Starting phenix.real_space_refine on Thu Feb 5 04:12:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jf7_61429/02_2026/9jf7_61429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jf7_61429/02_2026/9jf7_61429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jf7_61429/02_2026/9jf7_61429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jf7_61429/02_2026/9jf7_61429.map" model { file = "/net/cci-nas-00/data/ceres_data/9jf7_61429/02_2026/9jf7_61429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jf7_61429/02_2026/9jf7_61429.cif" } resolution = 3.03 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 5613 2.51 5 N 1329 2.21 5 O 1584 1.98 5 H 5988 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14580 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 4860 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Restraints were copied for chains: B, C Time building chain proxies: 4.17, per 1000 atoms: 0.29 Number of scatterers: 14580 At special positions: 0 Unit cell: (95.79, 101.37, 107.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 1584 8.00 N 1329 7.00 C 5613 6.00 H 5988 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 295 " distance=2.03 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: 1.30 Conformation dependent library (CDL) restraints added in 528.4 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1998 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 38.8% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 46 through 67 Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 123 through 132 removed outlier: 3.512A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP A 132 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 255 through 279 removed outlier: 3.877A pdb=" N ASP A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.649A pdb=" N LYS A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 381 removed outlier: 3.892A pdb=" N SER A 371 " --> pdb=" O TYR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'B' and resid 47 through 67 Processing helix chain 'B' and resid 93 through 96 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 109 through 120 Processing helix chain 'B' and resid 123 through 132 removed outlier: 3.511A pdb=" N THR B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 132 " --> pdb=" O TRP B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 255 through 279 removed outlier: 3.876A pdb=" N ASP B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 313 removed outlier: 3.649A pdb=" N LYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 removed outlier: 3.891A pdb=" N SER B 371 " --> pdb=" O TYR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'C' and resid 47 through 67 Processing helix chain 'C' and resid 93 through 96 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 109 through 120 Processing helix chain 'C' and resid 123 through 132 removed outlier: 3.511A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP C 132 " --> pdb=" O TRP C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 255 through 279 removed outlier: 3.875A pdb=" N ASP C 274 " --> pdb=" O PHE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.649A pdb=" N LYS C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 381 removed outlier: 3.891A pdb=" N SER C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 removed outlier: 9.353A pdb=" N THR A 356 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 240 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU A 358 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN A 242 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLU A 360 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE A 244 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 234 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR A 350 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 236 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASN A 194 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR A 137 " --> pdb=" O ASN A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 77 removed outlier: 9.353A pdb=" N THR A 356 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 240 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU A 358 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN A 242 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLU A 360 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE A 244 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU A 235 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN A 335 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A 237 " --> pdb=" O GLN A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 166 removed outlier: 7.122A