Starting phenix.real_space_refine on Sat Sep 12 17:19:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6j_47570/09_2026/9e6j_47570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6j_47570/09_2026/9e6j_47570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e6j_47570/09_2026/9e6j_47570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6j_47570/09_2026/9e6j_47570.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6j_47570/09_2026/9e6j_47570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6j_47570/09_2026/9e6j_47570.cif" } resolution = 2.98 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= 0.024 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 75 5.16 5 C 10512 2.51 5 N 2889 2.21 5 O 3267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16743 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3843 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 20, 'TRANS': 463} Chain breaks: 3 Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 96} Restraints were copied for chains: B, C, I, J, M, N Time building chain proxies: 4.23, per 1000 atoms: 0.25 Number of scatterers: 16743 At special positions: 0 Unit cell: (130.9, 126.5, 147.4, 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 75 16.00 O 3267 8.00 N 2889 7.00 C 10512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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: 1.41 Conformation dependent library (CDL) restraints added in 747.2 milliseconds 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 54 sheets defined 21.0% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.238A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 387 Processing helix chain 'A' and resid 403 through 456 removed outlier: 3.883A pdb=" N GLN A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'A' and resid 487 through 501 removed outlier: 3.916A pdb=" N TYR A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.043A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 122 through 127 removed outlier: 4.238A pdb=" N TRP B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 403 through 456 removed outlier: 3.883A pdb=" N GLN B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 487 through 501 removed outlier: 3.916A pdb=" N TYR B 491 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.043A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.238A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 387 Processing helix chain 'C' and resid 403 through 456 removed outlier: 3.883A pdb=" N GLN C 454 " --> pdb=" O LYS C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 487 through 501 removed outlier: 3.916A pdb=" N TYR C 491 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.043A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.061A pdb=" N ASP A 18 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 48 removed outlier: 5.675A pdb=" N LEU A 45 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.584A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 83 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 119 removed outlier: 3.658A pdb=" N SER A 114 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 119 removed outlier: 3.658A pdb=" N SER A 114 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.696A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 288 through 289 removed outlier: 4.317A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.747A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.585A pdb=" N VAL H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.656A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.253A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 361 through 365 Processing sheet with id=AC2, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.062A pdb=" N ASP B 18 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC4, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AC5, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.675A pdb=" N LEU B 45 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N CYS B 278 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.585A pdb=" N LEU B 54 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 83 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 112 through 119 removed outlier: 3.659A pdb=" N SER B 114 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 175 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 112 through 119 removed outlier: 3.659A pdb=" N SER B 114 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 175 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.696A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'B' and resid 288 through 289 removed outlier: 4.316A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.747A pdb=" N MET I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.585A pdb=" N VAL I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 98 through 100 Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AD8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.657A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.252A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 365 Processing sheet with id=AE2, first strand: chain 'C' and resid 18 through 20 removed outlier: 4.061A pdb=" N ASP C 18 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE4, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AE5, first strand: chain 'C' and resid 45 through 48 removed outlier: 5.675A pdb=" N LEU C 45 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N CYS C 278 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.585A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 83 " --> pdb=" O ILE C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 112 through 119 removed outlier: 3.658A pdb=" N SER C 114 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 112 through 119 removed outlier: 3.658A pdb=" N SER C 114 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.695A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AF2, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.317A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.747A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.584A pdb=" N VAL J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 98 through 100 Processing sheet with id=AF7, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.656A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.252A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2034 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: 3.70 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5530 1.34 - 1.46: 3856 1.46 - 1.58: 7630 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 17118 Sorted by residual: bond pdb=" CB VAL C 112 " pdb=" CG1 VAL C 112 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.46e-01 bond pdb=" CB VAL B 112 " pdb=" CG1 VAL B 112 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.41e-01 bond pdb=" CB VAL A 112 " pdb=" CG1 VAL A 112 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.35e-01 bond pdb=" CB VAL A 318 " pdb=" CG2 VAL A 318 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.89e-01 bond pdb=" CG1 ILE A 252 " pdb=" CD1 ILE A 252 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.80e-01 ... (remaining 17113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 21570 1.18 - 2.36: 1342 2.36 - 3.54: 228 3.54 - 4.72: 35 4.72 - 5.90: 18 Bond angle restraints: 23193 Sorted by residual: angle pdb=" CA GLN H 96 " pdb=" CB GLN H 96 " pdb=" CG GLN H 96 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.46e+00 angle pdb=" CA GLN J 96 " pdb=" CB GLN J 96 " pdb=" CG GLN J 96 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.40e+00 angle pdb=" CA GLN I 96 " pdb=" CB GLN I 96 " pdb=" CG GLN I 96 " ideal model delta sigma weight residual 114.10 119.88 -5.78 2.00e+00 2.50e-01 8.35e+00 angle pdb=" CA CYS B 139 " pdb=" CB CYS B 139 " pdb=" SG CYS B 139 " ideal model delta sigma weight residual 114.40 108.50 5.90 2.30e+00 1.89e-01 6.59e+00 angle pdb=" CA CYS A 139 " pdb=" CB CYS A 139 " pdb=" SG CYS A 139 " ideal model delta sigma weight residual 114.40 108.52 5.88 2.30e+00 1.89e-01 6.54e+00 ... (remaining 23188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 9534 17.83 - 35.65: 543 35.65 - 53.48: 87 53.48 - 71.30: 42 71.30 - 89.13: 15 Dihedral angle restraints: 10221 sinusoidal: 4074 harmonic: 6147 Sorted by residual: dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sinusoidal sigma weight residual -86.00 -152.40 66.40 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual -86.00 -152.39 66.39 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS B 94 " pdb=" SG CYS B 94 " pdb=" SG CYS B 139 " pdb=" CB CYS B 139 " ideal model delta sinusoidal sigma weight residual -86.00 -152.36 66.36 1 1.00e+01 1.00e-02 5.75e+01 ... (remaining 10218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1279 0.029 - 0.058: 760 0.058 - 0.087: 246 0.087 - 0.116: 147 0.116 - 0.145: 64 Chirality restraints: 2496 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA VAL I 37 " pdb=" N VAL I 37 " pdb=" C VAL I 37 " pdb=" CB VAL I 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA VAL J 37 " pdb=" N VAL J 37 " pdb=" C VAL J 37 " pdb=" CB VAL J 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2493 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 77 " 0.275 9.50e-02 1.11e+02 1.24e-01 1.17e+01 pdb=" NE ARG A 77 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 77 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG A 77 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 77 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 77 " -0.274 9.50e-02 1.11e+02 1.24e-01 1.16e+01 pdb=" NE ARG B 77 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 77 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 77 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 77 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 77 " 0.274 9.50e-02 1.11e+02 1.24e-01 1.16e+01 pdb=" NE ARG C 77 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 77 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 77 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 77 " 0.001 2.00e-02 2.50e+03 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3055 2.78 - 3.31: 15295 3.31 - 3.84: 27722 3.84 - 4.37: 34816 4.37 - 4.90: 60443 Nonbonded interactions: 141331 Sorted by model distance: nonbonded pdb=" OE1 GLU A 72 " pdb=" NZ LYS A 149 " model vdw 2.248 3.120 nonbonded pdb=" OE1 GLU B 72 " pdb=" NZ LYS B 149 " model vdw 2.249 3.120 nonbonded pdb=" OE1 GLU C 72 " pdb=" NZ LYS C 149 " model vdw 2.249 3.120 nonbonded pdb=" O TYR I 32 " pdb=" NH2 ARG I 71 " model vdw 2.325 3.120 nonbonded pdb=" O TYR H 32 " pdb=" NH2 ARG H 71 " model vdw 2.325 3.120 ... (remaining 141326 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: 0.05 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.870 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.003 0.034 17142 Z= 0.139 Angle : 0.655 5.904 23241 Z= 0.382 Chirality : 0.047 0.145 2496 Planarity : 0.008 0.124 3024 Dihedral : 12.741 89.128 6231 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.32 % Allowed : 3.25 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.17), residues: 2109 helix: -0.90 (0.22), residues: 357 sheet: -0.12 (0.22), residues: 504 loop : -0.76 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.004 ARG A 77 TYR 0.035 0.005 TYR I 35 PHE 0.023 0.002 PHE C 115 TRP 0.020 0.002 TRP H 103 HIS 0.007 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (17118) covalent geometry : angle 0.65376 / 0.38 (23193) SS BOND : bond 0.00469 / 0.28 ( 24) SS BOND : angle 1.20826 / 0.76 ( 48) hydrogen bonds : bond 0.18953 / 12.65 ( 711) hydrogen bonds : angle 8.51544 / 5.89 ( 2034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 318 time to evaluate : 0.612 Fit side-chains REVERT: A 26 LYS cc_start: 0.8815 (mttt) cc_final: 0.8290 (mmtt) REVERT: A 116 GLU cc_start: 0.8152 (pt0) cc_final: 0.7806 (pt0) REVERT: A 219 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7938 (tppp) REVERT: A 248 ASN cc_start: 0.8337 (p0) cc_final: 0.8011 (p0) REVERT: A 281 LYS cc_start: 0.8753 (mttt) cc_final: 0.8471 (mtmt) REVERT: A 317 MET cc_start: 0.8820 (ttm) cc_final: 0.8600 (ttt) REVERT: A 357 ASN cc_start: 0.8069 (p0) cc_final: 0.7847 (p0) REVERT: A 406 MET cc_start: 0.8347 (mtp) cc_final: 0.7851 (mmt) REVERT: A 445 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7722 (mttp) REVERT: A 479 GLU cc_start: 0.7832 (pt0) cc_final: 0.7390 (mm-30) REVERT: H 7 SER cc_start: 0.8157 (p) cc_final: 0.7678 (m) REVERT: H 20 LEU cc_start: 0.8563 (mt) cc_final: 0.8260 (mp) REVERT: H 43 LYS cc_start: 0.7684 (mttt) cc_final: 0.7415 (mtpm) REVERT: H 82 SER cc_start: 0.8559 (m) cc_final: 0.8152 (p) REVERT: H 101 ASP cc_start: 0.8467 (t0) cc_final: 0.8248 (t70) REVERT: L 42 LYS cc_start: 0.8485 (mttt) cc_final: 0.8252 (mptt) REVERT: B 26 LYS cc_start: 0.8941 (mttt) cc_final: 0.8374 (mptt) REVERT: B 116 GLU cc_start: 0.8162 (pt0) cc_final: 0.7732 (pt0) REVERT: B 214 THR cc_start: 0.8527 (m) cc_final: 0.8098 (p) REVERT: B 219 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7920 (tppt) REVERT: B 277 GLU cc_start: 0.7143 (tp30) cc_final: 0.6769 (tm-30) REVERT: B 317 MET cc_start: 0.8791 (ttm) cc_final: 0.8550 (ttt) REVERT: B 445 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7366 (mptt) REVERT: B 478 MET cc_start: 0.8118 (mmt) cc_final: 0.7904 (mmm) REVERT: B 479 GLU cc_start: 0.7738 (pt0) cc_final: 0.7443 (mm-30) REVERT: I 7 SER cc_start: 0.8561 (p) cc_final: 0.8063 (m) REVERT: I 20 LEU cc_start: 0.8432 (mt) cc_final: 0.8168 (mp) REVERT: I 39 GLN cc_start: 0.8675 (tt0) cc_final: 0.8467 (tt0) REVERT: I 43 LYS cc_start: 0.8076 (mttt) cc_final: 0.7768 (mttm) REVERT: I 82 SER cc_start: 0.8632 (m) cc_final: 0.8189 (p) REVERT: M 42 LYS cc_start: 0.8378 (mttt) cc_final: 0.8110 (mmtp) REVERT: C 26 LYS cc_start: 0.8883 (mttt) cc_final: 0.8451 (mmtt) REVERT: C 175 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7405 (mm-30) REVERT: C 214 THR cc_start: 0.8442 (m) cc_final: 0.8124 (p) REVERT: C 277 GLU cc_start: 0.6965 (tp30) cc_final: 0.6405 (tm-30) REVERT: C 289 ILE cc_start: 0.8456 (mt) cc_final: 0.8249 (mt) REVERT: C 317 MET cc_start: 0.8863 (ttm) cc_final: 0.8576 (ttt) REVERT: C 338 PHE cc_start: 0.8970 (p90) cc_final: 0.8767 (p90) REVERT: C 388 MET cc_start: 0.9300 (tpp) cc_final: 0.8947 (tpt) REVERT: C 441 ASP cc_start: 0.8502 (m-30) cc_final: 