553 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8207 (mm) REVERT: B 661 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8019 (mm) REVERT: B 710 GLU cc_start: 0.7616 (tt0) cc_final: 0.7375 (mt-10) REVERT: B 711 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7482 (mttp) REVERT: B 725 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7476 (ptmt) REVERT: B 748 VAL cc_start: 0.8596 (t) cc_final: 0.8126 (p) REVERT: C 429 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7165 (mtm110) REVERT: C 433 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7020 (mmt180) REVERT: C 461 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6902 (mm) REVERT: C 553 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8208 (mm) REVERT: C 661 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8018 (mm) REVERT: C 710 GLU cc_start: 0.7616 (tt0) cc_final: 0.7371 (mt-10) REVERT: C 711 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7479 (mttp) REVERT: C 725 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7470 (ptmt) REVERT: C 748 VAL cc_start: 0.8594 (t) cc_final: 0.8127 (p) REVERT: D 429 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7163 (mtm110) REVERT: D 433 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7027 (mmt180) REVERT: D 461 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6900 (mm) REVERT: D 553 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8209 (mm) REVERT: D 710 GLU cc_start: 0.7602 (tt0) cc_final: 0.7357 (mt-10) REVERT: D 711 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7468 (mttp) REVERT: D 725 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7468 (ptmt) REVERT: D 748 VAL cc_start: 0.8595 (t) cc_final: 0.8130 (p) outliers start: 75 outliers final: 44 residues processed: 283 average time/residue: 0.5584 time to fit residues: 178.3416 Evaluate side-chains 280 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 751 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 133 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 224 ASN A 498 GLN B 214 ASN B 224 ASN B 498 GLN C 214 ASN C 224 ASN C 498 GLN D 214 ASN D 224 ASN D 498 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.157538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123574 restraints weight = 16059.033| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.62 r_work: 0.3186 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18092 Z= 0.130 Angle : 0.506 5.098 24404 Z= 0.277 Chirality : 0.038 0.140 2720 Planarity : 0.003 0.037 2968 Dihedral : 13.745 166.989 2824 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.53 % Allowed : 19.49 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.38 (0.18), residues: 2108 helix: 2.06 (0.14), residues: 1272 sheet: 0.97 (0.59), residues: 76 loop : -1.12 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.016 0.002 TYR A 199 PHE 0.016 0.001 PHE A 305 TRP 0.012 0.001 TRP A 698 HIS 0.004 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (18092) covalent geometry : angle 0.50571 / 0.28 (24404) hydrogen bonds : bond 0.04477 / 3.05 ( 1016) hydrogen bonds : angle 3.91576 / 2.85 ( 2976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7106 (mtm110) REVERT: A 433 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7036 (mmt180) REVERT: A 553 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8208 (mm) REVERT: A 661 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8017 (mm) REVERT: A 710 GLU cc_start: 0.7539 (tt0) cc_final: 0.7332 (mt-10) REVERT: A 711 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7512 (mttp) REVERT: A 725 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7455 (ptmm) REVERT: A 738 ASP cc_start: 0.8011 (p0) cc_final: 0.7528 (p0) REVERT: A 748 VAL cc_start: 0.8554 (t) cc_final: 0.8049 (p) REVERT: B 429 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7106 (mtm110) REVERT: B 433 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7020 (mmt180) REVERT: B 553 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8207 (mm) REVERT: B 661 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8019 (mm) REVERT: B 710 GLU cc_start: 0.7546 (tt0) cc_final: 0.7344 (mt-10) REVERT: B 711 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7498 (mttp) REVERT: B 725 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7449 (ptmm) REVERT: B 738 ASP cc_start: 0.8000 (p0) cc_final: 0.7527 (p0) REVERT: B 748 VAL cc_start: 0.8553 (t) cc_final: 0.8043 (p) REVERT: C 429 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7116 (mtm110) REVERT: C 433 ARG cc_start: 0.7618 (mtt90) cc_final: 0.7023 (mmt180) REVERT: C 461 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6745 (mm) REVERT: C 553 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8206 (mm) REVERT: C 661 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8019 (mm) REVERT: C 710 GLU cc_start: 0.7534 (tt0) cc_final: 0.7328 (mt-10) REVERT: C 711 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7512 (mttp) REVERT: C 725 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7457 (ptmm) REVERT: C 738 ASP cc_start: 0.8010 (p0) cc_final: 0.7566 (p0) REVERT: C 748 VAL cc_start: 0.8551 (t) cc_final: 0.8041 (p) REVERT: D 429 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7114 (mtm110) REVERT: D 433 ARG cc_start: 0.7624 (mtt90) cc_final: 0.7031 (mmt180) REVERT: D 461 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6741 (mm) REVERT: D 553 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8209 (mm) REVERT: D 710 GLU cc_start: 0.7540 (tt0) cc_final: 0.7332 (mt-10) REVERT: D 711 LYS cc_start: 0.7839 (ttpt) cc_final: 0.7495 (mttp) REVERT: D 725 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7460 (ptmm) REVERT: D 738 ASP cc_start: 0.8010 (p0) cc_final: 0.7530 (p0) REVERT: D 748 VAL cc_start: 0.8550 (t) cc_final: 0.8047 (p) outliers start: 66 outliers final: 36 residues processed: 286 average time/residue: 0.5957 time to fit residues: 191.4685 Evaluate side-chains 273 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 751 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 224 ASN A 498 GLN B 214 ASN B 224 ASN B 420 ASN B 498 GLN C 214 ASN C 224 ASN C 498 GLN D 214 ASN D 224 ASN D 498 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.155222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120944 restraints weight = 16084.080| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.61 r_work: 0.3148 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18092 Z= 0.172 Angle : 0.571 5.401 24404 Z= 0.308 Chirality : 0.040 0.155 2720 Planarity : 0.004 0.040 2968 Dihedral : 13.815 170.399 2824 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.85 % Allowed : 19.38 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.16 (0.18), residues: 2108 helix: 1.87 (0.14), residues: 1268 sheet: 0.97 (0.58), residues: 76 loop : -1.18 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 429 TYR 0.020 0.002 TYR D 199 PHE 0.018 0.002 PHE B 267 TRP 0.013 0.002 TRP A 698 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (18092) covalent geometry : angle 0.57135 / 0.31 (24404) hydrogen bonds : bond 0.05164 / 3.51 ( 1016) hydrogen bonds : angle 4.01471 / 2.91 ( 2976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 224 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7193 (mtm110) REVERT: A 433 ARG cc_start: 0.7613 (mtt90) cc_final: 0.7018 (mmt180) REVERT: A 553 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8215 (mm) REVERT: A 661 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8028 (mm) REVERT: A 710 GLU cc_start: 0.7632 (tt0) cc_final: 0.7405 (mt-10) REVERT: A 711 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7503 (mttp) REVERT: A 725 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7470 (ptmt) REVERT: A 738 ASP cc_start: 0.8092 (p0) cc_final: 0.7695 (p0) REVERT: A 748 VAL cc_start: 0.8577 (t) cc_final: 0.8109 (p) REVERT: B 429 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7192 (mtm110) REVERT: B 433 ARG cc_start: 0.7609 (mtt90) cc_final: 0.7009 (mmt180) REVERT: B 553 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8207 (mm) REVERT: B 661 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8026 (mm) REVERT: B 710 GLU cc_start: 0.7636 (tt0) cc_final: 0.7409 (mt-10) REVERT: B 711 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7484 (mttp) REVERT: B 725 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7482 (ptmt) REVERT: B 738 ASP cc_start: 0.8083 (p0) cc_final: 0.7703 (p0) REVERT: B 748 VAL cc_start: 0.8580 (t) cc_final: 0.8109 (p) REVERT: C 429 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7191 (mtm110) REVERT: C 433 ARG cc_start: 0.7614 (mtt90) cc_final: 0.7028 (mmt180) REVERT: C 461 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6916 (mm) REVERT: C 553 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8209 (mm) REVERT: C 661 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8032 (mm) REVERT: C 710 GLU cc_start: 0.7639 (tt0) cc_final: 0.7407 (mt-10) REVERT: C 711 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7481 (mttp) REVERT: C 725 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7484 (ptmt) REVERT: C 738 ASP cc_start: 0.8081 (p0) cc_final: 0.7707 (p0) REVERT: C 748 VAL cc_start: 0.8584 (t) cc_final: 0.8112 (p) REVERT: D 429 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7196 (mtm110) REVERT: D 433 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7026 (mmt180) REVERT: D 461 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6907 (mm) REVERT: D 553 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8210 (mm) REVERT: D 710 GLU cc_start: 0.7629 (tt0) cc_final: 0.7399 (mt-10) REVERT: D 711 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7479 (mttp) REVERT: D 725 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7474 (ptmt) REVERT: D 738 ASP cc_start: 0.8085 (p0) cc_final: 0.7691 (p0) REVERT: D 748 VAL cc_start: 0.8581 (t) cc_final: 0.8115 (p) outliers start: 72 outliers final: 44 residues processed: 282 average time/residue: 0.5767 time to fit residues: 183.2473 Evaluate side-chains 280 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 751 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 111 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 0.0670 chunk 189 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 498 GLN B 214 ASN B 420 ASN B 498 GLN C 214 ASN C 498 GLN D 214 ASN D 498 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.159001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125043 restraints weight = 15996.764| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.59 r_work: 0.3201 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18092 Z= 0.119 Angle : 0.491 5.094 24404 Z= 0.270 Chirality : 0.038 0.178 2720 Planarity : 0.003 0.037 2968 Dihedral : 13.092 167.540 2824 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.48 % Allowed : 19.65 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2108 helix: 2.12 (0.14), residues: 1272 sheet: 1.18 (0.59), residues: 76 loop : -1.12 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 212 TYR 0.015 0.001 TYR C 199 PHE 0.015 0.001 PHE D 305 TRP 0.012 0.001 TRP A 698 HIS 0.003 0.001 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (18092) covalent geometry : angle 0.49141 / 0.27 (24404) hydrogen bonds : bond 0.04282 / 2.93 ( 1016) hydrogen bonds : angle 3.88655 / 2.83 ( 2976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 241 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7107 (mtm110) REVERT: A 433 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7050 (mmt180) REVERT: A 553 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8186 (mm) REVERT: A 710 GLU cc_start: 0.7547 (tt0) cc_final: 0.7337 (mt-10) REVERT: A 711 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7502 (mttp) REVERT: A 725 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7484 (ptmm) REVERT: A 738 ASP cc_start: 0.8003 (p0) cc_final: 0.7460 (p0) REVERT: A 748 VAL cc_start: 0.8545 (t) cc_final: 0.8061 (p) REVERT: B 429 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7116 (mtm110) REVERT: B 433 ARG cc_start: 0.7623 (mtt90) cc_final: 0.7042 (mmt180) REVERT: B 553 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8191 (mm) REVERT: B 710 GLU cc_start: 0.7538 (tt0) cc_final: 0.7329 (mt-10) REVERT: B 711 LYS cc_start: 0.7835 (ttpt) cc_final: 0.7505 (mttp) REVERT: B 725 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7493 (ptmm) REVERT: B 738 ASP cc_start: 0.8006 (p0) cc_final: 0.7499 (p0) REVERT: B 748 VAL cc_start: 0.8548 (t) cc_final: 0.8068 (p) REVERT: C 429 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7115 (mtm110) REVERT: C 433 ARG cc_start: 0.7629 (mtt90) cc_final: 0.7046 (mmt180) REVERT: C 553 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8194 (mm) REVERT: C 710 GLU cc_start: 0.7539 (tt0) cc_final: 0.7329 (mt-10) REVERT: C 711 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7499 (mttp) REVERT: C 725 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7479 (ptmm) REVERT: C 738 ASP cc_start: 0.7996 (p0) cc_final: 0.7495 (p0) REVERT: C 748 VAL cc_start: 0.8550 (t) cc_final: 0.8063 (p) REVERT: D 429 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7115 (mtm110) REVERT: D 433 ARG cc_start: 0.7626 (mtt90) cc_final: 0.7047 (mmt180) REVERT: D 553 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8196 (mm) REVERT: D 710 GLU cc_start: 0.7539 (tt0) cc_final: 0.7329 (mt-10) REVERT: D 711 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7499 (mttp) REVERT: D 725 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7489 (ptmm) REVERT: D 738 ASP cc_start: 0.8008 (p0) cc_final: 0.7465 (p0) REVERT: D 748 VAL cc_start: 0.8549 (t) cc_final: 0.8070 (p) outliers start: 65 outliers final: 35 residues processed: 294 average time/residue: 0.5935 