pdb=" N LYS A 170 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 77 removed outlier: 9.352A pdb=" N THR B 356 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 240 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLU B 358 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN B 242 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU B 360 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE B 244 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR B 234 " --> pdb=" O LYS B 348 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR B 350 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL B 236 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASN B 194 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR B 137 " --> pdb=" O ASN B 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 77 removed outlier: 9.352A pdb=" N THR B 356 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 240 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLU B 358 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN B 242 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU B 360 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE B 244 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU B 235 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN B 335 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN B 237 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 removed outlier: 7.123A pdb=" N LYS B 170 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 77 removed outlier: 9.353A pdb=" N THR C 356 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 240 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU C 358 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN C 242 " --> pdb=" O GLU C 358 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU C 360 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE C 244 " --> pdb=" O GLU C 360 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR C 234 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR C 350 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL C 236 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASN C 194 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR C 137 " --> pdb=" O ASN C 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 77 removed outlier: 9.353A pdb=" N THR C 356 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 240 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU C 358 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN C 242 " --> pdb=" O GLU C 358 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU C 360 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE C 244 " --> pdb=" O GLU C 360 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU C 235 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN C 335 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN C 237 " --> pdb=" O GLN C 333 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 166 removed outlier: 7.123A pdb=" N LYS C 170 " --> pdb=" O PRO C 91 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1101 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: 3.90 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 5982 1.01 - 1.21: 35 1.21 - 1.41: 3778 1.41 - 1.61: 4932 1.61 - 1.81: 96 Bond restraints: 14823 Sorted by residual: bond pdb=" SG CYS C 389 " pdb=" HG CYS C 389 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" SG CYS A 389 " pdb=" HG CYS A 389 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" SG CYS C 51 " pdb=" HG CYS C 51 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" SG CYS B 51 " pdb=" HG CYS B 51 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" SG CYS A 51 " pdb=" HG CYS A 51 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 14818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.97: 25485 7.97 - 15.94: 45 15.94 - 23.91: 0 23.91 - 31.89: 57 31.89 - 39.86: 33 Bond angle restraints: 25620 Sorted by residual: angle pdb=" C PRO B 179 " pdb=" CA PRO B 179 " pdb=" HA PRO B 179 " ideal model delta sigma weight residual 109.00 69.14 39.86 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C PRO A 179 " pdb=" CA PRO A 179 " pdb=" HA PRO A 179 " ideal model delta sigma weight residual 109.00 69.22 39.78 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C PRO C 179 " pdb=" CA PRO C 179 " pdb=" HA PRO C 179 " ideal model delta sigma weight residual 109.00 69.26 39.74 3.00e+00 1.11e-01 1.75e+02 angle pdb=" N MET A 233 " pdb=" CA MET A 233 " pdb=" HA MET A 233 " ideal model delta sigma weight residual 110.00 74.27 35.73 3.00e+00 1.11e-01 1.42e+02 angle pdb=" N MET C 233 " pdb=" CA MET C 233 " pdb=" HA MET C 233 " ideal model delta sigma weight residual 