0.8267 (m-30) REVERT: C 445 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7457 (mptt) REVERT: C 468 GLU cc_start: 0.8280 (tt0) cc_final: 0.8048 (tt0) REVERT: C 479 GLU cc_start: 0.7943 (pt0) cc_final: 0.7377 (mm-30) REVERT: J 17 SER cc_start: 0.7764 (m) cc_final: 0.7418 (t) REVERT: J 32 TYR cc_start: 0.8734 (m-80) cc_final: 0.8361 (m-80) REVERT: J 43 LYS cc_start: 0.7604 (mttt) cc_final: 0.7363 (mtpm) REVERT: J 82 SER cc_start: 0.8528 (m) cc_final: 0.8214 (p) REVERT: N 42 LYS cc_start: 0.8291 (mttt) cc_final: 0.7997 (mtmt) REVERT: N 45 LYS cc_start: 0.8415 (tttt) cc_final: 0.7880 (mttp) outliers start: 6 outliers final: 1 residues processed: 324 average time/residue: 0.5883 time to fit residues: 212.3711 Evaluate side-chains 211 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 129 ASN A 196 HIS A 424 ASN A 483 ASN H 73 ASN L 91 HIS B 35 ASN B 142 ASN B 424 ASN I 76 ASN M 91 HIS C 35 ASN C 129 ASN C 424 ASN J 76 ASN J 105 GLN N 91 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.180940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148353 restraints weight = 16781.527| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.52 r_work: 0.3361 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17142 Z= 0.137 Angle : 0.553 5.713 23241 Z= 0.307 Chirality : 0.044 0.147 2496 Planarity : 0.004 0.040 3024 Dihedral : 5.266 36.976 2312 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.19 % Allowed : 9.15 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2109 helix: 1.54 (0.26), residues: 360 sheet: 0.05 (0.21), residues: 498 loop : -0.41 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 220 TYR 0.011 0.002 TYR B 363 PHE 0.016 0.002 PHE B 439 TRP 0.011 0.001 TRP C 350 HIS 0.007 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (17118) covalent geometry : angle 0.55190 / 0.31 (23193) SS BOND : bond 0.00340 / 0.21 ( 24) SS BOND : angle 0.96232 / 0.60 ( 48) hydrogen bonds : bond 0.05099 / 3.48 ( 711) hydrogen bonds : angle 5.66607 / 3.97 ( 2034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.567 Fit side-chains REVERT: A 26 LYS cc_start: 0.8694 (mttt) cc_final: 0.8262 (mmtt) REVERT: A 116 GLU cc_start: 0.8062 (pt0) cc_final: 0.7791 (pt0) REVERT: A 214 THR cc_start: 0.8485 (m) cc_final: 0.8176 (p) REVERT: A 219 LYS cc_start: 0.8293 (ttmt) cc_final: 0.8056 (tppp) REVERT: A 246 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: A 248 ASN cc_start: 0.8346 (p0) cc_final: 0.8106 (p0) REVERT: A 281 LYS cc_start: 0.8769 (mttt) cc_final: 0.8479 (mtmt) REVERT: A 406 MET cc_start: 0.8251 (mtp) cc_final: 0.7912 (mmt) REVERT: A 445 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7426 (mttp) REVERT: A 468 GLU cc_start: 0.8343 (tt0) cc_final: 0.8080 (tt0) REVERT: A 479 GLU cc_start: 0.7679 (pt0) cc_final: 0.7197 (mm-30) REVERT: A 495 SER cc_start: 0.7331 (p) cc_final: 0.7046 (t) REVERT: H 7 SER cc_start: 0.8289 (p) cc_final: 0.7937 (m) REVERT: H 82 SER cc_start: 0.8631 (m) cc_final: 0.8404 (p) REVERT: H 101 ASP cc_start: 0.8409 (t0) cc_final: 0.8134 (t70) REVERT: L 42 LYS cc_start: 0.8622 (mttt) cc_final: 0.8316 (mptt) REVERT: L 45 LYS cc_start: 0.8465 (tttt) cc_final: 0.7941 (mtpt) REVERT: L 53 THR cc_start: 0.8986 (t) cc_final: 0.8751 (m) REVERT: B 4 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5365 (tp30) REVERT: B 26 LYS cc_start: 0.8890 (mttt) cc_final: 0.8387 (mptt) REVERT: B 116 GLU cc_start: 0.7991 (pt0) cc_final: 0.7572 (pt0) REVERT: B 214 THR cc_start: 0.8561 (m) cc_final: 0.8098 (p) REVERT: B 246 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: B 277 GLU cc_start: 0.7206 (tp30) cc_final: 0.6860 (tm-30) REVERT: B 445 LYS cc_start: 0.7859 (ttmt) cc_final: 0.7255 (mptt) REVERT: B 468 GLU cc_start: 0.8235 (tt0) cc_final: 0.8018 (tt0) REVERT: B 479 GLU cc_start: 0.7772 (pt0) cc_final: 0.7317 (mm-30) REVERT: I 7 SER cc_start: 0.8550 (p) cc_final: 0.8229 (m) REVERT: I 43 LYS cc_start: 0.8111 (mttt) cc_final: 0.7823 (mttm) REVERT: I 59 TYR cc_start: 0.9173 (m-80) cc_final: 0.8878 (m-80) REVERT: I 82 SER cc_start: 0.8861 (m) cc_final: 0.8554 (p) REVERT: I 84 VAL cc_start: 0.7648 (t) cc_final: 0.7296 (m) REVERT: I 105 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: M 42 LYS cc_start: 0.8496 (mttt) cc_final: 0.8104 (mmtp) REVERT: M 45 LYS cc_start: 0.8535 (tttt) cc_final: 0.7952 (mttp) REVERT: M 53 THR cc_start: 0.8942 (t) cc_final: 0.8731 (m) REVERT: C 21 ASP cc_start: 0.8406 (m-30) cc_final: 0.8092 (m-30) REVERT: C 26 LYS cc_start: 0.8788 (mttt) cc_final: 0.8401 (mmtt) REVERT: C 175 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7336 (mm-30) REVERT: C 214 THR cc_start: 0.8491 (m) cc_final: 0.8161 (p) REVERT: C 277 GLU cc_start: 0.7098 (tp30) cc_final: 0.6539 (tm-30) REVERT: C 317 MET cc_start: 0.8822 (ttm) cc_final: 0.8578 (ttt) REVERT: C 338 PHE cc_start: 0.8928 (p90) cc_final: 0.8698 (p90) REVERT: C 441 ASP cc_start: 0.8466 (m-30) cc_final: 0.8194 (m-30) REVERT: C 445 LYS cc_start: 0.7811 (ttmt) cc_final: 0.7251 (mptt) REVERT: C 468 GLU cc_start: 0.8254 (tt0) cc_final: 0.8042 (tt0) REVERT: C 479 GLU cc_start: 0.7795 (pt0) cc_final: 0.7196 (mm-30) REVERT: J 32 TYR cc_start: 0.8913 (m-80) cc_final: 0.8616 (m-80) REVERT: J 43 LYS cc_start: 0.7744 (mttt) cc_final: 0.7535 (mtpm) REVERT: N 42 LYS cc_start: 0.8371 (mttt) cc_final: 0.7932 (mtmt) REVERT: N 45 LYS cc_start: 0.8462 (tttt) cc_final: 0.7944 (mttp) outliers start: 22 outliers final: 11 residues processed: 237 average time/residue: 0.5495 time to fit residues: 146.5841 Evaluate side-chains 206 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 132 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 202 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 142 ASN H 76 ASN B 58 ASN B 130 HIS B 498 ASN C 58 ASN C 142 ASN C 483 ASN C 498 ASN J 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.142099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.108140 restraints weight = 18025.696| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.91 r_work: 0.2840 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17142 Z= 0.196 Angle : 0.576 5.985 23241 Z= 0.315 Chirality : 0.046 0.150 2496 Planarity : 0.004 0.044 3024 Dihedral : 5.066 37.199 2312 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.33 % Allowed : 9.85 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2109 helix: 1.86 (0.27), residues: 360 sheet: 0.08 (0.21), residues: 528 loop : -0.41 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 220 TYR 0.018 0.002 TYR M 49 PHE 0.023 0.002 PHE B 439 TRP 0.012 0.001 TRP J 103 HIS 0.011 0.002 HIS M 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (17118) covalent geometry : angle 0.57443 / 0.31 (23193) SS BOND : bond 0.00478 / 0.31 ( 24) SS BOND : angle 0.99210 / 0.64 ( 48) hydrogen bonds : bond 0.05130 / 3.50 ( 711) hydrogen bonds : angle 5.43230 / 3.82 ( 2034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 1.136 Fit side-chains REVERT: A 26 LYS cc_start: 0.8665 (mttt) cc_final: 0.7910 (mmtt) REVERT: A 116 GLU cc_start: 0.7817 (pt0) cc_final: 0.7526 (pt0) REVERT: A 149 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8519 (mmtt) REVERT: A 212 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7486 (mtpm) REVERT: A 