Starting phenix.real_space_refine on Thu Jul 2 10:43:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wq4_32699/07_2026/7wq4_32699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wq4_32699/07_2026/7wq4_32699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wq4_32699/07_2026/7wq4_32699.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wq4_32699/07_2026/7wq4_32699.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wq4_32699/07_2026/7wq4_32699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wq4_32699/07_2026/7wq4_32699.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wq4_32699/07_2026/7wq4_32699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wq4_32699/07_2026/7wq4_32699.map" } resolution = 2.6 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5277 2.51 5 N 1451 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8290 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2225 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain breaks: 1 Chain: "L" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 95 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "A" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1927 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.01, per 1000 atoms: 0.24 Number of scatterers: 8290 At special positions: 0 Unit cell: (88.218, 97.344, 123.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1509 8.00 N 1451 7.00 C 5277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 0.60 Conformation dependent library (CDL) restraints added in 463.2 milliseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'R' and resid 26 through 52 removed outlier: 3.907A pdb=" N LEU R 30 " --> pdb=" O VAL R 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 88 Proline residue: R 80 - end of helix Processing helix chain 'R' and resid 95 through 100 removed outlier: 4.096A pdb=" N LYS R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 129 removed outlier: 3.720A pdb=" N PHE R 106 " --> pdb=" O HIS R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 158 Processing helix chain 'R' and resid 159 through 164 removed outlier: 4.166A pdb=" N TYR R 164 " --> pdb=" O TYR R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 196 Processing helix chain 'R' and resid 196 through 215 Processing helix chain 'R' and resid 224 through 249 removed outlier: 3.794A pdb=" N ARG R 228 " --> pdb=" O GLY R 224 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TRP R 249 " --> pdb=" O PHE R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 262 removed outlier: 3.515A pdb=" N HIS R 253 " --> pdb=" O TRP R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 293 removed outlier: 3.696A pdb=" N ASN R 284 " --> pdb=" O VAL R 280 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 296 through 301 removed outlier: 3.642A pdb=" N ARG R 300 " --> pdb=" O SER R 296 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 296 through 301' Processing helix chain 'R' and resid 302 through 307 removed outlier: 3.528A pdb=" N ILE R 306 " --> pdb=" O GLY R 302 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 302 through 307' Processing helix chain 'L' and resid 3 through 12 removed outlier: 3.554A pdb=" N GLY L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.583A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.077A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.588A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.549A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 removed outlier: 3.840A pdb=" N PHE A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.602A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.641A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.022A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.845A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.518A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'R' and resid 165 through 169 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.181A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.508A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.688A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.541A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.683A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.110A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.068A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.608A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.316A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1212 