110.00 74.29 35.71 3.00e+00 1.11e-01 1.42e+02 ... (remaining 25615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6228 17.92 - 35.85: 776 35.85 - 53.77: 265 53.77 - 71.70: 102 71.70 - 89.62: 33 Dihedral angle restraints: 7404 sinusoidal: 3747 harmonic: 3657 Sorted by residual: dihedral pdb=" C LEU C 125 " pdb=" N LEU C 125 " pdb=" CA LEU C 125 " pdb=" CB LEU C 125 " ideal model delta harmonic sigma weight residual -122.60 -155.88 33.28 0 2.50e+00 1.60e-01 1.77e+02 dihedral pdb=" C LEU A 125 " pdb=" N LEU A 125 " pdb=" CA LEU A 125 " pdb=" CB LEU A 125 " ideal model delta harmonic sigma weight residual -122.60 -155.80 33.20 0 2.50e+00 1.60e-01 1.76e+02 dihedral pdb=" C LEU B 125 " pdb=" N LEU B 125 " pdb=" CA LEU B 125 " pdb=" CB LEU B 125 " ideal model delta harmonic sigma weight residual -122.60 -155.79 33.19 0 2.50e+00 1.60e-01 1.76e+02 ... (remaining 7401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 1245 0.287 - 0.574: 17 0.574 - 0.861: 1 0.861 - 1.149: 3 1.149 - 1.436: 15 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA LEU C 125 " pdb=" N LEU C 125 " pdb=" C LEU C 125 " pdb=" CB LEU C 125 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.15e+01 chirality pdb=" CA LEU A 125 " pdb=" N LEU A 125 " pdb=" C LEU A 125 " pdb=" CB LEU A 125 " both_signs ideal model delta sigma weight residual False 2.51 1.08 1.43 2.00e-01 2.50e+01 5.13e+01 chirality pdb=" CA LEU B 125 " pdb=" N LEU B 125 " pdb=" C LEU B 125 " pdb=" CB LEU B 125 " both_signs ideal model delta sigma weight residual False 2.51 1.08 1.43 2.00e-01 2.50e+01 5.11e+01 ... (remaining 1278 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 161 " 0.255 2.00e-02 2.50e+03 4.59e-01 3.16e+03 pdb=" CG ASN C 161 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 161 " -0.256 2.00e-02 2.50e+03 pdb=" ND2 ASN C 161 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 161 " 0.757 2.00e-02 2.50e+03 pdb="HD22 ASN C 161 " -0.747 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 161 " 0.256 2.00e-02 2.50e+03 4.59e-01 3.15e+03 pdb=" CG ASN B 161 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 161 " -0.256 2.00e-02 2.50e+03 pdb=" ND2 ASN B 161 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 161 " 0.757 2.00e-02 2.50e+03 pdb="HD22 ASN B 161 " -0.747 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 161 " 0.255 2.00e-02 2.50e+03 4.58e-01 3.15e+03 pdb=" CG ASN A 161 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 161 " -0.255 2.00e-02 2.50e+03 pdb=" ND2 ASN A 161 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 161 " 0.756 2.00e-02 2.50e+03 pdb="HD22 ASN A 161 " -0.747 2.00e-02 2.50e+03 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 271 2.07 - 2.70: 19196 2.70 - 3.33: 38413 3.33 - 3.97: 51970 3.97 - 4.60: 78992 Nonbonded interactions: 188842 Sorted by model distance: nonbonded pdb=" H ILE A 385 " pdb=" O LEU B 379 " model vdw 1.437 2.450 nonbonded pdb=" O LEU A 379 " pdb=" H ILE C 385 " model vdw 1.448 2.450 nonbonded pdb=" H ILE B 385 " pdb=" O LEU C 379 " model vdw 1.506 2.450 nonbonded pdb="HD22 ASN B 184 " pdb=" O PHE C 314 " model vdw 1.553 2.450 nonbonded pdb="HD22 ASN A 184 " pdb=" O PHE B 314 " model vdw 1.554 2.450 ... (remaining 188837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.700 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: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.270 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8850 Z= 0.446 Angle : 1.145 15.078 12009 Z= 0.743 Chirality : 0.166 1.436 1281 Planarity : 0.005 0.059 1521 Dihedral : 19.297 85.281 3237 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.71 % Allowed : 26.52 % Favored : 66.77 % Cbeta Deviations : 1.80 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.26), residues: 1026 helix: -0.77 (0.30), residues: 330 sheet: 0.11 (0.33), residues: 246 loop : -1.83 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 306 TYR 0.034 0.002 TYR B 122 PHE 0.019 0.002 PHE A 100 TRP 0.018 0.002 TRP A 96 HIS 0.005 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 8835) covalent geometry : angle 1.14671 (11979) SS BOND : bond 0.00223 ( 15) SS BOND : angle 0.40399 ( 30) hydrogen bonds : bond 0.14176 ( 385) hydrogen bonds : angle 7.19386 ( 1101) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 363 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6251 (ptp-170) REVERT: A 159 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.6187 (tp) REVERT: A 217 SER cc_start: 0.7709 (t) cc_final: 0.6968 (m) REVERT: A 263 PHE cc_start: 0.6828 (m-80) cc_final: 0.6204 (m-80) REVERT: A 274 ASP cc_start: 0.7420 (m-30) cc_final: 0.6871 (t70) REVERT: B 155 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6475 (ptp-170) REVERT: B 159 ILE cc_start: 0.6400 (OUTLIER) cc_final: 0.6106 (tp) REVERT: B 217 SER cc_start: 0.7802 (t) cc_final: 0.7499 (m) REVERT: B 274 ASP cc_start: 0.7005 (m-30) cc_final: 0.6235 (t70) REVERT: C 217 SER cc_start: 0.7722 (t) cc_final: 0.7439 (m) REVERT: C 263 PHE cc_start: 0.6648 (m-80) cc_final: 0.5833 (m-80) REVERT: C 274 ASP cc_start: 0.7317 (m-30) cc_final: 0.6616 (t70) outliers start: 66 outliers final: 31 residues processed: 341 average time/residue: 0.1586 time to fit residues: 76.4003 Evaluate side-chains 242 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 387 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 172 HIS A 184 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 172 HIS C 184 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.181130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.163619 restraints weight = 25871.737| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.28 r_work: 0.3796 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8850 Z= 0.138 Angle : 0.658 11.012 12009 Z= 0.360 Chirality : 0.095 1.332 1281 Planarity : 0.003 0.024 1521 Dihedral : 8.888 59.223 1196 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 7.22 % Allowed : 26.32 % Favored : 66.46 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1026 helix: 0.24 (0.29), residues: 312 sheet: 0.09 (0.31), residues: 279 loop : -1.71 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 306 TYR 0.014 0.001 TYR C 122 PHE 0.018 0.001 PHE B 135 TRP 0.008 0.001 TRP B 96 HIS 0.004 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8835) covalent geometry : angle 0.64708 (11979) SS BOND : bond 0.00381 ( 15) SS BOND : angle 2.43639 ( 30) hydrogen bonds : bond 0.03453 ( 385) hydrogen bonds : angle 5.09274 ( 1101) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 208 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 MET cc_start: 0.7729 (mmm) cc_final: 0.6930 (mmm) REVERT: A 242 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6396 (mt0) REVERT: A 274 ASP cc_start: 0.7851 (m-30) cc_final: 0.6918 (t70) REVERT: A 353 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.6558 (m110) REVERT: B 155 ARG cc_start: 0.6625 (mtm180) cc_final: 0.6270 (ptp-170) REVERT: B 159 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.6323 (tp) REVERT: B 197 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7677 (ttpt) REVERT: C 274 ASP cc_start: 0.7739 (m-30) cc_final: 0.6479 (t70) REVERT: C 278 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7118 (mm) outliers start: 71 outliers final: 36 residues processed: 259 average time/residue: 0.1445 time to fit residues: 53.7581 Evaluate side-chains 223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 356 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN A 269 ASN ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 279 HIS ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.179510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162894 restraints weight = 26663.686| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.00 r_work: 0.3804 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8850 Z= 0.191 Angle : 0.692 10.974 12009 Z= 0.380 Chirality : 0.096 1.350 1281 Planarity : 0.004 0.026 1521 Dihedral : 7.679 58.865 1166 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 7.62 % Allowed : 27.03 % Favored : 65.35 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.25), residues: 1026 helix: 0.50 (0.27), residues: 312 sheet: -0.10 (0.32), residues: 267 loop : -1.41 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 282 TYR 0.020 0.002 TYR C 334 PHE 0.024 0.002 PHE C 135 TRP 0.010 0.001 TRP B 96 HIS 0.010 0.002 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8835) covalent geometry : angle 0.68326 (11979) SS BOND : bond 0.00467 ( 15) SS BOND : angle 2.31906 ( 30) hydrogen bonds : bond 0.03651 ( 385) hydrogen bonds : angle 4.99713 ( 1101) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 195 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: A 165 MET cc_start: 0.7635 (mmm) cc_final: 0.6738 (mmm) REVERT: A 174 TYR cc_start: 0.6746 (m-80) cc_final: 0.6517 (m-80) REVERT: A 230 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7050 (mp) REVERT: A 242 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6630 (mt0) REVERT: A 276 SER cc_start: 0.8743 (p) cc_final: 0.8299 (m) REVERT: A 353 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.6795 (m110) REVERT: B 60 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7284 (mm-30) REVERT: B 84 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: B 93 LEU cc_start: 0.8087 (mt) cc_final: 0.7867 (mp) REVERT: B 115 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: B 155 ARG cc_start: 0.6842 (mtm180) cc_final: 0.6285 (mtm180) REVERT: B 159 ILE cc_start: 0.6565 (OUTLIER) cc_final: 0.6362 (tp) REVERT: B 242 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6742 (mt0) REVERT: B 387 SER cc_start: 0.7631 (t) cc_final: 0.7290 (p) REVERT: C 60 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7394 (mm-30) REVERT: C 84 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: C 93 LEU cc_start: 0.7979 (mt) cc_final: 0.7760 (mp) REVERT: C 242 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6811 (mt0) outliers start: 75 outliers final: 38 residues processed: 250 average time/residue: 0.1645 time to fit residues: 57.5525 Evaluate side-chains 221 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 356 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 GLN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.181216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.163830 restraints weight = 26403.584| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.09 r_work: 0.3837 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8850 Z= 0.107 Angle : 0.617 11.046 12009 Z= 0.338 Chirality : 0.094 1.331 1281 Planarity : 0.003 0.022 1521 Dihedral : 6.545 58.056 1155 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.79 % Allowed : 27.03 % Favored : 67.17 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.25), residues: 1026 helix: 0.92 (0.28), residues: 330 sheet: -0.16 (0.32), residues: 282 loop : -1.79 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 329 TYR 0.015 0.001 TYR C 122 PHE 0.015 0.001 PHE B 84 TRP 0.006 0.000 TRP B 96 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8835) covalent geometry : angle 0.61016 (11979) SS BOND : bond 0.00322 ( 15) SS BOND : angle 1.92621 ( 30) hydrogen bonds : bond 0.02934 ( 385) hydrogen bonds : angle 4.52966 ( 1101) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7085 (m-80) REVERT: A 115 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: A 198 ILE cc_start: 0.7358 (mm) cc_final: 0.6967 (tt) REVERT: A 242 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6629 (tt0) REVERT: A 276 SER cc_start: 0.8673 (p) cc_final: 0.8159 (m) REVERT: A 353 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.6922 (m110) REVERT: B 74 PHE cc_start: 0.8011 (t80) cc_final: 0.7761 (t80) REVERT: B 84 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: B 93 LEU cc_start: 0.7977 (mt) cc_final: 0.7768 (mp) REVERT: B 115 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: B 155 ARG cc_start: 0.6623 (mtm180) cc_final: 0.6259 (ptp-170) REVERT: B 177 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: B 271 MET cc_start: 0.6331 (mtt) cc_final: 0.6119 (mtm) REVERT: B 274 ASP cc_start: 0.7585 (m-30) cc_final: 0.6465 (t70) REVERT: B 276 SER cc_start: 0.8674 (p) cc_final: 0.8155 (m) REVERT: C 60 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7407 (mm-30) REVERT: C 84 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: C 93 LEU cc_start: 0.7935 (mt) cc_final: 0.7695 (mp) REVERT: C 159 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6201 (tp) REVERT: C 242 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6727 (tt0) REVERT: C 263 PHE cc_start: 0.7005 (m-80) cc_final: 0.6190 (m-80) outliers start: 57 outliers final: 26 residues processed: 234 average time/residue: 0.1488 time to fit residues: 49.9141 Evaluate side-chains 216 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 242 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160980 restraints weight = 26560.208| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.11 r_work: 0.3806 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8850 Z= 0.143 Angle : 0.634 11.132 12009 Z= 0.349 Chirality : 0.095 1.362 1281 Planarity : 0.003 0.023 1521 Dihedral : 6.165 54.921 1145 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.00 % Allowed : 26.83 % Favored : 67.17 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.25), residues: 1026 helix: 1.12 (0.28), residues: 330 sheet: -0.25 (0.31), residues: 285 loop : -1.75 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.017 0.001 TYR A 334 PHE 0.020 0.002 PHE B 135 TRP 0.005 0.001 TRP B 96 HIS 0.004 0.001 HIS C 279 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8835) covalent geometry : angle 0.62336 (11979) SS BOND : bond 0.00313 ( 15) SS BOND : angle 2.40764 ( 30) hydrogen bonds : bond 0.03095 ( 385) hydrogen bonds : angle 4.53725 ( 1101) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: A 84 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: A 115 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: A 198 ILE cc_start: 0.7370 (mm) cc_final: 0.7001 (tt) REVERT: A 242 