214 THR cc_start: 0.8453 (m) cc_final: 0.8061 (p) REVERT: A 219 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8049 (tppp) REVERT: A 246 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: A 281 LYS cc_start: 0.8533 (mttt) cc_final: 0.8031 (mtmt) REVERT: A 406 MET cc_start: 0.7990 (mtp) cc_final: 0.7432 (mmm) REVERT: A 445 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7097 (mttp) REVERT: A 468 GLU cc_start: 0.8279 (tt0) cc_final: 0.7833 (tt0) REVERT: A 479 GLU cc_start: 0.7351 (pt0) cc_final: 0.6712 (mm-30) REVERT: H 7 SER cc_start: 0.8116 (p) cc_final: 0.7656 (m) REVERT: H 82 SER cc_start: 0.8523 (m) cc_final: 0.8085 (p) REVERT: L 42 LYS cc_start: 0.8442 (mttt) cc_final: 0.7872 (mptt) REVERT: L 45 LYS cc_start: 0.8231 (tttt) cc_final: 0.7441 (mtpt) REVERT: B 4 GLU cc_start: 0.5463 (OUTLIER) cc_final: 0.4822 (tp30) REVERT: B 26 LYS cc_start: 0.8716 (mttt) cc_final: 0.7949 (mptt) REVERT: B 116 GLU cc_start: 0.7750 (pt0) cc_final: 0.7309 (pt0) REVERT: B 175 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: B 212 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8328 (ttmt) REVERT: B 214 THR cc_start: 0.8453 (m) cc_final: 0.8051 (p) REVERT: B 246 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: B 276 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.6780 (m-30) REVERT: B 445 LYS cc_start: 0.7639 (ttmt) cc_final: 0.6729 (mptt) REVERT: B 468 GLU cc_start: 0.8133 (tt0) cc_final: 0.7877 (tt0) REVERT: B 479 GLU cc_start: 0.7446 (pt0) cc_final: 0.6758 (mm-30) REVERT: B 490 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7689 (ttpp) REVERT: I 7 SER cc_start: 0.8408 (p) cc_final: 0.7963 (m) REVERT: I 43 LYS cc_start: 0.7978 (mttt) cc_final: 0.7616 (mttm) REVERT: I 82 SER cc_start: 0.8653 (m) cc_final: 0.8174 (p) REVERT: I 105 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7720 (pt0) REVERT: M 42 LYS cc_start: 0.8354 (mttt) cc_final: 0.7770 (mmtp) REVERT: M 45 LYS cc_start: 0.8328 (tttt) cc_final: 0.7357 (mttp) REVERT: M 53 THR cc_start: 0.8848 (t) cc_final: 0.8557 (m) REVERT: C 26 LYS cc_start: 0.8742 (mttt) cc_final: 0.8087 (mptt) REVERT: C 148 TYR cc_start: 0.8579 (m-80) cc_final: 0.8359 (m-80) REVERT: C 149 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8469 (mttm) REVERT: C 175 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7154 (mm-30) REVERT: C 214 THR cc_start: 0.8486 (m) cc_final: 0.8085 (p) REVERT: C 219 LYS cc_start: 0.8214 (tptm) cc_final: 0.7937 (tptm) REVERT: C 276 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: C 317 MET cc_start: 0.8996 (ttm) cc_final: 0.8746 (ttt) REVERT: C 338 PHE cc_start: 0.8862 (p90) cc_final: 0.8606 (p90) REVERT: C 402 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8002 (mt) REVERT: C 445 LYS cc_start: 0.7598 (ttmt) cc_final: 0.6724 (mptt) REVERT: C 468 GLU cc_start: 0.8173 (tt0) cc_final: 0.7812 (tt0) REVERT: C 479 GLU cc_start: 0.7395 (pt0) cc_final: 0.6551 (mm-30) REVERT: J 52 ASN cc_start: 0.8951 (p0) cc_final: 0.8737 (p0) REVERT: N 42 LYS cc_start: 0.8133 (mttt) cc_final: 0.7551 (mtmt) REVERT: N 45 LYS cc_start: 0.8175 (tttt) cc_final: 0.7280 (mttp) outliers start: 43 outliers final: 18 residues processed: 225 average time/residue: 0.5383 time to fit residues: 136.5947 Evaluate side-chains 208 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.143912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109863 restraints weight = 17878.290| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.98 r_work: 0.2863 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17142 Z= 0.135 Angle : 0.509 6.690 23241 Z= 0.277 Chirality : 0.043 0.150 2496 Planarity : 0.004 0.044 3024 Dihedral : 4.713 38.121 2312 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.44 % Allowed : 11.15 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2109 helix: 2.20 (0.27), residues: 363 sheet: 0.16 (0.21), residues: 537 loop : -0.38 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 220 TYR 0.014 0.002 TYR A 491 PHE 0.016 0.002 PHE B 439 TRP 0.009 0.001 TRP C 421 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (17118) covalent geometry : angle 0.50851 / 0.28 (23193) SS BOND : bond 0.00387 / 0.25 ( 24) SS BOND : angle 0.81582 / 0.51 ( 48) hydrogen bonds : bond 0.04460 / 3.03 ( 711) hydrogen bonds : angle 5.07617 / 3.59 ( 2034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.570 Fit side-chains REVERT: A 26 LYS cc_start: 0.8666 (mttt) cc_final: 0.7890 (mmtt) REVERT: A 116 GLU cc_start: 0.7842 (pt0) cc_final: 0.7557 (pt0) REVERT: A 214 THR cc_start: 0.8337 (m) cc_final: 0.7950 (p) REVERT: A 219 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8066 (tppp) REVERT: A 246 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: A 281 LYS cc_start: 0.8438 (mttt) cc_final: 0.8025 (mtmt) REVERT: A 406 MET cc_start: 0.7943 (mtp) cc_final: 0.7402 (mmm) REVERT: A 445 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7062 (mttp) REVERT: A 468 GLU cc_start: 0.8282 (tt0) cc_final: 0.7822 (tt0) REVERT: A 479 GLU cc_start: 0.7377 (pt0) cc_final: 0.6672 (mm-30) REVERT: A 495 SER cc_start: 0.6566 (t) cc_final: 0.6225 (p) REVERT: H 7 SER cc_start: 0.8131 (p) cc_final: 0.7638 (m) REVERT: H 82 SER cc_start: 0.8515 (m) cc_final: 0.8057 (p) REVERT: L 42 LYS cc_start: 0.8443 (mttt) cc_final: 0.7865 (mptt) REVERT: L 45 LYS cc_start: 0.8214 (tttt) cc_final: 0.7406 (mtpt) REVERT: B 4 GLU cc_start: 0.5487 (OUTLIER) cc_final: 0.4877 (tp30) REVERT: B 26 LYS cc_start: 0.8676 (mttt) cc_final: 0.7913 (mptt) REVERT: B 116 GLU cc_start: 0.7723 (pt0) cc_final: 0.7263 (pt0) REVERT: B 175 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: B 214 THR cc_start: 0.8531 (m) cc_final: 0.8146 (p) REVERT: B 246 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: B 276 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.6848 (m-30) REVERT: B 445 LYS cc_start: 0.7566 (ttmt) cc_final: 0.6602 (mptt) REVERT: B 468 GLU cc_start: 0.8152 (tt0) cc_final: 0.7801 (tt0) REVERT: B 479 GLU cc_start: 0.7442 (pt0) cc_final: 0.6736 (mm-30) REVERT: I 7 SER cc_start: 0.8342 (p) cc_final: 0.7844 (m) REVERT: I 43 LYS cc_start: 0.8036 (mttt) cc_final: 0.7654 (mttm) REVERT: I 82 SER cc_start: 0.8763 (m) cc_final: 0.8170 (p) REVERT: I 105 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: M 42 LYS cc_start: 0.8334 (mttt) cc_final: 0.7737 (mmtp) REVERT: M 45 LYS cc_start: 0.8309 (tttt) cc_final: 0.7308 (mtmm) REVERT: M 53 THR cc_start: 0.8789 (t) cc_final: 0.8445 (m) REVERT: C 21 ASP cc_start: 0.8802 (m-30) cc_final: 0.8579 (m-30) REVERT: C 26 LYS cc_start: 0.8583 (mttt) cc_final: 0.8009 (mptt) REVERT: C 149 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8436 (mttm) REVERT: C 175 GLU cc_start: 0.7836 (mt-10) cc_final: 0.6942 (mm-30) REVERT: C 214 THR cc_start: 0.8357 (m) cc_final: 0.7981 (p) REVERT: C 219 LYS cc_start: 0.8218 (tptm) cc_final: 0.7953 (tptm) REVERT: C 317 MET cc_start: 0.8952 (ttm) cc_final: 0.8696 (ttt) REVERT: C 338 PHE cc_start: 0.8774 (p90) cc_final: 0.8537 (p90) REVERT: C 445 LYS cc_start: 0.7499 (ttmt) cc_final: 0.6570 (mptt) REVERT: C 468 GLU cc_start: 0.8119 (tt0) cc_final: 0.7708 (tt0) REVERT: C 479 GLU cc_start: 0.7351 (pt0) cc_final: 0.6428 (mm-30) REVERT: N 42 LYS cc_start: 0.8099 (mttt) cc_final: 0.7532 (mtmt) REVERT: N 45 LYS cc_start: 0.8153 (tttt) cc_final: 0.7269 (mttp) REVERT: N 53 THR cc_start: 0.8658 (t) cc_final: 0.8369 (m) outliers start: 45 outliers final: 18 residues processed: 225 average time/residue: 0.5363 time to fit residues: 135.7497 Evaluate side-chains 203 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 146 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 154 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 148 optimal weight: 0.0000 chunk 187 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.145057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.112122 restraints weight = 17826.659| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.80 r_work: 0.2897 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17142 Z= 0.117 Angle : 0.492 7.752 23241 Z= 0.263 Chirality : 0.042 0.144 2496 Planarity : 0.004 0.042 3024 Dihedral : 4.474 38.430 2312 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.16 % Allowed : 11.96 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2109 helix: 2.45 (0.27), residues: 363 sheet: 0.35 (0.22), residues: 537 loop : -0.37 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 220 TYR 0.015 0.001 TYR C 491 PHE 0.014 0.001 PHE B 439 TRP 0.008 0.001 TRP C 421 HIS 0.005 0.001 HIS N 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17118) covalent geometry : angle 0.49156 / 0.26 (23193) SS BOND : bond 0.00363 / 0.23 ( 24) SS BOND : angle 0.75280 / 0.46 ( 48) hydrogen bonds : bond 0.04193 / 2.85 ( 711) hydrogen bonds : angle 4.88315 / 3.45 ( 2034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.521 Fit side-chains REVERT: A 26 LYS cc_start: 0.8649 (mttt) cc_final: 0.7953 (mmtt) REVERT: A 116 GLU cc_start: 0.7847 (pt0) cc_final: 0.7578 (pt0) REVERT: A 149 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8377 (mmtp) REVERT: A 212 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7469 (mtpm) REVERT: A 214 THR cc_start: 0.8328 (m) cc_final: 0.7957 (p) REVERT: A 219 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8105 (tppp) REVERT: A 246 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: A 281 LYS cc_start: 0.8368 (mttt) cc_final: 0.8032 (mtmt) REVERT: A 406 MET cc_start: 0.7945 (mtp) cc_final: 0.7418 (mmt) REVERT: A 445 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7036 (mttp) REVERT: A 468 GLU cc_start: 0.8275 (tt0) cc_final: 0.7865 (tt0) REVERT: A 479 GLU cc_start: 0.7414 (pt0) cc_final: 0.6742 (mm-30) REVERT: H 7 SER cc_start: 0.8210 (p) cc_final: 0.7715 (m) REVERT: H 43 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7640 (mtpm) REVERT: H 72 ASP cc_start: 0.7697 (t70) cc_final: 0.7401 (t0) REVERT: H 82 SER cc_start: 0.8523 (m) cc_final: 0.8078 (p) REVERT: L 42 LYS cc_start: 0.8383 (mttt) cc_final: 0.7889 (mptt) REVERT: L 45 LYS cc_start: 0.8248 (tttt) cc_final: 0.7461 (mtpt) REVERT: B 4 GLU cc_start: 0.5567 (OUTLIER) cc_final: 0.4992 (tp30) REVERT: B 116 GLU cc_start: 0.7729 (pt0) cc_final: 0.7275 (pt0) REVERT: B 219 LYS cc_start: 0.8232 (ttpt) cc_final: 0.7989 (tttm) REVERT: B 246 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: B 276 ASP cc_start: 0.7640 (t70) cc_final: 0.6894 (OUTLIER) REVERT: B 445 LYS cc_start: 0.7580 (ttmt) cc_final: 0.6660 (mptt) REVERT: B 468 GLU cc_start: 0.8163 (tt0) cc_final: 0.7792 (tt0) REVERT: B 479 GLU cc_start: 0.7507 (pt0) cc_final: 0.6815 (mm-30) REVERT: I 7 SER cc_start: 0.8414 (p) cc_final: 0.7923 (m) REVERT: I 43 LYS cc_start: 0.8103 (mttt) cc_final: 0.7739 (mttm) REVERT: I 59 TYR cc_start: 0.9130 (m-80) cc_final: 0.8834 (m-80) REVERT: I 82 SER cc_start: 0.8776 (m) cc_final: 0.8205 (p) REVERT: I 105 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: M 42 LYS cc_start: 0.8311 (mttt) cc_final: 0.7748 (mmtp) REVERT: M 45 LYS cc_start: 0.8329 (tttt) cc_final: 0.7366 (mttp) REVERT: C 21 ASP cc_start: 0.8778 (m-30) cc_final: 0.8538 (m-30) REVERT: C 26 LYS cc_start: 0.8582 (mttt) cc_final: 0.8050 (mptt) REVERT: C 149 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8220 (mmtm) REVERT: C 175 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7060 (mm-30) REVERT: C 214 THR cc_start: 0.8379 (m) cc_final: 0.8002 (p) REVERT: C 219 LYS cc_start: 0.8219 (tptm) cc_final: 0.7968 (tptm) REVERT: C 246 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7721 (mm-30) REVERT: C 275 MET cc_start: 0.7660 (ttp) cc_final: 0.7388 (ttm) REVERT: C 276 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.6932 (m-30) REVERT: C 338 PHE cc_start: 0.8747 (p90) cc_final: 0.8520 (p90) REVERT: C 445 LYS cc_start: 0.7614 (ttmt) cc_final: 0.6736 (mptt) REVERT: C 468 GLU cc_start: 0.8148 (tt0) cc_final: 0.7768 (tt0) REVERT: C 479 GLU cc_start: 0.7412 (pt0) cc_final: 0.6503 (mm-30) REVERT: N 42 LYS cc_start: 0.8172 (mttt) cc_final: 0.7598 (mtmt) REVERT: N 45 LYS cc_start: 0.8246 (tttt) cc_final: 0.7359 (mttp) outliers start: 40 outliers final: 19 residues processed: 210 average time/residue: 0.5226 time to fit residues: 123.2601 Evaluate side-chains 195 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 140 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.140760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.106574 restraints weight = 17809.124| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.94 r_work: 0.2818 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17142 Z= 0.248 Angle : 0.599 7.792 23241 Z= 0.319 Chirality : 0.046 0.155 2496 Planarity : 0.005 0.048 3024 Dihedral : 4.901 38.553 2312 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.71 % Allowed : 12.55 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2109 helix: 2.09 (0.27), residues: 363 sheet: 0.22 (0.21), residues: 540 loop : -0.54 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 220 TYR 0.022 0.002 TYR M 49 PHE 0.025 0.002 PHE B 439 TRP 0.009 0.002 TRP C 234 HIS 0.011 0.002 HIS M 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.25 (17118) covalent geometry : angle 0.59824 / 0.32 (23193) SS BOND : bond 0.00573 / 0.38 ( 24) SS BOND : angle 0.97985 / 0.62 ( 48) hydrogen bonds : bond 0.05095 / 3.47 ( 711) hydrogen bonds : angle 5.22816 / 3.70 ( 2034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.632 Fit side-chains REVERT: A 26 LYS cc_start: 0.8670 (mttt) cc_final: 0.7925 (mmtt) REVERT: A 116 GLU cc_start: 0.7788 (pt0) cc_final: 0.7489 (pt0) REVERT: A 149 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8531 (mttm) REVERT: A 212 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7479 (mtpm) REVERT: A 214 THR cc_start: 0.8486 (m) cc_final: 0.8116 (p) REVERT: A 219 LYS cc_start: 0.8390 (ttmt) cc_final: 0.8102 (tppp) REVERT: A 246 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: A 281 LYS cc_start: 0.8381 (mttt) cc_final: 0.7998 (mtmt) REVERT: A 402 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7995 (mt) REVERT: A 406 MET cc_start: 0.7978 (mtp) cc_final: 0.7395 (mmm) REVERT: A 445 LYS cc_start: 0.7779 (ttmt) cc_final: 0.7266 (mttp) REVERT: A 468 GLU cc_start: 0.8273 (tt0) cc_final: 0.7836 (tt0) REVERT: A 479 GLU cc_start: 0.7440 (pt0) cc_final: 0.6706 (mm-30) REVERT: H 7 SER cc_start: 0.8175 (p) cc_final: 0.7628 (m) REVERT: H 82 SER cc_start: 0.8451 (m) cc_final: 0.7938 (p) REVERT: L 42 LYS