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: 1.30 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2702 1.34 - 1.46: 1972 1.46 - 1.58: 3709 1.58 - 1.70: 10 1.70 - 1.81: 74 Bond restraints: 8467 Sorted by residual: bond pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.650 -0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" C15 CLR R 402 " pdb=" C16 CLR R 402 " ideal model delta sigma weight residual 1.541 1.708 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C15 CLR R 401 " pdb=" C16 CLR R 401 " ideal model delta sigma weight residual 1.541 1.705 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C8 CLR R 402 " pdb=" C9 CLR R 402 " ideal model delta sigma weight residual 1.535 1.671 -0.136 2.00e-02 2.50e+03 4.62e+01 ... (remaining 8462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 11412 2.71 - 5.41: 58 5.41 - 8.12: 12 8.12 - 10.83: 3 10.83 - 13.53: 4 Bond angle restraints: 11489 Sorted by residual: angle pdb=" N VAL R 295 " pdb=" CA VAL R 295 " pdb=" C VAL R 295 " ideal model delta sigma weight residual 113.71 106.66 7.05 9.50e-01 1.11e+00 5.51e+01 angle pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " pdb=" C7 CLR R 401 " ideal model delta sigma weight residual 125.11 111.58 13.53 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" CA ALA R 170 " pdb=" C ALA R 170 " pdb=" O ALA R 170 " ideal model delta sigma weight residual 122.03 117.50 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" C10 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 122.94 111.81 11.13 3.00e+00 1.11e-01 1.38e+01 ... (remaining 11484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.16: 4765 12.16 - 24.32: 178 24.32 - 36.47: 56 36.47 - 48.63: 16 48.63 - 60.79: 8 Dihedral angle restraints: 5023 sinusoidal: 1982 harmonic: 3041 Sorted by residual: dihedral pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sinusoidal sigma weight residual -180.00 -120.16 -59.84 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG R 184 " pdb=" CA ARG R 184 " pdb=" CB ARG R 184 " pdb=" CG ARG R 184 " ideal model delta sinusoidal sigma weight residual -60.00 -117.77 57.77 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG ARG R 184 " pdb=" CD ARG R 184 " pdb=" NE ARG R 184 " pdb=" CZ ARG R 184 " ideal model delta sinusoidal sigma weight residual 180.00 139.10 40.90 2 1.50e+01 4.44e-03 9.14e+00 ... (remaining 5020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1271 0.110 - 0.221: 27 0.221 - 0.331: 4 0.331 - 0.442: 2 0.442 - 0.552: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.38 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.39 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" C9 CLR R 402 " pdb=" C10 CLR R 402 " pdb=" C11 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.45 -2.86 0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 1303 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 101 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C VAL R 101 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL R 101 " -0.008 2.00e-02 2.50e+03 pdb=" N HIS R 102 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO B 236 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 158 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO R 159 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 159 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 159 " -0.015 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 2 2.10 - 2.80: 2089 2.80 - 3.50: 11004 3.50 - 4.20: 19240 4.20 - 4.90: 34386 Nonbonded interactions: 66721 Sorted by model distance: nonbonded pdb=" OD1 ASN N 35 " pdb=" CB ASP N 50 " model vdw 1.399 3.440 nonbonded pdb=" CG2 VAL R 174 " pdb=" NE2 HIS R 176 " model vdw 2.067 3.540 nonbonded pdb=" O TYR R 129 " pdb=" OG SER R 133 " model vdw 2.247 3.040 nonbonded pdb=" O THR R 191 " pdb=" OG SER R 195 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.289 3.040 ... (remaining 66716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.007 