Starting phenix.real_space_refine on Thu Mar 5 04:22:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ui0_26521/03_2026/7ui0_26521_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ui0_26521/03_2026/7ui0_26521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ui0_26521/03_2026/7ui0_26521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ui0_26521/03_2026/7ui0_26521.map" model { file = "/net/cci-nas-00/data/ceres_data/7ui0_26521/03_2026/7ui0_26521_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ui0_26521/03_2026/7ui0_26521_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 12123 2.51 5 N 3330 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19203 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4660 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Restraints were copied for chains: B, C, I, J, M, N Time building chain proxies: 4.54, per 1000 atoms: 0.24 Number of scatterers: 19203 At special positions: 0 Unit cell: (137.775, 138.6, 186.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3660 8.00 N 3330 7.00 C 12123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.05 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.05 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.05 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: 1.60 Conformation dependent library (CDL) restraints added in 806.5 milliseconds 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 42 sheets defined 16.3% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 303 through 310 removed outlier: 4.022A pdb=" N GLY A 306 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 411 through 428 removed outlier: 4.479A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 543 removed outlier: 4.844A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.937A pdb=" N ILE A 550 " --> pdb=" O ASN A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 303 through 310 removed outlier: 4.022A pdb=" N GLY B 306 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS B 308 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 411 through 428 removed outlier: 4.479A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 543 removed outlier: 4.843A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 removed outlier: 3.938A pdb=" N ILE B 550 " --> pdb=" O ASN B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 303 through 310 removed outlier: 4.022A pdb=" N GLY C 306 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS C 308 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 411 through 428 removed outlier: 4.479A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 543 removed outlier: 4.844A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.937A pdb=" N ILE C 550 " --> pdb=" O ASN C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 7.042A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.212A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 372 current: chain 'A' and resid 449 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 157 through 175 removed outlier: 8.577A pdb=" N TYR A 164 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS A 166 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG A 189 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 168 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU A 187 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 170 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 185 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN A 172 " --> pdb=" O MET A 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 191 current: chain 'A' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 246 through 248 current: chain 'A' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 294 through 295 current: chain 'A' and resid 340 through 345 Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 563 Processing sheet with id=AA9, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 643 removed outlier: 5.804A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AB3, first strand: chain 'B' and resid 574 through 576 removed outlier: 7.043A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.212A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 372 current: chain 'B' and resid 449 through 457 Processing sheet with id=AB5, first strand: chain 'B' and resid 157 through 175 removed outlier: 8.578A pdb=" N TYR B 164 " --> pdb=" O PRO B 191 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS B 166 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG B 189 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 168 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU B 187 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 170 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE B 185 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN B 172 " --> pdb=" O MET B 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 180 through 191 current: chain 'B' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 246 through 248 current: chain 'B' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 294 through 295 current: chain 'B' and resid 340 through 345 Processing sheet with id=AB6, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AB7, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AB8, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AB9, first strand: chain 'B' and resid 559 through 563 Processing sheet with id=AC1, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'B' and resid 638 through 643 removed outlier: 5.803A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 666 through 667 Processing sheet with id=AC4, first strand: chain 'C' and resid 574 through 576 removed outlier: 7.042A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 145 through 152 removed