cc_start: 0.8378 (mttt) cc_final: 0.7831 (mptt) REVERT: L 45 LYS cc_start: 0.8272 (tttt) cc_final: 0.7457 (mtpt) REVERT: B 4 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5493 (tt0) REVERT: B 26 LYS cc_start: 0.8728 (mttt) cc_final: 0.7946 (mptt) REVERT: B 116 GLU cc_start: 0.7691 (pt0) cc_final: 0.7197 (pt0) REVERT: B 148 TYR cc_start: 0.8522 (m-80) cc_final: 0.8321 (m-80) REVERT: B 175 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: B 212 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8292 (ttmt) REVERT: B 214 THR cc_start: 0.8486 (m) cc_final: 0.8223 (p) REVERT: B 219 LYS cc_start: 0.8260 (ttpt) cc_final: 0.8002 (tttm) REVERT: B 246 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: B 276 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.6842 (OUTLIER) REVERT: B 445 LYS cc_start: 0.7561 (ttmt) cc_final: 0.6632 (mptt) REVERT: B 468 GLU cc_start: 0.8106 (tt0) cc_final: 0.7781 (tt0) REVERT: B 479 GLU cc_start: 0.7486 (pt0) cc_final: 0.6785 (mm-30) REVERT: I 7 SER cc_start: 0.8250 (p) cc_final: 0.7724 (m) REVERT: I 43 LYS cc_start: 0.8108 (mttt) cc_final: 0.7749 (mtpm) REVERT: I 57 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7601 (mtp180) REVERT: I 82 SER cc_start: 0.8764 (m) cc_final: 0.8166 (p) REVERT: I 105 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: M 42 LYS cc_start: 0.8344 (mttt) cc_final: 0.7732 (mmtp) REVERT: C 26 LYS cc_start: 0.8526 (mttt) cc_final: 0.7901 (mmtt) REVERT: C 55 GLN cc_start: 0.8257 (tp-100) cc_final: 0.8051 (tp-100) REVERT: C 148 TYR cc_start: 0.8529 (m-80) cc_final: 0.8302 (m-80) REVERT: C 175 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7033 (mm-30) REVERT: C 212 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7460 (mtpm) REVERT: C 214 THR cc_start: 0.8507 (m) cc_final: 0.8128 (p) REVERT: C 219 LYS cc_start: 0.8288 (tptm) cc_final: 0.8017 (tptm) REVERT: C 276 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7226 (t70) REVERT: C 338 PHE cc_start: 0.8870 (p90) cc_final: 0.8646 (p90) REVERT: C 445 LYS cc_start: 0.7719 (ttmt) cc_final: 0.6666 (mptt) REVERT: C 468 GLU cc_start: 0.8200 (tt0) cc_final: 0.7870 (tt0) REVERT: C 479 GLU cc_start: 0.7272 (pt0) cc_final: 0.6412 (mm-30) REVERT: J 32 TYR cc_start: 0.8737 (m-80) cc_final: 0.8464 (m-80) REVERT: J 105 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8150 (pt0) REVERT: N 42 LYS cc_start: 0.8078 (mttt) cc_final: 0.7494 (mtmt) REVERT: N 45 LYS cc_start: 0.8276 (tttt) cc_final: 0.7234 (mttp) outliers start: 50 outliers final: 27 residues processed: 211 average time/residue: 0.5330 time to fit residues: 127.0559 Evaluate side-chains 212 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.143408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.109385 restraints weight = 17673.605| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.95 r_work: 0.2859 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17142 Z= 0.132 Angle : 0.508 7.219 23241 Z= 0.271 Chirality : 0.042 0.148 2496 Planarity : 0.004 0.043 3024 Dihedral : 4.600 39.435 2312 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.06 % Allowed : 13.47 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2109 helix: 2.41 (0.27), residues: 363 sheet: 0.35 (0.22), residues: 540 loop : -0.49 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 220 TYR 0.013 0.001 TYR M 49 PHE 0.015 0.001 PHE B 439 TRP 0.010 0.001 TRP C 421 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (17118) covalent geometry : angle 0.50718 / 0.27 (23193) SS BOND : bond 0.00369 / 0.24 ( 24) SS BOND : angle 0.73240 / 0.45 ( 48) hydrogen bonds : bond 0.04367 / 2.97 ( 711) hydrogen bonds : angle 4.95150 / 3.50 ( 2034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.587 Fit side-chains REVERT: A 26 LYS cc_start: 0.8643 (mttt) cc_final: 0.7912 (mmtt) REVERT: A 116 GLU cc_start: 0.7813 (pt0) cc_final: 0.7535 (pt0) REVERT: A 149 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8585 (mttm) REVERT: A 212 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7459 (mtpm) REVERT: A 214 THR cc_start: 0.8389 (m) cc_final: 0.8033 (p) REVERT: A 219 LYS cc_start: 0.8411 (ttmt) cc_final: 0.8124 (tppp) REVERT: A 246 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: A 281 LYS cc_start: 0.8334 (mttt) cc_final: 0.7984 (mtmt) REVERT: A 402 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 406 MET cc_start: 0.7957 (mtp) cc_final: 0.7391 (mmt) REVERT: A 445 LYS cc_start: 0.7631 (ttmt) cc_final: 0.7039 (mttp) REVERT: A 468 GLU cc_start: 0.8274 (tt0) cc_final: 0.7819 (tt0) REVERT: A 479 GLU cc_start: 0.7372 (pt0) cc_final: 0.6648 (mm-30) REVERT: H 7 SER cc_start: 0.8121 (p) cc_final: 0.7651 (m) REVERT: H 82 SER cc_start: 0.8436 (m) cc_final: 0.7912 (p) REVERT: L 42 LYS cc_start: 0.8380 (mttt) cc_final: 0.7838 (mptt) REVERT: L 45 LYS cc_start: 0.8257 (tttt) cc_final: 0.7396 (mttm) REVERT: B 4 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5073 (tp30) REVERT: B 26 LYS cc_start: 0.8685 (mttt) cc_final: 0.7922 (mptt) REVERT: B 116 GLU cc_start: 0.7680 (pt0) cc_final: 0.7197 (pt0) REVERT: B 212 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8292 (ttmt) REVERT: B 219 LYS cc_start: 0.8267 (ttpt) cc_final: 0.8013 (tttm) REVERT: B 246 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: B 276 ASP cc_start: 0.7595 (t70) cc_final: 0.6854 (m-30) REVERT: B 445 LYS cc_start: 0.7468 (ttmt) cc_final: 0.6561 (mptt) REVERT: B 468 GLU cc_start: 0.8167 (tt0) cc_final: 0.7818 (tt0) REVERT: B 479 GLU cc_start: 0.7453 (pt0) cc_final: 0.6742 (mm-30) REVERT: I 43 LYS cc_start: 0.8017 (mttt) cc_final: 0.7657 (mtpm) REVERT: I 82 SER cc_start: 0.8762 (m) cc_final: 0.8171 (p) REVERT: I 105 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: M 42 LYS cc_start: 0.8302 (mttt) cc_final: 0.7701 (mmtp) REVERT: C 26 LYS cc_start: 0.8490 (mttt) cc_final: 0.7896 (mptt) REVERT: C 148 TYR cc_start: 0.8387 (m-80) cc_final: 0.8176 (m-80) REVERT: C 175 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7026 (mm-30) REVERT: C 214 THR cc_start: 0.8451 (m) cc_final: 0.8067 (p) REVERT: C 219 LYS cc_start: 0.8284 (tptm) cc_final: 0.8013 (tptm) REVERT: C 246 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7663 (mm-30) REVERT: C 338 PHE cc_start: 0.8814 (p90) cc_final: 0.8581 (p90) REVERT: C 445 LYS cc_start: 0.7518 (ttmt) cc_final: 0.6608 (mptt) REVERT: C 468 GLU cc_start: 0.8197 (tt0) cc_final: 0.7832 (tt0) REVERT: C 479 GLU cc_start: 0.7306 (pt0) cc_final: 0.6432 (mm-30) REVERT: N 42 LYS cc_start: 0.8091 (mttt) cc_final: 0.7495 (mtmt) REVERT: N 45 LYS cc_start: 0.8230 (tttt) cc_final: 0.7251 (mttp) REVERT: N 74 THR cc_start: 0.8304 (m) cc_final: 0.7927 (p) outliers start: 38 outliers final: 24 residues processed: 207 average time/residue: 0.5114 time to fit residues: 118.8581 Evaluate side-chains 199 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 172 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 49 optimal weight: 0.0000 chunk 154 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 79 GLN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.144069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.110774 restraints weight = 17771.383| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.90 