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6698 (tt0) REVERT: A 353 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.6601 (m110) REVERT: B 60 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 84 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: B 93 LEU cc_start: 0.8046 (mt) cc_final: 0.7786 (mp) REVERT: B 115 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: B 155 ARG cc_start: 0.6498 (mtm180) cc_final: 0.6253 (ptp-170) REVERT: B 177 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: C 60 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7415 (mm-30) REVERT: C 84 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: C 93 LEU cc_start: 0.8010 (mt) cc_final: 0.7774 (mp) REVERT: C 137 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7772 (t80) REVERT: C 159 ILE cc_start: 0.6625 (OUTLIER) cc_final: 0.6230 (tp) REVERT: C 242 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: C 263 PHE cc_start: 0.6915 (m-80) cc_final: 0.6115 (m-80) outliers start: 59 outliers final: 34 residues processed: 226 average time/residue: 0.1380 time to fit residues: 45.2119 Evaluate side-chains 223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 356 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.180402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163045 restraints weight = 26990.976| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.13 r_work: 0.3825 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8850 Z= 0.114 Angle : 0.603 11.064 12009 Z= 0.332 Chirality : 0.094 1.348 1281 Planarity : 0.003 0.023 1521 Dihedral : 5.871 54.399 1145 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.98 % Allowed : 28.46 % Favored : 66.57 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.26), residues: 1026 helix: 1.40 (0.28), residues: 330 sheet: -0.27 (0.31), residues: 285 loop : -1.69 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 329 TYR 0.016 0.001 TYR C 122 PHE 0.015 0.001 PHE C 84 TRP 0.004 0.001 TRP C 96 HIS 0.004 0.001 HIS C 279 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8835) covalent geometry : angle 0.59710 (11979) SS BOND : bond 0.00219 ( 15) SS BOND : angle 1.80688 ( 30) hydrogen bonds : bond 0.02849 ( 385) hydrogen bonds : angle 4.35388 ( 1101) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: A 84 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: A 115 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: A 137 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7500 (t80) REVERT: A 198 ILE cc_start: 0.7255 (mm) cc_final: 0.6882 (tt) REVERT: A 353 ASN cc_start: 0.7366 (OUTLIER) cc_final: 0.6675 (m110) REVERT: B 74 PHE cc_start: 0.8105 (t80) cc_final: 0.7853 (t80) REVERT: B 84 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7234 (m-80) REVERT: B 115 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: B 155 ARG cc_start: 0.6537 (mtm180) cc_final: 0.6133 (ptp-170) REVERT: B 177 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: C 60 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7429 (mm-30) REVERT: C 84 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: C 93 LEU cc_start: 0.7986 (mt) cc_final: 0.7743 (mp) REVERT: C 137 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7760 (t80) REVERT: C 159 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6213 (tp) REVERT: C 242 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: C 263 PHE cc_start: 0.6940 (m-80) cc_final: 0.6110 (m-80) outliers start: 49 outliers final: 31 residues processed: 227 average time/residue: 0.1395 time to fit residues: 45.9418 Evaluate side-chains 221 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 356 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.177345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159995 restraints weight = 27008.237| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.12 r_work: 0.3791 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8850 Z= 0.158 Angle : 0.635 11.089 12009 Z= 0.349 Chirality : 0.096 1.372 1281 Planarity : 0.003 0.024 1521 Dihedral : 5.862 51.194 1143 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.00 % Allowed : 27.85 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1026 helix: 1.26 (0.28), residues: 330 sheet: -0.44 (0.31), residues: 279 loop : -1.41 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 282 TYR 0.016 0.002 TYR C 334 PHE 0.023 0.002 PHE B 135 TRP 0.005 0.001 TRP B 362 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8835) covalent geometry : angle 0.62941 (11979) SS BOND : bond 0.00328 ( 15) SS BOND : angle 1.78995 ( 30) hydrogen bonds : bond 0.03124 ( 385) hydrogen bonds : angle 4.50103 ( 1101) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: A 84 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: A 115 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: A 137 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 198 ILE cc_start: 0.7191 (mm) cc_final: 0.6880 (tt) REVERT: B 84 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: B 93 LEU cc_start: 0.8099 (mt) cc_final: 0.7795 (mp) REVERT: B 115 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6931 (mm-30) REVERT: C 60 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7451 (mm-30) REVERT: C 84 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: C 93 LEU cc_start: 0.8048 (mt) cc_final: 0.7797 (mp) REVERT: C 137 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7752 (t80) REVERT: C 138 ASP cc_start: 0.7126 (t70) cc_final: 0.6867 (t70) REVERT: C 159 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6252 (tp) REVERT: C 242 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: C 263 PHE cc_start: 0.6955 (m-80) cc_final: 0.6206 (m-80) outliers start: 59 outliers final: 38 residues processed: 222 average time/residue: 0.1372 time to fit residues: 43.8953 Evaluate side-chains 222 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 359 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.181868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.164781 restraints weight = 26890.754| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.08 r_work: 0.3807 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8850 Z= 0.125 Angle : 0.611 11.045 12009 Z= 0.336 Chirality : 0.095 1.361 1281 Planarity : 0.003 0.022 1521 Dihedral : 5.368 44.391 1139 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.98 % Allowed : 29.37 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.26), residues: 1026 helix: 1.38 (0.28), residues: 330 sheet: -0.52 (0.31), residues: 279 loop : -1.32 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 329 TYR 0.015 0.001 TYR C 122 PHE 0.017 0.001 PHE A 135 TRP 0.004 0.001 TRP C 96 HIS 0.003 0.001 HIS C 279 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8835) covalent geometry : angle 0.60750 (11979) SS BOND : bond 0.00226 ( 15) SS BOND : angle 1.42813 ( 30) hydrogen bonds : bond 0.02962 ( 385) hydrogen bonds : angle 4.36265 ( 1101) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: A 84 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: A 115 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: A 137 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7437 (t80) REVERT: A 198 ILE cc_start: 0.7229 (mm) cc_final: 0.6903 (tt) REVERT: B 84 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: B 93 LEU cc_start: 0.8065 (mt) cc_final: 0.7743 (mp) REVERT: B 115 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: B 177 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: C 60 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7483 (mm-30) REVERT: C 84 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: C 93 LEU cc_start: 0.8005 (mt) cc_final: 0.7740 (mp) REVERT: C 137 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7719 (t80) REVERT: C 138 ASP cc_start: 0.7048 (t70) cc_final: 0.6810 (t70) REVERT: C 159 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6300 (tp) REVERT: C 242 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: C 263 PHE cc_start: 0.6987 (m-80) cc_final: 0.6222 (m-80) outliers start: 49 outliers final: 28 residues processed: 223 average time/residue: 0.1445 time to fit residues: 46.5906 Evaluate side-chains 219 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 356 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 279 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.177816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160760 restraints weight = 27018.798| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.10 r_work: 0.3799 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8850 Z= 0.137 Angle : 0.623 11.209 12009 Z= 0.341 Chirality : 0.096 1.403 1281 Planarity : 0.003 0.023 1521 Dihedral : 4.800 28.641 1127 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.47 % Allowed : 29.98 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.26), residues: 1026 helix: 1.38 (0.28), residues: 330 sheet: -0.56 (0.30), residues: 279 loop : -1.33 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.014 0.001 TYR C 122 PHE 0.020 0.001 PHE B 135 TRP 0.004 0.001 TRP B 362 HIS 0.003 0.001 HIS C 279 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8835) covalent geometry : angle 0.61873 (11979) SS BOND : bond 0.00302 ( 15) SS BOND : angle 1.52556 ( 30) hydrogen bonds : bond 0.03035 ( 385) hydrogen bonds : angle 4.39834 ( 1101) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: A 84 