outlier: 6.212A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 372 current: chain 'C' and resid 449 through 457 Processing sheet with id=AC6, first strand: chain 'C' and resid 157 through 175 removed outlier: 8.577A pdb=" N TYR C 164 " --> pdb=" O PRO C 191 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS C 166 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG C 189 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 168 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU C 187 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 170 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE C 185 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN C 172 " --> pdb=" O MET C 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 180 through 191 current: chain 'C' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 246 through 248 current: chain 'C' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 294 through 295 current: chain 'C' and resid 340 through 345 Processing sheet with id=AC7, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AC8, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AC9, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AD1, first strand: chain 'C' and resid 559 through 563 Processing sheet with id=AD2, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD3, first strand: chain 'C' and resid 638 through 643 removed outlier: 5.804A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AD5, first strand: chain 'H' and resid 9 through 12 removed outlier: 5.546A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AD7, first strand: chain 'I' and resid 9 through 12 removed outlier: 5.546A pdb=" N GLU I 10 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE I 34 " --> pdb=" O MET I 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AD9, first strand: chain 'J' and resid 9 through 12 removed outlier: 5.546A pdb=" N GLU J 10 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE J 34 " --> pdb=" O MET J 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.893A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.893A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.892A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1578 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: 3.76 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6235 1.34 - 1.46: 4418 1.46 - 1.58: 8895 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 19683 Sorted by residual: bond pdb=" CZ ARG B 624 " pdb=" NH2 ARG B 624 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.59e+00 bond pdb=" CZ ARG A 624 " pdb=" NH2 ARG A 624 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.47e+00 bond pdb=" CZ ARG C 624 " pdb=" NH2 ARG C 624 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.38e+00 bond pdb=" CZ ARG C 588 " pdb=" NH2 ARG C 588 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.13e+00 bond pdb=" CZ ARG A 588 " pdb=" NH2 ARG A 588 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.74e+00 ... (remaining 19678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 26023 2.30 - 4.59: 689 4.59 - 6.89: 30 6.89 - 9.19: 3 9.19 - 11.48: 3 Bond angle restraints: 26748 Sorted by residual: angle pdb=" CB HIS B 637 " pdb=" CG HIS B 637 " pdb=" CD2 HIS B 637 " ideal model delta sigma weight residual 131.20 125.37 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" CB HIS A 637 " pdb=" CG HIS A 637 " pdb=" CD2 HIS A 637 " ideal model delta sigma weight residual 131.20 125.37 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" CB HIS C 637 " pdb=" CG HIS C 637 " pdb=" CD2 HIS C 637 " ideal model delta sigma weight residual 131.20 125.39 5.81 1.30e+00 5.92e-01 2.00e+01 angle pdb=" CB MET I 81 " pdb=" CG MET I 81 " pdb=" SD MET I 81 " ideal model delta sigma weight residual 112.70 101.22 11.48 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CB MET J 81 " pdb=" CG MET J 81 " pdb=" SD MET J 81 " ideal model delta sigma weight residual 112.70 101.24 11.46 3.00e+00 1.11e-01 1.46e+01 ... (remaining 26743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 10490 17.61 - 35.22: 946 35.22 - 52.83: 153 52.83 - 70.43: 42 70.43 - 88.04: 12 Dihedral angle restraints: 11643 sinusoidal: 4599 harmonic: 7044 Sorted by residual: dihedral pdb=" CA SER J 101 " pdb=" C SER J 101 " pdb=" N SER J 102 " pdb=" CA SER J 102 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA SER I 101 " pdb=" C SER I 101 " pdb=" N SER I 102 " pdb=" CA SER I 102 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA SER H 101 " pdb=" C SER H 101 " pdb=" N SER H 102 " pdb=" CA SER H 102 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 11640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2258 0.053 - 0.106: 545 0.106 - 0.159: 83 0.159 - 0.212: 15 0.212 - 0.265: 6 Chirality restraints: 2907 Sorted by residual: chirality pdb=" CA TYR A 653 " pdb=" N TYR A 653 " pdb=" C TYR A 653 " pdb=" CB TYR A 653 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA TYR B 653 " pdb=" N TYR B 653 " pdb=" C TYR B 653 " pdb=" CB TYR B 653 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA TYR C 653 " pdb=" N TYR C 653 " pdb=" C TYR C 653 " pdb=" CB TYR C 653 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2904 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 653 " -0.066 2.00e-02 2.50e+03 3.43e-02 2.35e+01 pdb=" CG TYR C 653 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 653 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C 653 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR C 653 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR C 653 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 653 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 653 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 653 " -0.066 