r_work: 0.2874 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17142 Z= 0.128 Angle : 0.493 6.933 23241 Z= 0.263 Chirality : 0.042 0.147 2496 Planarity : 0.004 0.042 3024 Dihedral : 4.454 39.166 2312 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.44 % Allowed : 13.20 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2109 helix: 2.55 (0.27), residues: 363 sheet: 0.52 (0.22), residues: 540 loop : -0.46 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 220 TYR 0.012 0.001 TYR M 49 PHE 0.015 0.001 PHE B 439 TRP 0.009 0.001 TRP C 421 HIS 0.005 0.001 HIS N 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17118) covalent geometry : angle 0.49290 / 0.26 (23193) SS BOND : bond 0.00364 / 0.24 ( 24) SS BOND : angle 0.70453 / 0.44 ( 48) hydrogen bonds : bond 0.04226 / 2.87 ( 711) hydrogen bonds : angle 4.85176 / 3.43 ( 2034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.705 Fit side-chains REVERT: A 26 LYS cc_start: 0.8624 (mttt) cc_final: 0.7923 (mmtt) REVERT: A 116 GLU cc_start: 0.7821 (pt0) cc_final: 0.7557 (pt0) REVERT: A 149 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8378 (mmtp) REVERT: A 212 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7484 (mtpm) REVERT: A 214 THR cc_start: 0.8410 (m) cc_final: 0.8049 (p) REVERT: A 219 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8171 (tppp) REVERT: A 246 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: A 281 LYS cc_start: 0.8335 (mttt) cc_final: 0.7995 (mtmt) REVERT: A 406 MET cc_start: 0.7991 (mtp) cc_final: 0.7446 (mmt) REVERT: A 445 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7083 (mttp) REVERT: A 468 GLU cc_start: 0.8280 (tt0) cc_final: 0.7846 (tt0) REVERT: A 479 GLU cc_start: 0.7418 (pt0) cc_final: 0.6736 (mm-30) REVERT: H 82 SER cc_start: 0.8465 (m) cc_final: 0.7960 (p) REVERT: L 42 LYS cc_start: 0.8401 (mttt) cc_final: 0.7887 (mptt) REVERT: L 45 LYS cc_start: 0.8291 (tttt) cc_final: 0.7489 (mtpt) REVERT: B 4 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5170 (tp30) REVERT: B 26 LYS cc_start: 0.8687 (mttt) cc_final: 0.7960 (mptt) REVERT: B 116 GLU cc_start: 0.7780 (pt0) cc_final: 0.7314 (pt0) REVERT: B 212 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8308 (ttmt) REVERT: B 219 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7804 (tppp) REVERT: B 246 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: B 276 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.6980 (OUTLIER) REVERT: B 445 LYS cc_start: 0.7537 (ttmt) cc_final: 0.6647 (mptt) REVERT: B 468 GLU cc_start: 0.8178 (tt0) cc_final: 0.7842 (tt0) REVERT: B 479 GLU cc_start: 0.7469 (pt0) cc_final: 0.6810 (mm-30) REVERT: I 43 LYS cc_start: 0.8034 (mttt) cc_final: 0.7688 (mtpm) REVERT: I 82 SER cc_start: 0.8844 (m) cc_final: 0.8262 (p) REVERT: I 105 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: M 42 LYS cc_start: 0.8327 (mttt) cc_final: 0.7753 (mmtp) REVERT: C 26 LYS cc_start: 0.8438 (mttt) cc_final: 0.7922 (mmtt) REVERT: C 175 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7065 (mm-30) REVERT: C 212 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7459 (mtpm) REVERT: C 214 THR cc_start: 0.8465 (m) cc_final: 0.8082 (p) REVERT: C 219 LYS cc_start: 0.8227 (tptm) cc_final: 0.7973 (tptm) REVERT: C 246 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7685 (mm-30) REVERT: C 338 PHE cc_start: 0.8796 (p90) cc_final: 0.8547 (p90) REVERT: C 445 LYS cc_start: 0.7640 (ttmt) cc_final: 0.6751 (mptt) REVERT: C 468 GLU cc_start: 0.8210 (tt0) cc_final: 0.7854 (tt0) REVERT: C 479 GLU cc_start: 0.7362 (pt0) cc_final: 0.6498 (mm-30) REVERT: J 32 TYR cc_start: 0.8690 (m-80) cc_final: 0.8459 (m-80) REVERT: N 27 GLN cc_start: 0.7608 (mt0) cc_final: 0.7382 (mt0) REVERT: N 42 LYS cc_start: 0.8120 (mttt) cc_final: 0.7539 (mtmt) REVERT: N 45 LYS cc_start: 0.8279 (tttt) cc_final: 0.7318 (mttp) REVERT: N 74 THR cc_start: 0.8315 (m) cc_final: 0.7959 (p) outliers start: 45 outliers final: 27 residues processed: 202 average time/residue: 0.5497 time to fit residues: 124.6653 Evaluate side-chains 200 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 157 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.142173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108086 restraints weight = 17838.415| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.98 r_work: 0.2839 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17142 Z= 0.188 Angle : 0.545 7.031 23241 Z= 0.289 Chirality : 0.044 0.159 2496 Planarity : 0.004 0.044 3024 Dihedral : 4.651 39.118 2312 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.22 % Allowed : 13.74 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2109 helix: 2.35 (0.27), residues: 363 sheet: 0.44 (0.22), residues: 540 loop : -0.53 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 220 TYR 0.016 0.002 TYR M 49 PHE 0.020 0.002 PHE B 439 TRP 0.007 0.001 TRP C 421 HIS 0.008 0.001 HIS N 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (17118) covalent geometry : angle 0.54445 / 0.29 (23193) SS BOND : bond 0.00446 / 0.29 ( 24) SS BOND : angle 0.79728 / 0.50 ( 48) hydrogen bonds : bond 0.04648 / 3.16 ( 711) hydrogen bonds : angle 5.02465 / 3.56 ( 2034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.663 Fit side-chains REVERT: A 26 LYS cc_start: 0.8635 (mttt) cc_final: 0.7908 (mmtt) REVERT: A 116 GLU cc_start: 0.7785 (pt0) cc_final: 0.7505 (pt0) REVERT: A 149 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8556 (mttm) REVERT: A 212 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7470 (mtpm) REVERT: A 214 THR cc_start: 0.8493 (m) cc_final: 0.8113 (p) REVERT: A 219 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8191 (tppp) REVERT: A 246 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: A 281 LYS cc_start: 0.8286 (mttt) cc_final: 0.7929 (mtmt) REVERT: A 406 MET cc_start: 0.7998 (mtp) cc_final: 0.7420 (mmt) REVERT: A 445 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7136 (mttp) REVERT: A 468 GLU cc_start: 0.8272 (tt0) cc_final: 0.7797 (tt0) REVERT: A 479 GLU cc_start: 0.7398 (pt0) cc_final: 0.6670 (mm-30) REVERT: H 7 SER cc_start: 0.8111 (p) cc_final: 0.7605 (m) REVERT: H 82 SER cc_start: 0.8464 (m) cc_final: 0.7970 (p) REVERT: L 42 LYS cc_start: 0.8380 (mttt) cc_final: 0.7839 (mptt) REVERT: L 45 LYS cc_start: 0.8324 (tttt) cc_final: 0.7508 (mtpt) REVERT: B 4 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.5502 (tt0) REVERT: B 26 LYS cc_start: 0.8719 (mttt) cc_final: 0.7936 (mptt) REVERT: B 116 GLU cc_start: 0.7745 (pt0) cc_final: 0.7257 (pt0) REVERT: B 212 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8285 (ttmt) REVERT: B 246 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: B 276 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.6872 (OUTLIER) REVERT: B 445 LYS cc_start: 0.7601 (ttmt) cc_final: 0.6652 (mptt) REVERT: B 468 GLU cc_start: 0.8167 (tt0) cc_final: 0.7807 (tt0) REVERT: B 479 GLU cc_start: 0.7459 (pt0) cc_final: 0.6762 (mm-30) REVERT: I 43 LYS cc_start: 0.8030 (mttt) cc_final: 0.7668 (mtpm) REVERT: I 82 SER cc_start: 0.8806 (m) cc_final: 0.8220 (p) REVERT: I 105 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: M 42 LYS cc_start: 0.8301 (mttt) cc_final: 0.7707 (mmtp) REVERT: C 26 