time to fit residues: 195.6632 Evaluate side-chains 272 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 751 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 124 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 0.0970 chunk 173 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 261 GLN A 498 GLN B 214 ASN B 261 GLN B 498 GLN C 498 GLN D 214 ASN D 261 GLN D 498 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123995 restraints weight = 15913.460| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.59 r_work: 0.3188 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18092 Z= 0.131 Angle : 0.533 12.388 24404 Z= 0.284 Chirality : 0.038 0.146 2720 Planarity : 0.003 0.037 2968 Dihedral : 13.128 167.960 2824 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.32 % Allowed : 19.54 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.42 (0.18), residues: 2108 helix: 2.09 (0.14), residues: 1272 sheet: 1.14 (0.59), residues: 76 loop : -1.15 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.016 0.002 TYR A 199 PHE 0.016 0.001 PHE C 305 TRP 0.011 0.001 TRP A 698 HIS 0.004 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (18092) covalent geometry : angle 0.53317 / 0.28 (24404) hydrogen bonds : bond 0.04504 / 3.08 ( 1016) hydrogen bonds : angle 3.90788 / 2.84 ( 2976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7116 (mtm110) REVERT: A 433 ARG cc_start: 0.7659 (mtt90) cc_final: 0.7048 (mmt180) REVERT: A 553 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8186 (mm) REVERT: A 710 GLU cc_start: 0.7543 (tt0) cc_final: 0.7332 (mt-10) REVERT: A 711 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7479 (mttp) REVERT: A 725 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7489 (ptmm) REVERT: A 738 ASP cc_start: 0.8029 (p0) cc_final: 0.7549 (p0) REVERT: A 748 VAL cc_start: 0.8533 (t) cc_final: 0.8070 (p) REVERT: B 429 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7112 (mtm110) REVERT: B 433 ARG cc_start: 0.7642 (mtt90) cc_final: 0.7031 (mmt180) REVERT: B 553 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8181 (mm) REVERT: B 710 GLU cc_start: 0.7530 (tt0) cc_final: 0.7318 (mt-10) REVERT: B 711 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7480 (mttp) REVERT: B 717 MET cc_start: 0.0372 (pmm) cc_final: -0.0984 (pp-130) REVERT: B 725 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7495 (ptmm) REVERT: B 738 ASP cc_start: 0.8033 (p0) cc_final: 0.7583 (p0) REVERT: B 748 VAL cc_start: 0.8545 (t) cc_final: 0.8077 (p) REVERT: C 429 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7117 (mtm110) REVERT: C 433 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7030 (mmt180) REVERT: C 553 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8181 (mm) REVERT: C 710 GLU cc_start: 0.7537 (tt0) cc_final: 0.7323 (mt-10) REVERT: C 711 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7475 (mttp) REVERT: C 725 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7489 (ptmm) REVERT: C 738 ASP cc_start: 0.8029 (p0) cc_final: 0.7586 (p0) REVERT: C 748 VAL cc_start: 0.8540 (t) cc_final: 0.8070 (p) REVERT: D 429 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7123 (mtm110) REVERT: D 433 ARG cc_start: 0.7642 (mtt90) cc_final: 0.7038 (mmt180) REVERT: D 553 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8186 (mm) REVERT: D 710 GLU cc_start: 0.7530 (tt0) cc_final: 0.7316 (mt-10) REVERT: D 711 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7474 (mttp) REVERT: D 725 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7489 (ptmm) REVERT: D 738 ASP cc_start: 0.8032 (p0) cc_final: 0.7551 (p0) REVERT: D 748 VAL cc_start: 0.8543 (t) cc_final: 0.8082 (p) outliers start: 62 outliers final: 39 residues processed: 285 average time/residue: 0.5319 time to fit residues: 170.9908 Evaluate side-chains 275 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 751 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 420 ASN A 498 GLN B 214 ASN B 498 GLN C 498 GLN D 214 ASN D 420 ASN D 498 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.159138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125164 restraints weight = 15851.510| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.56 r_work: 0.3201 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18092 Z= 0.123 Angle : 0.523 12.624 24404 Z= 0.277 Chirality : 0.037 0.141 2720 Planarity : 0.003 0.036 2968 Dihedral : 12.983 166.658 2824 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.78 % Allowed : 20.29 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.57 (0.18), residues: 2108 helix: 