0.319 8470 Z= 0.384 Angle : 0.615 13.533 11495 Z= 0.339 Chirality : 0.052 0.552 1306 Planarity : 0.003 0.027 1450 Dihedral : 8.043 60.788 3050 Min Nonbonded Distance : 1.399 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.45 % Allowed : 3.38 % Favored : 96.17 % 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: -1.07 (0.24), residues: 1032 helix: 0.15 (0.26), residues: 373 sheet: -0.58 (0.31), residues: 237 loop : -1.48 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 72 TYR 0.005 0.001 TYR N 60 PHE 0.010 0.001 PHE R 103 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.38 ( 8467) covalent geometry : angle 0.61460 / 0.34 (11489) SS BOND : bond 0.00085 / 0.04 ( 3) SS BOND : angle 0.48101 / 0.34 ( 6) hydrogen bonds : bond 0.12329 / 8.48 ( 430) hydrogen bonds : angle 5.57269 / 3.89 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: R 184 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.4897 (mtp-110) REVERT: A 15 ARG cc_start: 0.6050 (ttt90) cc_final: 0.5842 (ttm-80) REVERT: A 17 LYS cc_start: 0.6310 (mttt) cc_final: 0.5857 (pttp) REVERT: A 69 ILE cc_start: 0.8297 (mt) cc_final: 0.8074 (mm) REVERT: A 75 GLN cc_start: 0.7309 (tt0) cc_final: 0.6941 (tm130) REVERT: A 191 TYR cc_start: 0.7616 (m-10) cc_final: 0.7346 (m-10) REVERT: A 208 ARG cc_start: 0.6356 (mtm-85) cc_final: 0.5995 (tpt90) REVERT: B 44 GLN cc_start: 0.7850 (mt0) cc_final: 0.7582 (mt0) REVERT: B 188 MET cc_start: 0.8239 (mmm) cc_final: 0.8029 (mmm) REVERT: B 197 ARG cc_start: 0.6792 (mtm180) cc_final: 0.6497 (mtp85) REVERT: B 234 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: B 254 ASP cc_start: 0.7784 (p0) cc_final: 0.7549 (p0) REVERT: N 65 LYS cc_start: 0.7321 (mttt) cc_final: 0.6892 (tmtt) REVERT: N 80 TYR cc_start: 0.6848 (m-80) cc_final: 0.6631 (m-80) outliers start: 4 outliers final: 0 residues processed: 255 average time/residue: 0.5696 time to fit residues: 153.9658 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 55 GLN R 82 GLN R 253 HIS A 52 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN A 244 ASN B 35 ASN B 91 HIS B 176 GLN B 220 GLN N 77 ASN G 11 GLN G 24 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.158496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125064 restraints weight = 8933.051| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.81 r_work: 0.3332 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8470 Z= 0.174 Angle : 0.592 7.833 11495 Z= 0.313 Chirality : 0.044 0.147 1306 Planarity : 0.004 0.029 1450 Dihedral : 5.066 55.066 1174 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.72 % Allowed : 13.96 % Favored : 82.32 % 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: 0.00 (0.26), residues: 1032 helix: 1.13 (0.26), residues: 398 sheet: -0.18 (0.32), residues: 229 loop : -0.96 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 137 TYR 0.012 0.002 TYR A 243 PHE 0.018 0.002 PHE A 215 TRP 0.018 0.002 TRP B 339 HIS 0.012 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 8467) covalent geometry : angle 0.59222 / 0.31 (11489) SS BOND : bond 0.00222 / 0.11 ( 3) SS BOND : angle 0.89084 / 0.64 ( 6) hydrogen bonds : bond 0.04626 / 3.16 ( 430) hydrogen bonds : angle 4.44293 / 3.16 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7157 (mt) REVERT: R 88 LEU cc_start: 0.6879 (mt) cc_final: 0.6477 (mt) REVERT: R 96 LEU cc_start: 0.6283 (pt) cc_final: 0.5695 (tp) REVERT: R 166 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: R 298 HIS cc_start: 0.7006 (t70) cc_final: 0.6364 (m-70) REVERT: A 8 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6829 (mm-30) REVERT: A 15 ARG cc_start: 0.7323 (ttt90) cc_final: 0.7030 (ttm-80) REVERT: A 71 GLU cc_start: 0.8094 (tt0) cc_final: 0.7685 (tt0) REVERT: A 208 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.6671 (tpt90) REVERT: A 222 GLU cc_start: 0.7731 (pm20) cc_final: 0.7366 (pt0) REVERT: B 57 LYS cc_start: 0.9045 (pttm) cc_final: 0.8781 (pttt) REVERT: B 186 ASP cc_start: 0.8532 (m-30) cc_final: 0.8240 (m-30) REVERT: B 188 MET cc_start: 0.8967 (mmm) cc_final: 0.8586 (mmm) REVERT: B 197 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7499 (mtp85) REVERT: B 212 ASP cc_start: 0.8092 (t0) cc_final: 0.7862 (t0) REVERT: B 214 ARG cc_start: 0.7754 (mmt180) cc_final: 0.7512 (mmt180) REVERT: B 263 THR cc_start: 0.8658 (t) cc_final: 0.8151 (m) REVERT: G 21 MET cc_start: 0.6333 (ttp) cc_final: 0.6130 (ttp) REVERT: G 38 MET cc_start: 0.8218 (ttp) cc_final: 0.8008 (ttp) outliers start: 33 outliers final: 15 residues processed: 189 average time/residue: 0.5790 time to fit residues: 116.1957 Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 36 optimal weight: 0.0060 chunk 79 optimal weight: 0.