LYS cc_start: 0.8447 (mttt) cc_final: 0.7835 (mmtt) REVERT: C 148 TYR cc_start: 0.8556 (m-80) cc_final: 0.8339 (m-80) REVERT: C 175 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7050 (mm-30) REVERT: C 212 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7443 (mtpm) REVERT: C 214 THR cc_start: 0.8479 (m) cc_final: 0.8091 (p) REVERT: C 219 LYS cc_start: 0.8283 (tptm) cc_final: 0.8011 (tptm) REVERT: C 246 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7661 (mm-30) REVERT: C 338 PHE cc_start: 0.8839 (p90) cc_final: 0.8590 (p90) REVERT: C 445 LYS cc_start: 0.7615 (ttmt) cc_final: 0.6676 (mptt) REVERT: C 468 GLU cc_start: 0.8191 (tt0) cc_final: 0.7809 (tt0) REVERT: C 479 GLU cc_start: 0.7290 (pt0) cc_final: 0.6427 (mm-30) REVERT: J 32 TYR cc_start: 0.8705 (m-80) cc_final: 0.8437 (m-80) REVERT: J 82 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.6326 (mtp) REVERT: N 27 GLN cc_start: 0.7639 (mt0) cc_final: 0.7409 (mt0) REVERT: N 42 LYS cc_start: 0.8094 (mttt) cc_final: 0.7501 (mtmt) REVERT: N 45 LYS cc_start: 0.8246 (tttt) cc_final: 0.7223 (mttp) REVERT: N 74 THR cc_start: 0.8265 (m) cc_final: 0.7883 (p) REVERT: N 82 ASP cc_start: 0.7752 (m-30) cc_final: 0.7412 (m-30) outliers start: 41 outliers final: 26 residues processed: 200 average time/residue: 0.5174 time to fit residues: 116.6365 Evaluate side-chains 205 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 87 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 152 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS J 105 GLN 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 = 0.143683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109719 restraints weight = 17697.011| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.96 r_work: 0.2863 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17142 Z= 0.135 Angle : 0.501 6.966 23241 Z= 0.266 Chirality : 0.042 0.149 2496 Planarity : 0.004 0.041 3024 Dihedral : 4.492 39.612 2312 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.06 % Allowed : 13.91 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 2109 helix: 2.51 (0.27), residues: 363 sheet: 0.51 (0.22), residues: 540 loop : -0.48 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 220 TYR 0.012 0.001 TYR M 49 PHE 0.015 0.001 PHE B 439 TRP 0.011 0.001 TRP C 421 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (17118) covalent geometry : angle 0.50058 / 0.27 (23193) SS BOND : bond 0.00369 / 0.24 ( 24) SS BOND : angle 0.71492 / 0.45 ( 48) hydrogen bonds : bond 0.04270 / 2.90 ( 711) hydrogen bonds : angle 4.88240 / 3.45 ( 2034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.646 Fit side-chains REVERT: A 26 LYS cc_start: 0.8545 (mttt) cc_final: 0.7791 (mmtt) REVERT: A 116 GLU cc_start: 0.7805 (pt0) cc_final: 0.7538 (pt0) REVERT: A 149 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8347 (mmtp) REVERT: A 212 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7468 (mtpm) REVERT: A 214 THR cc_start: 0.8392 (m) cc_final: 0.8038 (p) REVERT: A 219 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8189 (tppp) REVERT: A 246 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: A 281 LYS cc_start: 0.8295 (mttt) cc_final: 0.7935 (mtpt) REVERT: A 406 MET cc_start: 0.7964 (mtp) cc_final: 0.7397 (mmt) REVERT: A 445 LYS cc_start: 0.7618 (ttmt) cc_final: 0.7110 (mttp) REVERT: A 468 GLU cc_start: 0.8259 (tt0) cc_final: 0.7766 (tt0) REVERT: A 479 GLU cc_start: 0.7406 (pt0) cc_final: 0.6667 (mm-30) REVERT: H 82 SER cc_start: 0.8450 (m) cc_final: 0.7954 (p) REVERT: L 42 LYS cc_start: 0.8393 (mttt) cc_final: 0.7850 (mptt) REVERT: L 45 LYS cc_start: 0.8309 (tttt) cc_final: 0.7487 (mtpt) REVERT: B 26 LYS cc_start: 0.8705 (mttt) cc_final: 0.7957 (mptt) REVERT: B 116 GLU cc_start: 0.7737 (pt0) cc_final: 0.7259 (pt0) REVERT: B 212 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8275 (ttmt) REVERT: B 246 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: B 276 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.6950 (OUTLIER) REVERT: B 335 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7941 (mm) REVERT: B 445 LYS cc_start: 0.7545 (ttmt) cc_final: 0.6612 (mptt) REVERT: B 468 GLU cc_start: 0.8147 (tt0) cc_final: 0.7759 (tt0) REVERT: B 479 GLU cc_start: 0.7437 (pt0) cc_final: 0.6741 (mm-30) REVERT: I 43 LYS cc_start: 0.8003 (mttt) cc_final: 0.7640 (mtpm) REVERT: I 82 SER cc_start: 0.8720 (m) cc_final: 0.8155 (p) REVERT: I 105 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: M 42 LYS cc_start: 0.8302 (mttt) cc_final: 0.7709 (mmtp) REVERT: C 26 LYS cc_start: 0.8440 (mttt) cc_final: 0.7859 (mptt) REVERT: C 58 ASN cc_start: 0.7408 (m-40) cc_final: 0.7164 (m-40) REVERT: C 175 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7025 (mm-30) REVERT: C 212 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7428 (mtpm) REVERT: C 214 THR cc_start: 0.8453 (m) cc_final: 0.8051 (p) REVERT: C 219 LYS cc_start: 0.8232 (tptm) cc_final: 0.7965 (tptm) REVERT: C 246 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7648 (mm-30) REVERT: C 338 PHE cc_start: 0.8804 (p90) cc_final: 0.8555 (p90) REVERT: C 445 LYS cc_start: 0.7547 (ttmt) cc_final: 0.6609 (mptt) REVERT: C 468 GLU cc_start: 0.8200 (tt0) cc_final: 0.7791 (tt0) REVERT: C 479 GLU cc_start: 0.7284 (pt0) cc_final: 0.6423 (mm-30) REVERT: C 495 SER cc_start: 0.6994 (t) cc_final: 0.6688 (p) REVERT: J 32 TYR cc_start: 0.8680 (m-80) cc_final: 0.8418 (m-80) REVERT: J 82 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6286 (mtp) REVERT: N 27 GLN cc_start: 0.7694 (mt0) cc_final: 0.7370 (mt0) REVERT: N 42 LYS cc_start: 0.8095 (mttt) cc_final: 0.7494 (mtmt) REVERT: N 45 LYS cc_start: 0.8229 (tttt) cc_final: 0.7194 (mttp) REVERT: N 74 THR cc_start: 0.8224 (m) cc_final: 0.7920 (p) outliers start: 38 outliers final: 25 residues processed: 202 average time/residue: 0.5347 time to fit residues: 121.7123 Evaluate side-chains 201 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 76 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS M 27 GLN J 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.143186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.109217 restraints weight = 17660.020| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.95 r_work: 0.2856 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17142 Z= 0.151 Angle : 0.516 6.928 23241 Z= 0.274 Chirality : 0.043 0.152 2496 Planarity : 0.004 0.042 3024 Dihedral : 4.519 39.334 2312 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.95 % Allowed : 14.18 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2109 helix: 2.45 (0.27), residues: 363 sheet: 0.50 (0.22), residues: 540 loop : -0.49 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 220 TYR 0.014 0.002 TYR M 49 PHE 0.017 0.002 PHE A 439 TRP 0.009 0.001 TRP C 421 HIS 0.007 0.001 HIS N 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (17118) covalent geometry : angle 0.51548 / 0.27 (23193) SS BOND : bond 0.00415 / 0.26 ( 24) SS BOND : angle 0.76337 / 0.49 ( 48) hydrogen bonds : bond 0.04373 / 2.97 ( 711) hydrogen bonds : angle 4.92033 / 3.48 ( 2034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5402.72 seconds wall clock time: 93 minutes 8.43 seconds (5588.43 seconds total)