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: A 115 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: A 137 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7415 (t80) REVERT: A 198 ILE cc_start: 0.7291 (mm) cc_final: 0.6980 (tt) REVERT: B 84 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7231 (m-80) REVERT: B 93 LEU cc_start: 0.8083 (mt) cc_final: 0.7746 (mp) REVERT: B 115 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: C 60 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7503 (mm-30) REVERT: C 84 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: C 93 LEU cc_start: 0.8011 (mt) cc_final: 0.7742 (mp) REVERT: C 102 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5792 (pt0) REVERT: C 137 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7733 (t80) REVERT: C 138 ASP cc_start: 0.7117 (t70) cc_final: 0.6891 (t70) REVERT: C 159 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6308 (tp) REVERT: C 242 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: C 263 PHE cc_start: 0.7077 (m-80) cc_final: 0.6373 (m-80) outliers start: 44 outliers final: 31 residues processed: 214 average time/residue: 0.1465 time to fit residues: 44.5867 Evaluate side-chains 220 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 356 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 299 ASN ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.171322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155380 restraints weight = 27437.201| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.97 r_work: 0.3753 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8850 Z= 0.264 Angle : 0.730 11.218 12009 Z= 0.403 Chirality : 0.100 1.424 1281 Planarity : 0.004 0.035 1521 Dihedral : 5.432 29.282 1125 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.88 % Allowed : 29.57 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.25), residues: 1026 helix: 0.60 (0.27), residues: 330 sheet: -0.74 (0.31), residues: 276 loop : -1.66 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 282 TYR 0.020 0.002 TYR C 334 PHE 0.032 0.003 PHE A 135 TRP 0.007 0.002 TRP B 362 HIS 0.005 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 8835) covalent geometry : angle 0.72398 (11979) SS BOND : bond 0.00466 ( 15) SS BOND : angle 2.06504 ( 30) hydrogen bonds : bond 0.03901 ( 385) hydrogen bonds : angle 5.00789 ( 1101) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7223 (m-80) REVERT: A 84 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: A 137 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7554 (t80) REVERT: A 198 ILE cc_start: 0.7310 (mm) cc_final: 0.6976 (tt) REVERT: B 84 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: B 115 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: C 60 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7629 (mm-30) REVERT: C 84 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: C 93 LEU cc_start: 0.8101 (mt) cc_final: 0.7856 (mp) REVERT: C 102 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5937 (pt0) REVERT: C 137 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7754 (t80) REVERT: C 242 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6699 (tt0) REVERT: C 263 PHE cc_start: 0.7214 (m-80) cc_final: 0.6554 (m-80) outliers start: 48 outliers final: 32 residues processed: 227 average time/residue: 0.1483 time to fit residues: 46.9140 Evaluate side-chains 224 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 359 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 0.0000 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.180773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164221 restraints weight = 26838.521| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.04 r_work: 0.3822 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8850 Z= 0.111 Angle : 0.623 11.297 12009 Z= 0.342 Chirality : 0.095 1.414 1281 Planarity : 0.003 0.030 1521 Dihedral : 4.948 29.231 1125 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.25 % Allowed : 30.79 % Favored : 65.96 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.26), residues: 1026 helix: 1.09 (0.28), residues: 330 sheet: -0.81 (0.31), residues: 279 loop : -1.34 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.014 0.001 TYR C 122 PHE 0.016 0.001 PHE C 84 TRP 0.008 0.001 TRP A 56 HIS 0.003 0.001 HIS C 279 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8835) covalent geometry : angle 0.62021 (11979) SS BOND : bond 0.00238 ( 15) SS BOND : angle 1.37239 ( 30) hydrogen bonds : bond 0.03089 ( 385) hydrogen bonds : angle 4.49327 ( 1101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3953.08 seconds wall clock time: 67 minutes 58.64 seconds (4078.64 seconds total)