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 82 GLN A 75 GLN B 35 ASN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121137 restraints weight = 8851.857| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.85 r_work: 0.3280 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8470 Z= 0.171 Angle : 0.578 8.525 11495 Z= 0.305 Chirality : 0.044 0.191 1306 Planarity : 0.004 0.030 1450 Dihedral : 4.881 59.944 1168 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.62 % Allowed : 14.53 % Favored : 80.86 % 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: 1032 helix: 1.41 (0.26), residues: 396 sheet: 0.22 (0.33), residues: 222 loop : -0.73 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 134 TYR 0.011 0.002 TYR R 86 PHE 0.015 0.002 PHE B 151 TRP 0.014 0.002 TRP B 332 HIS 0.009 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 8467) covalent geometry : angle 0.57129 / 0.30 (11489) SS BOND : bond 0.00302 / 0.15 ( 3) SS BOND : angle 3.81901 / 2.90 ( 6) hydrogen bonds : bond 0.04587 / 3.15 ( 430) hydrogen bonds : angle 4.43645 / 3.16 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7218 (mt) REVERT: R 166 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: R 298 HIS cc_start: 0.7010 (t70) cc_final: 0.6553 (m-70) REVERT: A 15 ARG cc_start: 0.7433 (ttt90) cc_final: 0.7094 (ttm-80) REVERT: A 51 LYS cc_start: 0.7475 (pptt) cc_final: 0.7233 (mmmt) REVERT: A 194 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8189 (ttt-90) REVERT: A 208 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.6889 (mmm-85) REVERT: A 238 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8251 (mtt) REVERT: B 57 LYS cc_start: 0.8956 (pttm) cc_final: 0.8679 (pttt) REVERT: B 59 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8509 (t80) REVERT: B 186 ASP cc_start: 0.8593 (m-30) cc_final: 0.8369 (m-30) REVERT: B 188 MET cc_start: 0.8861 (mmm) cc_final: 0.8470 (mmm) REVERT: B 197 ARG cc_start: 0.8081 (mtm180) cc_final: 0.7563 (mtp85) REVERT: B 212 ASP cc_start: 0.8289 (t0) cc_final: 0.8087 (t70) REVERT: B 214 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7499 (mpp-170) REVERT: B 220 GLN cc_start: 0.8149 (tt0) cc_final: 0.7824 (tt0) REVERT: B 234 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: B 263 THR cc_start: 0.8748 (t) cc_final: 0.8253 (m) REVERT: G 37 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8177 (mp) REVERT: G 42 GLU cc_start: 0.7837 (pp20) cc_final: 0.7295 (mm-30) outliers start: 41 outliers final: 20 residues processed: 164 average time/residue: 0.6332 time to fit residues: 109.8774 Evaluate side-chains 150 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 82 GLN A 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120936 restraints weight = 9103.547| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.96 r_work: 0.3302 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8470 Z= 0.125 Angle : 0.522 7.448 11495 Z= 0.276 Chirality : 0.042 0.181 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.735 58.152 1168 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.05 % Allowed : 17.23 % Favored : 78.72 % 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: 0.77 (0.26), residues: 1032 helix: 1.79 (0.27), residues: 392 sheet: 0.37 (0.32), residues: 230 loop : -0.63 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.009 0.001 TYR R 86 PHE 0.011 0.001 PHE B 151 TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8467) covalent geometry : angle 0.51599 / 0.27 (11489) SS BOND : bond 0.00323 / 0.16 ( 3) SS BOND : angle 3.36720 / 2.45 ( 6) hydrogen bonds : bond 0.03945 / 2.71 ( 430) hydrogen bonds : angle 4.26131 / 3.04 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7273 (mt) REVERT: R 85 