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 653 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 653 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 653 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 653 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 653 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 653 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 653 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 653 " -0.065 2.00e-02 2.50e+03 3.42e-02 2.33e+01 pdb=" CG TYR B 653 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 653 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 653 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR B 653 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 653 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 653 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 653 " -0.041 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 306 2.60 - 3.18: 16995 3.18 - 3.75: 29304 3.75 - 4.33: 41175 4.33 - 4.90: 68480 Nonbonded interactions: 156260 Sorted by model distance: nonbonded pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " model vdw 2.036 3.760 ... (remaining 156255 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.800 Find NCS groups from input model: 0.160 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 19698 Z= 0.365 Angle : 0.815 11.484 26778 Z= 0.487 Chirality : 0.049 0.265 2907 Planarity : 0.006 0.091 3456 Dihedral : 13.944 88.042 7086 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.17), residues: 2385 helix: 0.48 (0.29), residues: 309 sheet: -1.10 (0.17), residues: 798 loop : -1.08 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 627 TYR 0.066 0.002 TYR C 653 PHE 0.039 0.003 PHE A 641 TRP 0.031 0.002 TRP H 110 HIS 0.017 0.002 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00763 (19683) covalent geometry : angle 0.81192 (26748) SS BOND : bond 0.00877 ( 15) SS BOND : angle 2.23747 ( 30) hydrogen bonds : bond 0.12456 ( 616) hydrogen bonds : angle 7.15098 ( 1578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 419 ASP cc_start: 0.7559 (t70) cc_final: 0.7267 (t0) REVERT: C 297 MET cc_start: 0.8598 (ptm) cc_final: 0.8384 (ptp) REVERT: H 36 TRP cc_start: 0.7374 (m100) cc_final: 0.7052 (m100) REVERT: H 95 TYR cc_start: 0.6671 (m-80) cc_final: 0.6430 (m-80) REVERT: I 10 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6629 (mm-30) REVERT: J 36 TRP cc_start: 0.7687 (m100) cc_final: 0.7234 (m100) REVERT: J 50 MET cc_start: 0.8549 (ptt) cc_final: 0.8330 (ptt) REVERT: J 95 TYR cc_start: 0.6871 (m-80) cc_final: 0.6423 (m-80) REVERT: J 112 GLN cc_start: 0.6577 (pm20) cc_final: 0.6182 (pm20) REVERT: L 91 TYR cc_start: 0.8351 (p90) cc_final: 0.8132 (p90) REVERT: M 37 GLN cc_start: 0.7054 (tt0) cc_final: 0.6386 (tm-30) REVERT: M 91 TYR cc_start: 0.8425 (p90) cc_final: 0.8047 (p90) REVERT: N 37 GLN cc_start: 0.6862 (tt0) cc_final: 0.6458 (tt0) REVERT: N 79 GLN cc_start: 0.6698 (pt0) cc_final: 0.6480 (pt0) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1309 time to fit residues: 63.1716 Evaluate side-chains 237 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 534 HIS B 216 ASN B 458 ASN B 534 HIS C 129 GLN C 216 ASN C 534 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN M 28 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.092817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064905 restraints weight = 51906.341| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.30 r_work: 0.2904 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19698 Z= 0.164 Angle : 0.618 9.696 26778 Z= 0.325 Chirality : 0.044 0.175 2907 Planarity : 0.004 0.039 3456 Dihedral : 5.156 22.450 2688 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.30 % Allowed : 8.59 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.22 (0.17), residues: 2385 helix: 0.87 (0.29), residues: 315 sheet: -0.98 (0.17), residues: 801 loop : -1.07 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 627 TYR 0.025 0.002 TYR B 653 PHE 0.015 0.002 PHE A 294 TRP 0.023 0.002 TRP H 36 HIS 0.010 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00371 (19683) covalent geometry : angle 0.61645 (26748) SS BOND : bond 0.00302 ( 15) SS BOND : angle 1.42007 ( 30) hydrogen bonds : bond 0.04076 ( 616) hydrogen bonds : angle 6.02679 ( 1578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 653 TYR cc_start: 0.7939 (m-80) cc_final: 0.7710 (m-80) REVERT: C 456 LEU cc_start: 0.9235 (tp) cc_final: 0.8913 (tt) REVERT: C 587 MET cc_start: 0.8911 (mtp) cc_final: 0.8344 (mtp) REVERT: C 677 MET cc_start: 0.8728 (mmt) cc_final: 0.7855 (mmm) REVERT: H 3 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8031 (tm-30) REVERT: H 47 TRP cc_start: 0.8151 (t60) cc_final: 0.7620 (t60) REVERT: H 59 HIS cc_start: 0.7555 (m-70) cc_final: 0.7009 (m-70) REVERT: H 95 TYR cc_start: 0.6916 (m-80) cc_final: 0.6468 (m-80) REVERT: H 112 GLN cc_start: 0.7202 (pm20) cc_final: 0.6665 (pm20) REVERT: I 5 GLN cc_start: 0.8906 (mt0) cc_final: 0.8679 (tp40) REVERT: I 10 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6729 (mm-30) REVERT: I 36 TRP cc_start: 0.7661 (m100) cc_final: 0.7395 (m-10) REVERT: I 59 HIS cc_start: 0.7669 (m-70) cc_final: 0.7381 (m-70) REVERT: I 65 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8305 (mmtt) REVERT: J 3 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8018 (tm-30) REVERT: J 47 TRP cc_start: 0.7713 (t60) cc_final: 0.7226 (t60) REVERT: J 70 LEU cc_start: 0.9017 (mm) cc_final: 0.8781 (mm) REVERT: J 73 ASP cc_start: 0.8174 (t0) cc_final: 0.6660 (p0) REVERT: J 80 TYR cc_start: 0.7475 (m-80) cc_final: 0.6668 (m-10) REVERT: J 95 TYR cc_start: 0.6929 (m-80) cc_final: 0.6690 (m-80) REVERT: L 37 GLN cc_start: 0.7174 (tt0) cc_final: 0.6966 (tm-30) REVERT: L 79 GLN cc_start: 0.7662 (pt0) cc_final: 0.7419 (tm-30) REVERT: L 91 TYR cc_start: 0.8484 (p90) cc_final: 0.8111 (p90) REVERT: M 37 GLN cc_start: 0.7056 (tt0) cc_final: 0.6683 (tm-30) REVERT: M 91 TYR cc_start: 0.8621 (p90) cc_final: 0.8255 (p90) REVERT: N 30 ASN cc_start: 0.8920 (t0) cc_final: 0.8707 (t0) REVERT: N 69 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7358 (mtpp) outliers start: 27 outliers final: 16 residues processed: 270 average time/residue: 0.1320 time to fit residues: 55.7200 Evaluate side-chains 236 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 106 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 120 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 177 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.058551 restraints weight = 52259.954| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.25 r_work: 0.2753 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 19698 Z= 0.340 Angle : 0.709 12.910 26778 Z= 0.375 Chirality : 0.047 0.187 2907 Planarity : 0.005 0.051 3456 Dihedral : 5.421 26.247 2688 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.27 % Allowed : 11.43 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.48 (0.16), residues: 2385 helix: 0.60 (0.29), residues: 312 sheet: -1.40 (0.17), residues: 822 loop : -1.01 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 136 TYR 0.038 0.002 TYR A 653 PHE 0.019 0.002 PHE A 294 TRP 0.019 0.002 TRP B 528 HIS 0.011 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00778 (19683) covalent geometry : angle 0.70166 (26748) SS BOND : bond 0.00866 ( 15) SS BOND : angle 3.19811 ( 30) hydrogen bonds : bond 0.04460 ( 616) hydrogen bonds : angle 6.15175 ( 1578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8048 (mpp) REVERT: B 234 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8800 (mp) REVERT: B 421 MET cc_start: 0.8763 (mtm) cc_final: 0.8469 (mtt) REVERT: C 178 ARG cc_start: 0.8553 (mtt90) cc_final: 0.7766 (mtt90) REVERT: H 3 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8024 (tm-30) REVERT: H 36 TRP cc_start: 0.7111 (m100) cc_final: 0.6882 (m-10) REVERT: H 47 TRP cc_start: 0.8277 (t60) cc_final: 0.7912 (t60) REVERT: H 112 GLN cc_start: 0.7184 (pm20) cc_final: 0.6774 (pm20) REVERT: I 5 GLN cc_start: 0.8943 (mt0) cc_final: 0.8600 (tp40) REVERT: I 10 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6886 (mm-30) REVERT: I 65 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8341 (mmtp) REVERT: I 95 TYR cc_start: 0.6855 (m-80) cc_final: 0.6250 (m-80) REVERT: J 3 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8093 (tm-30) REVERT: J 27 TYR cc_start: 0.6868 (p90) cc_final: 0.6527 (p90) REVERT: J 70 LEU cc_start: 0.8972 (mm) cc_final: 0.8726 (mm) REVERT: J 95 TYR cc_start: 0.7034 (m-80) cc_final: 0.6649 (m-80) REVERT: J 112 GLN cc_start: 0.6898 (pm20) cc_final: 0.6340 (pm20) REVERT: L 79 GLN cc_start: 0.7715 (pt0) cc_final: 0.7458 (tm-30) REVERT: L 91 TYR cc_start: 0.8608 (p90) cc_final: 0.8164 (p90) REVERT: M 37 GLN cc_start: 0.7154 (tt0) cc_final: 0.6538 (tt0) REVERT: M 91 TYR cc_start: 0.8593 (p90) cc_final: 0.8258 (p90) REVERT: N 37 GLN cc_start: 0.7140 (tt0) cc_final: 0.6634 (tt0) REVERT: N 61 ARG cc_start: 0.7623 (ptt180) cc_final: 0.7163 (ptt90) REVERT: N 69 LYS cc_start: 0.7732 (mtpp) cc_final: 0.7509 (mtpp) outliers start: 47 outliers final: 23 residues processed: 247 average time/residue: 0.1263 time to fit residues: 49.3711 Evaluate side-chains 231 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain J residue 110 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 231 optimal weight: 20.0000 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 0.0670 chunk 140 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 222 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN I 54 ASN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.089591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.060808 restraints weight = 51156.536| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.27 r_work: 0.2808 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19698 Z= 0.121 Angle : 0.577 8.805 26778 Z= 0.302 Chirality : 0.042 0.149 2907 Planarity : 0.004 0.039 3456 Dihedral : 4.940 20.393 2688 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.27 % Allowed : 12.69 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.17), residues: 2385 helix: 1.43 (0.30), residues: 297 sheet: -1.12 (0.17), residues: 831 loop : -0.98 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.032 0.001 TYR B 653 PHE 0.015 0.001 PHE C 194 TRP 0.022 0.001 TRP I 36 HIS 0.005 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00276 (19683) covalent geometry : angle 0.56567 (26748) SS BOND : bond 0.00344 ( 15) SS BOND : angle 3.43298 ( 30) hydrogen bonds : bond 0.03650 ( 616) hydrogen bonds : angle 5.78143 ( 1578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 653 TYR cc_start: 0.7907 (m-80) cc_final: 0.7676 (m-80) REVERT: C 177 HIS cc_start: 0.8165 (p90) cc_final: 0.7888 (p90) REVERT: C 178 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8253 (mtt90) REVERT: H 47 TRP cc_start: 0.8232 (t60) cc_final: 0.7850 (t60) REVERT: H 59 HIS cc_start: 0.7647 (m-70) cc_final: 0.7155 (m-70) REVERT: H 65 LYS cc_start: 0.8466 (mmtp) cc_final: 0.8208 (mmtt) REVERT: H 95 TYR cc_start: 0.6716 (m-80) cc_final: 0.6478 (m-80) REVERT: H 112 GLN cc_start: 0.6871 (pm20) cc_final: 0.6500 (pm20) REVERT: I 3 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7954 (tm-30) REVERT: I 10 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6879 (mm-30) REVERT: I 36 TRP cc_start: 0.7241 (m-10) cc_final: 0.6708 (m-10) REVERT: I 59 HIS cc_start: 0.7638 (m-70) cc_final: 0.7239 (m-70) REVERT: I 65 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8354 (mmtt) REVERT: J 3 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8049 (tm-30) REVERT: J 70 LEU cc_start: 0.9096 (mm) cc_final: 0.8558 (mm) REVERT: J 73 ASP cc_start: 0.7919 (t0) cc_final: 0.6361 (p0) REVERT: J 80 TYR cc_start: 0.7714 (m-80) cc_final: 0.6718 (m-10) REVERT: J 95 TYR cc_start: 0.6838 (m-80) cc_final: 0.6542 (m-80) REVERT: J 112 GLN cc_start: 0.6865 (pm20) cc_final: 0.6348 (pm20) REVERT: L 3 GLN cc_start: 0.8822 (tp40) cc_final: 0.7874 (pp30) REVERT: L 37 GLN cc_start: 0.7176 (tt0) cc_final: 0.6496 (tm-30) REVERT: L 61 ARG cc_start: 0.7884 (ptt180) cc_final: 0.7431 (ptt90) REVERT: L 79 GLN cc_start: 0.7656 (pt0) cc_final: 0.7451 (tm-30) REVERT: M 37 GLN cc_start: 0.7163 (tt0) cc_final: 0.6564 (tt0) REVERT: M 61 ARG cc_start: 0.7922 (ptt-90) cc_final: 0.7374 (ptt180) REVERT: M 71 TYR cc_start: 0.6266 (m-80) cc_final: 0.5808 (m-80) REVERT: N 27 ASP cc_start: 0.8823 (t0) cc_final: 0.7898 (m-30) REVERT: N 37 GLN cc_start: 0.7107 (tt0) cc_final: 0.6586 (tt0) REVERT: N 61 ARG cc_start: 0.7524 (ptt180) cc_final: 0.7163 (ptt90) REVERT: N 69 LYS cc_start: 0.7790 (mtpp) cc_final: 0.7560 (mtpp) REVERT: N 87 TYR cc_start: 0.7764 (m-10) cc_final: 0.7449 (m-10) outliers start: 47 outliers final: 21 residues processed: 263 average time/residue: 0.1343 time to fit residues: 55.6984 Evaluate side-chains 230 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN N 30 ASN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.088004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.059171 restraints weight = 51530.086| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.25 r_work: 0.2767 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19698 Z= 0.221 Angle : 0.618 8.574 26778 Z= 0.324 Chirality : 0.043 0.221 2907 Planarity : 0.004 0.049 3456 Dihedral : 4.961 20.837 2688 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.27 % Allowed : 13.99 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.17), residues: 2385 helix: 1.03 (0.29), residues: 315 sheet: -1.30 (0.17), residues: 843 loop : -0.82 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 627 TYR 0.047 0.002 TYR B 653 PHE 0.025 0.002 PHE C 194 TRP 0.023 0.002 TRP J 36 HIS 0.007 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00509 (19683) covalent geometry : angle 0.60890 (26748) SS BOND : bond 0.00371 ( 15) SS BOND : angle 3.24097 ( 30) hydrogen bonds : bond 0.03847 ( 616) hydrogen bonds : angle 5.77893 ( 1578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 421 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8120 (mpp) REVERT: B 534 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.8224 (t-90) REVERT: C 627 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8455 (mtt180) REVERT: H 47 TRP cc_start: 0.8249 (t60) cc_final: 0.7905 (t60) REVERT: H 81 MET cc_start: 0.7393 (ttp) cc_final: 0.7028 (tpp) REVERT: H 95 TYR cc_start: 0.6816 (m-80) cc_final: 0.6195 (m-80) REVERT: H 112 GLN cc_start: 0.6741 (pm20) cc_final: 0.6448 (pm20) REVERT: I 3 GLN cc_start: 0.8286 (tm-30) cc_final: 0.8040 (tm-30) REVERT: I 10 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6841 (mm-30) REVERT: I 95 TYR cc_start: 0.6856 (m-80) cc_final: 0.6386 (m-80) REVERT: J 3 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8135 (tm-30) REVERT: J 70 LEU cc_start: 0.9127 (mm) cc_final: 0.8731 (mm) REVERT: J 73 ASP cc_start: 0.7964 (t0) cc_final: 0.6284 (p0) REVERT: J 80 TYR cc_start: 0.7636 (m-80) cc_final: 0.6552 (m-10) REVERT: J 95 TYR cc_start: 0.6896 (m-80) cc_final: 0.6546 (m-80) REVERT: J 112 GLN cc_start: 0.6773 (pm20) cc_final: 0.6380 (pm20) REVERT: L 37 GLN cc_start: 0.7242 (tt0) cc_final: 0.6543 (tm-30) REVERT: L 61 ARG cc_start: 0.7892 (ptt180) cc_final: 0.7395 (ptt90) REVERT: L 79 GLN cc_start: 0.7638 (pt0) cc_final: 0.7438 (tm-30) REVERT: M 37 GLN cc_start: 0.7172 (tt0) cc_final: 0.6572 (tt0) REVERT: M 61 ARG cc_start: 0.8020 (ptt-90) cc_final: 0.7478 (ptt180) REVERT: M 71 TYR cc_start: 0.6287 (m-80) cc_final: 0.5701 (m-80) REVERT: N 37 GLN cc_start: 0.7173 (tt0) cc_final: 0.6658 (tt0) REVERT: N 61 ARG cc_start: 0.7633 (ptt180) cc_final: 0.7080 (ptt90) REVERT: N 69 LYS cc_start: 0.7826 (mtpp) cc_final: 0.7599 (mtpp) outliers start: 47 outliers final: 29 residues processed: 251 average time/residue: 0.1374 time to fit residues: 53.9771 Evaluate side-chains 242 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain N residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 166 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.059874 restraints weight = 51128.365| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.25 r_work: 0.2784 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19698 Z= 0.163 Angle : 0.581 10.012 26778 Z= 0.306 Chirality : 0.042 0.150 2907 Planarity : 0.004 0.056 3456 Dihedral : 4.823 24.886 2688 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.22 % Allowed : 14.91 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.17), residues: 2385 helix: 1.52 (0.30), residues: 297 sheet: -1.25 (0.16), residues: 867 loop : -0.87 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 627 TYR 0.042 0.001 TYR B 653 PHE 0.022 0.001 PHE C 194 TRP 0.028 0.002 TRP I 36 HIS 0.005 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00373 (19683) covalent geometry : angle 0.57342 (26748) SS BOND : bond 0.00293 ( 15) SS BOND : angle 2.90240 ( 30) hydrogen bonds : bond 0.03635 ( 616) hydrogen bonds : angle 5.64923 ( 1578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 HIS cc_start: 0.7723 (p90) cc_final: 0.6270 (p-80) REVERT: A 178 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7375 (mtm-85) REVERT: A 421 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8114 (mpp) REVERT: B 534 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.8085 (t-90) REVERT: C 177 HIS cc_start: 0.8303 (p90) cc_final: 0.8069 (p90) REVERT: C 421 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: C 627 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8453 (mtt180) REVERT: H 47 TRP cc_start: 0.8219 (t60) cc_final: 0.7943 (t60) REVERT: H 59 HIS cc_start: 0.7695 (m-70) cc_final: 0.7276 (m-70) REVERT: H 81 MET cc_start: 0.7517 (ttp) cc_final: 0.7090 (tpp) REVERT: H 95 TYR cc_start: 0.6813 (m-80) cc_final: 0.6218 (m-80) REVERT: H 109 TYR cc_start: 0.8440 (m-80) cc_final: 0.8088 (m-80) REVERT: I 3 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8015 (tm-30) REVERT: I 10 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6810 (mm-30) REVERT: I 36 TRP cc_start: 0.6331 (m-10) cc_final: 0.6065 (m-10) REVERT: I 59 HIS cc_start: 0.7783 (m-70) cc_final: 0.7363 (m-70) REVERT: I 81 MET cc_start: 0.7382 (ttp) cc_final: 0.7091 (tpp) REVERT: I 95 TYR cc_start: 0.6795 (m-80) cc_final: 0.6451 (m-80) REVERT: J 3 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8178 (tm-30) REVERT: J 70 LEU cc_start: 0.9129 (mm) cc_final: 0.8839 (mm) REVERT: J 73 ASP cc_start: 0.8014 (t0) cc_final: 0.7742 (t0) REVERT: J 80 TYR cc_start: 0.7610 (m-80) cc_final: 0.7269 (m-10) REVERT: J 95 TYR cc_start: 0.6889 (m-80) cc_final: 0.6546 (m-80) REVERT: J 112 GLN cc_start: 0.6843 (pm20) cc_final: 0.6457 (pm20) REVERT: L 37 GLN cc_start: 0.7203 (tt0) cc_final: 0.6616 (tm-30) REVERT: L 61 ARG cc_start: 0.7899 (ptt180) cc_final: 0.7403 (ptt90) REVERT: M 37 GLN cc_start: 0.7188 (tt0) cc_final: 0.6771 (tm-30) REVERT: M 61 ARG cc_start: 0.7994 (ptt-90) cc_final: 0.7509 (ptt180) REVERT: N 27 ASP cc_start: 0.8691 (t0) cc_final: 0.7914 (m-30) REVERT: N 37 GLN cc_start: 0.7144 (tt0) cc_final: 0.6642 (tt0) REVERT: N 61 ARG cc_start: 0.7673 (ptt180) cc_final: 0.7116 (ptt90) REVERT: N 69 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7601 (mtpp) outliers start: 46 outliers final: 29 residues processed: 255 average time/residue: 0.1335 time to fit residues: 53.5443 Evaluate side-chains 242 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 529 CYS Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 95 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 137 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.089362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.060466 restraints weight = 51084.094| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.26 r_work: 0.2799 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19698 Z= 0.130 Angle : 0.567 9.804 26778 Z= 0.298 Chirality : 0.041 0.149 2907 Planarity : 0.004 0.047 3456 Dihedral : 4.701 23.575 2688 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.41 % Allowed : 15.00 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.03 (0.17), residues: 2385 helix: 1.67 (0.30), residues: 297 sheet: -1.16 (0.17), residues: 867 loop : -0.82 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 178 TYR 0.050 0.001 TYR C 653 PHE 0.018 0.001 PHE C 194 TRP 0.028 0.001 TRP J 36 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00297 (19683) covalent geometry : angle 0.55972 (26748) SS BOND : bond 0.00553 ( 15) SS BOND : angle 2.81572 ( 30) hydrogen bonds : bond 0.03467 ( 616) hydrogen bonds : angle 5.60058 ( 1578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.743 Fit side-chains REVERT: A 177 HIS cc_start: 0.7724 (p90) cc_final: 0.7308 (p90) REVERT: A 421 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8116 (mpp) REVERT: B 534 HIS cc_start: 0.8792 (OUTLIER) cc_final: 0.7994 (t-90) REVERT: C 177 HIS cc_start: 0.8323 (p90) cc_final: 0.7959 (p90) REVERT: C 178 ARG cc_start: 0.8602 (mtt90) cc_final: 0.8260 (mtt90) REVERT: C 421 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8171 (mpp) REVERT: C 534 HIS cc_start: 0.8885 (OUTLIER) cc_final: 0.7779 (t-90) REVERT: C 627 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8500 (mtt180) REVERT: H 47 TRP cc_start: 0.8200 (t60) cc_final: 0.7999 (t60) REVERT: H 59 HIS cc_start: 0.7638 (m-70) cc_final: 0.7239 (m-70) REVERT: H 81 MET cc_start: 0.7531 (ttp) cc_final: 0.7040 (tpp) REVERT: H 95 TYR cc_start: 0.6774 (m-80) cc_final: 0.6224 (m-80) REVERT: H 109 TYR cc_start: 0.8441 (m-80) cc_final: 0.8056 (m-80) REVERT: I 3 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7934 (mp10) REVERT: I 10 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6795 (mm-30) REVERT: I 59 HIS cc_start: 0.7749 (m-70) cc_final: 0.7338 (m-70) REVERT: I 65 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8386 (mmtt) REVERT: I 95 TYR cc_start: 0.6824 (m-80) cc_final: 0.6506 (m-80) REVERT: I 112 GLN cc_start: 0.6966 (pm20) cc_final: 0.6706 (pm20) REVERT: J 3 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8150 (tm-30) REVERT: J 70 LEU cc_start: 0.9108 (mm) cc_final: 0.8819 (mm) REVERT: J 73 ASP cc_start: 0.8063 (t0) cc_final: 0.7791 (t0) REVERT: J 80 TYR cc_start: 0.7619 (m-80) cc_final: 0.7285 (m-10) REVERT: J 95 TYR cc_start: 0.6857 (m-80) cc_final: 0.6500 (m-80) REVERT: J 112 GLN cc_start: 0.6867 (pm20) cc_final: 0.6376 (pm20) REVERT: L 3 GLN cc_start: 0.8807 (tp40) cc_final: 0.8479 (mm110) REVERT: L 37 GLN cc_start: 0.7190 (tt0) cc_final: 0.6613 (tm-30) REVERT: M 61 ARG cc_start: 0.8004 (ptt-90) cc_final: 0.7515 (ptt180) REVERT: N 27 ASP cc_start: 0.8704 (t0) cc_final: 0.7926 (m-30) REVERT: N 37 GLN cc_start: 0.7147 (tt0) cc_final: 0.6655 (tt0) REVERT: N 61 ARG cc_start: 0.7605 (ptt180) cc_final: 0.7027 (ptt90) REVERT: N 69 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7666 (mtpp) outliers start: 50 outliers final: 36 residues processed: 255 average time/residue: 0.1390 time to fit residues: 55.3831 Evaluate side-chains 252 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain L residue 30 