2.32 (0.14), residues: 1244 sheet: 1.16 (0.59), residues: 76 loop : -1.15 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.015 0.002 TYR D 199 PHE 0.015 0.001 PHE C 305 TRP 0.011 0.001 TRP A 698 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (18092) covalent geometry : angle 0.52257 / 0.28 (24404) hydrogen bonds : bond 0.04291 / 2.93 ( 1016) hydrogen bonds : angle 3.87144 / 2.81 ( 2976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 0.703 Fit side-chains REVERT: A 429 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7098 (mtm110) REVERT: A 433 ARG cc_start: 0.7673 (mtt90) cc_final: 0.7085 (mmt180) REVERT: A 553 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8161 (mm) REVERT: A 710 GLU cc_start: 0.7503 (tt0) cc_final: 0.7282 (mt-10) REVERT: A 711 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7466 (mttp) REVERT: A 717 MET cc_start: 0.0385 (pmm) cc_final: -0.0857 (pp-130) REVERT: A 725 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7482 (ptmm) REVERT: A 738 ASP cc_start: 0.8012 (p0) cc_final: 0.7524 (p0) REVERT: A 748 VAL cc_start: 0.8540 (t) cc_final: 0.8070 (p) REVERT: B 429 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7090 (mtm110) REVERT: B 433 ARG cc_start: 0.7657 (mtt90) cc_final: 0.7069 (mmt180) REVERT: B 553 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8175 (mm) REVERT: B 710 GLU cc_start: 0.7488 (tt0) cc_final: 0.7271 (mt-10) REVERT: B 711 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7470 (mttp) REVERT: B 717 MET cc_start: 0.0358 (pmm) cc_final: -0.0976 (pp-130) REVERT: B 725 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7477 (ptmm) REVERT: B 738 ASP cc_start: 0.8003 (p0) cc_final: 0.7529 (p0) REVERT: B 748 VAL cc_start: 0.8544 (t) cc_final: 0.8076 (p) REVERT: C 429 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7101 (mtm110) REVERT: C 433 ARG cc_start: 0.7655 (mtt90) cc_final: 0.7067 (mmt180) REVERT: C 553 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8171 (mm) REVERT: C 710 GLU cc_start: 0.7497 (tt0) cc_final: 0.7279 (mt-10) REVERT: C 711 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7466 (mttp) REVERT: C 717 MET cc_start: 0.0354 (pmm) cc_final: -0.0904 (pp-130) REVERT: C 725 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7481 (ptmm) REVERT: C 738 ASP cc_start: 0.8011 (p0) cc_final: 0.7567 (p0) REVERT: C 748 VAL cc_start: 0.8543 (t) cc_final: 0.8071 (p) REVERT: D 429 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7100 (mtm110) REVERT: D 433 ARG cc_start: 0.7671 (mtt90) cc_final: 0.7084 (mmt180) REVERT: D 553 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8176 (mm) REVERT: D 710 GLU cc_start: 0.7488 (tt0) cc_final: 0.7271 (mt-10) REVERT: D 711 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7467 (mttp) REVERT: D 717 MET cc_start: 0.0378 (pmm) cc_final: -0.0870 (pp-130) REVERT: D 725 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7480 (ptmm) REVERT: D 738 ASP cc_start: 0.7996 (p0) cc_final: 0.7491 (p0) REVERT: D 748 VAL cc_start: 0.8547 (t) cc_final: 0.8081 (p) outliers start: 52 outliers final: 34 residues processed: 275 average time/residue: 0.5923 time to fit residues: 183.3745 Evaluate side-chains 273 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 751 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 139 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 156 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 498 GLN B 214 ASN B 498 GLN C 498 GLN D 214 ASN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.158996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124942 restraints weight = 15873.481| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.57 r_work: 0.3198 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18092 Z= 0.122 Angle : 0.522 12.598 24404 Z= 0.277 Chirality : 0.037 0.147 2720 Planarity : 0.003 0.036 2968 Dihedral : 12.996 166.547 2824 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.46 % Allowed : 20.34 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.59 (0.18), residues: 2108 helix: 2.33 (0.14), residues: 1244 sheet: 1.17 (0.59), residues: 76 loop : -1.13 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.015 0.002 TYR C 199 PHE 0.015 0.001 PHE C 305 TRP 0.011 0.001 TRP A 698 HIS 0.004 0.001 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (18092) covalent geometry : angle 0.52183 / 0.28 (24404) hydrogen bonds : bond 0.04309 / 2.95 ( 1016) hydrogen bonds : angle 3.87789 / 2.82 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6890.46 seconds wall clock time: 117 minutes 58.81 seconds (7078.81 seconds total)