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 214 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN N 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.058707 restraints weight = 51607.826| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.24 r_work: 0.2758 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19698 Z= 0.254 Angle : 0.630 10.338 26778 Z= 0.332 Chirality : 0.043 0.157 2907 Planarity : 0.004 0.048 3456 Dihedral : 4.926 23.051 2688 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.56 % Allowed : 15.53 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.13 (0.17), residues: 2385 helix: 1.48 (0.30), residues: 297 sheet: -1.14 (0.17), residues: 837 loop : -0.95 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 178 TYR 0.047 0.002 TYR C 653 PHE 0.022 0.002 PHE C 194 TRP 0.040 0.002 TRP I 36 HIS 0.008 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00581 (19683) covalent geometry : angle 0.62140 (26748) SS BOND : bond 0.00334 ( 15) SS BOND : angle 3.07479 ( 30) hydrogen bonds : bond 0.03916 ( 616) hydrogen bonds : angle 5.69570 ( 1578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 HIS cc_start: 0.7743 (p90) cc_final: 0.7499 (p-80) REVERT: A 421 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8114 (mpp) REVERT: B 534 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.8145 (t-90) REVERT: C 178 ARG cc_start: 0.8627 (mtt90) cc_final: 0.7864 (mtm-85) REVERT: C 421 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8164 (mpp) REVERT: C 534 HIS cc_start: 0.8952 (OUTLIER) cc_final: 0.7889 (t-90) REVERT: C 627 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8591 (mtt180) REVERT: H 47 TRP cc_start: 0.8207 (t60) cc_final: 0.7980 (t60) REVERT: H 81 MET cc_start: 0.7654 (ttp) cc_final: 0.7095 (tpp) REVERT: H 95 TYR cc_start: 0.6739 (m-80) cc_final: 0.6379 (m-80) REVERT: H 109 TYR cc_start: 0.8417 (m-80) cc_final: 0.8083 (m-80) REVERT: H 112 GLN cc_start: 0.8147 (mp10) cc_final: 0.7515 (pm20) REVERT: I 10 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6250 (mm-30) REVERT: I 81 MET cc_start: 0.7142 (ttp) cc_final: 0.6709 (tpp) REVERT: I 95 TYR cc_start: 0.6868 (m-80) cc_final: 0.6637 (m-80) REVERT: J 3 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8233 (tm-30) REVERT: J 70 LEU cc_start: 0.9151 (mm) cc_final: 0.8918 (mm) REVERT: J 73 ASP cc_start: 0.8047 (t0) cc_final: 0.7750 (t0) REVERT: J 80 TYR cc_start: 0.7567 (m-80) cc_final: 0.7177 (m-80) REVERT: J 95 TYR cc_start: 0.6951 (m-80) cc_final: 0.6572 (m-80) REVERT: J 112 GLN cc_start: 0.6811 (pm20) cc_final: 0.6423 (pm20) REVERT: L 3 GLN cc_start: 0.8803 (tp40) cc_final: 0.7871 (pp30) REVERT: M 61 ARG cc_start: 0.8061 (ptt-90) cc_final: 0.7559 (ptt180) REVERT: N 37 GLN cc_start: 0.7179 (tt0) cc_final: 0.6654 (tt0) REVERT: N 61 ARG cc_start: 0.7643 (ptt180) cc_final: 0.7068 (ptt90) REVERT: N 69 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7687 (mtpp) outliers start: 53 outliers final: 39 residues processed: 247 average time/residue: 0.1310 time to fit residues: 51.1271 Evaluate side-chains 252 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain L residue 30 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 227 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 204 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN N 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.088887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.060046 restraints weight = 50961.077| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.24 r_work: 0.2788 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19698 Z= 0.145 Angle : 0.574 8.765 26778 Z= 0.303 Chirality : 0.042 0.146 2907 Planarity : 0.004 0.047 3456 Dihedral : 4.739 21.782 2688 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.36 % Allowed : 15.92 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.17), residues: 2385 helix: 1.69 (0.30), residues: 297 sheet: -1.19 (0.17), residues: 864 loop : -0.83 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 178 TYR 0.047 0.001 TYR A 653 PHE 0.016 0.001 PHE A 294 TRP 0.038 0.002 TRP J 36 HIS 0.004 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00334 (19683) covalent geometry : angle 0.56746 (26748) SS BOND : bond 0.00247 ( 15) SS BOND : angle 2.55446 ( 30) hydrogen bonds : bond 0.03529 ( 616) hydrogen bonds : angle 5.58351 ( 1578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8099 (mpp) REVERT: B 534 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.8034 (t-90) REVERT: C 177 HIS cc_start: 0.8298 (p90) cc_final: 0.8055 (p90) REVERT: C 384 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: C 421 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8179 (mpp) REVERT: C 534 HIS cc_start: 0.8850 (OUTLIER) cc_final: 0.7753 (t-90) REVERT: C 627 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8570 (mtt180) REVERT: H 59 HIS cc_start: 0.7674 (m-70) cc_final: 0.7332 (m-70) REVERT: H 81 MET cc_start: 0.7594 (ttp) cc_final: 0.7048 (tpp) REVERT: H 95 TYR cc_start: 0.6666 (m-80) cc_final: 0.6272 (m-80) REVERT: H 109 TYR cc_start: 0.8402 (m-80) cc_final: 0.8035 (m-80) REVERT: H 112 GLN cc_start: 0.8338 (mp10) cc_final: 0.7646 (pm20) REVERT: I 10 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6735 (mm-30) REVERT: I 36 TRP cc_start: 0.6036 (m-10) cc_final: 0.5615 (m-10) REVERT: I 59 HIS cc_start: 0.7660 (m-70) cc_final: 0.7323 (m-70) REVERT: I 80 TYR cc_start: 0.7858 (m-10) cc_final: 0.7643 (m-80) REVERT: I 81 MET cc_start: 0.7174 (ttp) cc_final: 0.6860 (tpp) REVERT: I 95 TYR cc_start: 0.6807 (m-80) cc_final: 0.6550 (m-80) REVERT: I 112 GLN cc_start: 0.7027 (pm20) cc_final: 0.6718 (pm20) REVERT: J 3 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8187 (tm-30) REVERT: J 70 LEU cc_start: 0.9154 (mm) cc_final: 0.8897 (mm) REVERT: J 73 ASP cc_start: 0.8033 (t0) cc_final: 0.7752 (t0) REVERT: J 80 TYR cc_start: 0.7593 (m-80) cc_final: 0.7287 (m-10) REVERT: J 95 TYR cc_start: 0.6854 (m-80) cc_final: 0.6474 (m-80) REVERT: J 112 GLN cc_start: 0.6881 (pm20) cc_final: 0.6194 (pm20) REVERT: L 3 GLN cc_start: 0.8825 (tp40) cc_final: 0.7950 (pp30) REVERT: M 61 ARG cc_start: 0.8065 (ptt-90) cc_final: 0.7570 (ptt180) REVERT: N 27 ASP cc_start: 0.8786 (t0) cc_final: 0.7960 (m-30) REVERT: N 61 ARG cc_start: 0.7618 (ptt180) cc_final: 0.7116 (ptt90) REVERT: N 69 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7707 (mtpp) REVERT: N 79 GLN cc_start: 0.6321 (pp30) cc_final: 0.6099 (pp30) outliers start: 49 outliers final: 37 residues processed: 251 average time/residue: 0.1299 time to fit residues: 51.8174 Evaluate side-chains 249 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.2980 chunk 124 optimal weight: 0.7980 chunk 223 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 12 optimal weight: 0.0670 chunk 48 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS H 5 GLN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.088190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.059374 restraints weight = 51279.596| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.24 r_work: 0.2772 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19698 Z= 0.191 Angle : 0.590 8.634 26778 Z= 0.311 Chirality : 0.042 0.170 2907 Planarity : 0.004 0.050 3456 Dihedral : 4.781 22.367 2688 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.22 % Allowed : 16.30 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.10 (0.17), residues: 2385 helix: 1.63 (0.30), residues: 297 sheet: -1.26 (0.17), residues: 843 loop : -0.83 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 178 TYR 0.055 0.001 TYR C 653 PHE 0.019 0.001 PHE A 294 TRP 0.041 0.002 TRP J 36 HIS 0.006 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00439 (19683) covalent geometry : angle 0.58287 (26748) SS BOND : bond 0.00318 ( 15) SS BOND : angle 2.76012 ( 30) hydrogen bonds : bond 0.03732 ( 616) hydrogen bonds : angle 5.60225 ( 1578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7727 (mtm-85) REVERT: A 421 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8096 (mpp) REVERT: B 534 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8092 (t-90) REVERT: C 421 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8166 (mpp) REVERT: C 534 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.7822 (t-90) REVERT: C 627 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8539 (mtt180) REVERT: H 47 TRP cc_start: 0.7957 (t60) cc_final: 0.7689 (t60) REVERT: H 59 HIS cc_start: 0.7716 (m-70) cc_final: 0.7356 (m-70) REVERT: H 81 MET cc_start: 0.7592 (ttp) cc_final: 0.7040 (tpp) REVERT: H 95 TYR cc_start: 0.6739 (m-80) cc_final: 0.6382 (m-80) REVERT: H 109 TYR cc_start: 0.8393 (m-80) cc_final: 0.8060 (m-80) REVERT: H 112 GLN cc_start: 0.8314 (mp10) cc_final: 0.7570 (pm20) REVERT: I 10 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6727 (mm-30) REVERT: I 59 HIS cc_start: 0.7691 (m-70) cc_final: 0.7351 (m-70) REVERT: I 80 TYR cc_start: 0.7963 (m-10) cc_final: 0.7526 (m-10) REVERT: I 95 TYR cc_start: 0.6892 (m-80) cc_final: 0.6664 (m-80) REVERT: I 112 GLN cc_start: 0.6988 (pm20) cc_final: 0.6683 (pm20) REVERT: J 3 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8213 (tm-30) REVERT: J 73 ASP cc_start: 0.8073 (t0) cc_final: 0.7784 (t0) REVERT: J 80 TYR cc_start: 0.7637 (m-80) cc_final: 0.7287 (m-80) REVERT: J 95 TYR cc_start: 0.6970 (m-80) cc_final: 0.6561 (m-80) REVERT: J 112 GLN cc_start: 0.6893 (pm20) cc_final: 0.6426 (pm20) REVERT: L 3 GLN cc_start: 0.8866 (tp40) cc_final: 0.8544 (mm-40) REVERT: L 79 GLN cc_start: 0.6332 (pp30) cc_final: 0.6124 (pp30) REVERT: M 61 ARG cc_start: 0.8079 (ptt-90) cc_final: 0.7582 (ptt180) REVERT: M 87 TYR cc_start: 0.7593 (m-10) cc_final: 0.7378 (m-10) REVERT: N 27 ASP cc_start: 0.8768 (t0) cc_final: 0.7947 (m-30) REVERT: N 61 ARG cc_start: 0.7616 (ptt180) cc_final: 0.7103 (ptt90) REVERT: N 69 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7676 (mtpp) REVERT: N 79 GLN cc_start: 0.6470 (pp30) cc_final: 0.6243 (pp30) outliers start: 46 outliers final: 37 residues processed: 240 average time/residue: 0.1417 time to fit residues: 53.0586 Evaluate side-chains 250 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain L residue 30 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 182 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 181 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.088344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.059538 restraints weight = 51128.776| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.23 r_work: 0.2776 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 19698 Z= 0.225 Angle : 0.876 59.199 26778 Z= 0.518 Chirality : 0.043 0.532 2907 Planarity : 0.004 0.061 3456 Dihedral : 4.790 22.303 2688 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 2.32 % Allowed : 16.21 % Favored : 81.48 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.71 % 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: -1.07 (0.17), residues: 2385 helix: 1.65 (0.30), residues: 297 sheet: -1.21 (0.16), residues: 861 loop : -0.83 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 178 TYR 0.050 0.001 TYR C 653 PHE 0.016 0.001 PHE A 294 TRP 0.035 0.002 TRP J 36 HIS 0.006 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00481 (19683) covalent geometry : angle 0.87156 (26748) SS BOND : bond 0.00375 ( 15) SS BOND : angle 2.73028 ( 30) hydrogen bonds : bond 0.03791 ( 616) hydrogen bonds : angle 5.61734 ( 1578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4337.93 seconds wall clock time: 75 minutes 29.33 seconds (4529.33 seconds total)