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6312 (mp) REVERT: R 136 LEU cc_start: 0.7910 (tt) cc_final: 0.7625 (tp) REVERT: R 166 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: R 298 HIS cc_start: 0.7067 (t70) cc_final: 0.6550 (m-70) REVERT: A 15 ARG cc_start: 0.7477 (ttt90) cc_final: 0.7113 (ttm-80) REVERT: A 51 LYS cc_start: 0.7529 (pptt) cc_final: 0.7292 (mmmt) REVERT: A 73 LYS cc_start: 0.9068 (mttp) cc_final: 0.8848 (mttt) REVERT: A 208 ARG cc_start: 0.7592 (mtm-85) cc_final: 0.6859 (mmm-85) REVERT: A 238 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8233 (mtt) REVERT: A 242 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7288 (tt0) REVERT: B 57 LYS cc_start: 0.8940 (pttm) cc_final: 0.8668 (pttt) REVERT: B 186 ASP cc_start: 0.8515 (m-30) cc_final: 0.8303 (m-30) REVERT: B 188 MET cc_start: 0.8915 (mmm) cc_final: 0.8608 (mmm) REVERT: B 197 ARG cc_start: 0.8154 (mtm180) cc_final: 0.7536 (mtp85) REVERT: B 212 ASP cc_start: 0.8244 (t0) cc_final: 0.8015 (t70) REVERT: B 214 ARG cc_start: 0.7849 (mmt180) cc_final: 0.7565 (mpp-170) REVERT: B 234 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: B 263 THR cc_start: 0.8762 (t) cc_final: 0.8230 (m) REVERT: G 37 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8103 (mp) REVERT: G 42 GLU cc_start: 0.7831 (pp20) cc_final: 0.7320 (mm-30) outliers start: 36 outliers final: 16 residues processed: 162 average time/residue: 0.6444 time to fit residues: 110.3156 Evaluate side-chains 152 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 61 ASN R 82 GLN R 102 HIS R 168 GLN A 75 GLN B 32 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117676 restraints weight = 8992.324| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.80 r_work: 0.3236 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8470 Z= 0.236 Angle : 0.654 8.659 11495 Z= 0.344 Chirality : 0.047 0.209 1306 Planarity : 0.005 0.040 1450 Dihedral : 5.300 57.353 1168 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.73 % Allowed : 18.02 % Favored : 77.25 % 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: 0.51 (0.26), residues: 1032 helix: 1.47 (0.26), residues: 393 sheet: 0.44 (0.32), residues: 226 loop : -0.79 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.017 0.002 TYR A 243 PHE 0.017 0.003 PHE B 151 TRP 0.017 0.002 TRP A 96 HIS 0.012 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 ( 8467) covalent geometry : angle 0.64824 / 0.34 (11489) SS BOND : bond 0.00440 / 0.22 ( 3) SS BOND : angle 3.73766 / 2.84 ( 6) hydrogen bonds : bond 0.05408 / 3.70 ( 430) hydrogen bonds : angle 4.63810 / 3.33 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7844 (tt) cc_final: 0.7411 (mp) REVERT: R 140 ARG cc_start: 0.7344 (ttt180) cc_final: 0.6987 (ttm-80) REVERT: R 166 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: R 298 HIS cc_start: 0.7491 (t70) cc_final: 0.6589 (m-70) REVERT: A 10 LYS cc_start: 0.7413 (mttt) cc_final: 0.7203 (mmtp) REVERT: A 15 ARG cc_start: 0.7340 (ttt90) cc_final: 0.6765 (ttm-80) REVERT: A 24 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7127 (tp-100) REVERT: A 73 LYS cc_start: 0.9106 (mttp) cc_final: 0.8851 (mttt) REVERT: A 194 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8189 (ttt-90) REVERT: A 208 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.6895 (mmm-85) REVERT: A 238 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8331 (mtt) REVERT: A 242 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7426 (tt0) REVERT: B 57 LYS cc_start: 0.8964 (pttm) cc_final: 0.8653 (pttt) REVERT: B 59 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8534 (t80) REVERT: B 134 ARG cc_start: 0.7388 (ptm-80) cc_final: 0.6609 (tpp-160) REVERT: B 155 ASN cc_start: 0.7677 (p0) cc_final: 0.7425 (t0) REVERT: B 188 MET cc_start: 0.8876 (mmm) cc_final: 0.8543 (mmm) REVERT: B 197 ARG cc_start: 0.8212 (mtm180) cc_final: 0.7787 (mtp85) REVERT: B 214 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7679 (mpp-170) REVERT: B 220 GLN cc_start: 0.8261 (tt0) cc_final: 0.7951 (tt0) REVERT: B 234 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: B 263 THR cc_start: 0.8869 (t) cc_final: 0.8292 (m) REVERT: B 304 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7984 (mtp85) REVERT: G 37 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8133 (mp) REVERT: G 42 GLU cc_start: 0.7855 (pp20) cc_final: 0.7359 (mm-30) outliers start: 42 outliers final: 19 residues processed: 157 average time/residue: 0.6640 time to fit residues: 110.0073 Evaluate side-chains 151 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 236 ARG Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 61 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120651 restraints weight = 8949.296| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.93 r_work: 0.3303 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8470 Z= 0.108 Angle : 0.496 5.649 11495 Z= 0.263 Chirality : 0.042 0.152 1306 Planarity : 0.003 0.030 1450 Dihedral : 4.873 59.238 1168 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.70 % Allowed : 19.93 % Favored : 77.36 % 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: 0.92 (0.26), residues: 1032 helix: 2.04 (0.27), residues: 390 sheet: 0.47 (0.32), residues: 228 loop : -0.69 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.014 0.001 TYR R 129 PHE 0.011 0.001 PHE B 199 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8467) covalent geometry : angle 0.49394 / 0.26 (11489) SS BOND : bond 0.00461 / 0.23 ( 3) SS BOND : angle 2.16548 / 1.79 ( 6) hydrogen bonds : bond 0.03703 / 2.55 ( 430) hydrogen bonds : angle 4.18676 / 2.99 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7738 (tt) cc_final: 0.7494 (tp) REVERT: R 166 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: R 298 HIS cc_start: 0.7422 (t70) cc_final: 0.6480 (m-70) REVERT: A 10 LYS cc_start: 0.7358 (mttt) cc_final: 0.7133 (mmtp) REVERT: A 15 ARG cc_start: 0.7439 (ttt90) cc_final: 0.6986 (ttm-80) REVERT: A 73 LYS cc_start: 0.9065 (mttp) cc_final: 0.8849 (mttt) REVERT: A 82 HIS cc_start: 0.8354 (m170) cc_final: 0.8116 (m170) REVERT: A 208 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.6831 (mmm-85) REVERT: A 242 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7448 (tt0) REVERT: B 57 LYS cc_start: 0.8926 (pttm) cc_final: 0.8545 (ptpt) REVERT: B 134 ARG cc_start: 0.7385 (ptm-80) cc_final: 0.6569 (tpp-160) REVERT: B 188 MET cc_start: 0.8902 (mmm) cc_final: 0.8612 (mmm) REVERT: B 197 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7752 (mtp85) REVERT: B 214 ARG cc_start: 0.7869 (mmt180) cc_final: 0.7585 (mpp-170) REVERT: B 220 GLN cc_start: 0.8051 (tt0) cc_final: 0.7731 (tt0) REVERT: B 234 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: B 263 THR cc_start: 0.8829 (t) cc_final: 0.8246 (m) REVERT: G 37 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8051 (mp) REVERT: G 42 GLU cc_start: 0.7764 (pp20) cc_final: 0.7321 (mm-30) outliers start: 24 outliers final: 12 residues processed: 158 average time/residue: 0.6085 time to fit residues: 101.6988 Evaluate side-chains 145 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 41 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 61 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 32 GLN B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122163 restraints weight = 8987.628| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.95 r_work: 0.3320 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8470 Z= 0.101 Angle : 0.493 9.991 11495 Z= 0.258 Chirality : 0.041 0.174 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.722 59.960 1168 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.59 % Allowed : 20.16 % Favored : 77.25 % 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: 1.10 (0.26), residues: 1032 helix: 2.24 (0.27), residues: 390 sheet: 0.53 (0.32), residues: 228 loop : -0.62 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.014 0.001 TYR B 124 PHE 0.011 0.001 PHE B 199 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 8467) covalent geometry : angle 0.49136 / 0.26 (11489) SS BOND : bond 0.00269 / 0.13 ( 3) SS BOND : angle 1.82485 / 1.60 ( 6) hydrogen bonds : bond 0.03494 / 2.40 ( 430) hydrogen bonds : angle 4.06675 / 2.91 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7718 (tt) cc_final: 0.7474 (tp) REVERT: R 166 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: R 298 HIS cc_start: 0.7376 (t70) cc_final: 0.6445 (m-70) REVERT: A 17 LYS cc_start: 0.7833 (mttt) cc_final: 0.7589 (mttt) REVERT: A 20 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7270 (tp30) REVERT: A 73 LYS cc_start: 0.9017 (mttp) cc_final: 0.8806 (mttt) REVERT: A 208 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.6850 (mmm-85) REVERT: A 222 GLU cc_start: 0.7820 (pm20) cc_final: 0.7462 (pt0) REVERT: A 238 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8195 (mtt) REVERT: A 242 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7255 (tt0) REVERT: B 57 LYS cc_start: 0.8942 (pttm) cc_final: 0.8591 (pttt) REVERT: B 59 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.8223 (t80) REVERT: B 134 ARG cc_start: 0.7354 (ptm-80) cc_final: 0.6559 (tpp-160) REVERT: B 197 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7732 (mtp85) REVERT: B 220 GLN cc_start: 0.7973 (tt0) cc_final: 0.7644 (tt0) REVERT: B 234 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: B 260 GLU cc_start: 0.7106 (tt0) cc_final: 0.6881 (tp30) REVERT: B 263 THR cc_start: 0.8765 (t) cc_final: 0.8161 (m) REVERT: G 42 GLU cc_start: 0.7819 (pp20) cc_final: 0.7357 (mm-30) outliers start: 23 outliers final: 11 residues processed: 159 average time/residue: 0.5842 time to fit residues: 98.2140 Evaluate side-chains 153 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 24 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 61 ASN A 75 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118032 restraints weight = 8887.832| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.93 r_work: 0.3269 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8470 Z= 0.154 Angle : 0.571 13.799 11495 Z= 0.298 Chirality : 0.043 0.196 1306 Planarity : 0.004 0.032 1450 Dihedral : 4.978 58.712 1168 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.15 % Allowed : 20.61 % Favored : 76.24 % 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: 0.96 (0.26), residues: 1032 helix: 2.03 (0.26), residues: 390 sheet: 0.56 (0.33), residues: 224 loop : -0.64 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 15 TYR 0.015 0.002 TYR R 129 PHE 0.012 0.002 PHE B 199 TRP 0.014 0.002 TRP B 82 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 8467) covalent geometry : angle 0.56867 / 0.30 (11489) SS BOND : bond 0.00351 / 0.17 ( 3) SS BOND : angle 2.24974 / 1.87 ( 6) hydrogen bonds : bond 0.04334 / 2.97 ( 430) hydrogen bonds : angle 4.32047 / 3.10 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7788 (tt) cc_final: 0.7536 (tp) REVERT: R 166 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: R 200 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7890 (p) REVERT: R 298 HIS cc_start: 0.7533 (t70) cc_final: 0.6583 (m-70) REVERT: A 73 LYS cc_start: 0.9070 (mttp) cc_final: 0.8866 (mttt) REVERT: A 82 HIS cc_start: 0.8327 (m170) cc_final: 0.8071 (m-70) REVERT: A 222 GLU cc_start: 0.7886 (pm20) cc_final: 0.7526 (pt0) REVERT: A 242 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7352 (mt-10) REVERT: B 57 LYS cc_start: 0.8961 (pttm) cc_final: 0.8590 (pttt) REVERT: B 59 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8514 (t80) REVERT: B 134 ARG cc_start: 0.7393 (ptm-80) cc_final: 0.6606 (tpp-160) REVERT: B 197 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7720 (mtp85) REVERT: B 220 GLN cc_start: 0.8172 (tt0) cc_final: 0.7801 (tt0) REVERT: B 234 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: B 260 GLU cc_start: 0.7401 (tt0) cc_final: 0.7114 (tp30) REVERT: B 263 THR cc_start: 0.8820 (t) cc_final: 0.8208 (m) REVERT: G 37 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8068 (mp) REVERT: G 42 GLU cc_start: 0.7890 (pp20) cc_final: 0.7423 (mm-30) outliers start: 28 outliers final: 14 residues processed: 150 average time/residue: 0.6664 time to fit residues: 105.3077 Evaluate side-chains 147 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 64 optimal weight: 0.0470 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 61 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121165 restraints weight = 9006.896| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.94 r_work: 0.3310 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8470 Z= 0.107 Angle : 0.516 14.380 11495 Z= 0.267 Chirality : 0.042 0.179 1306 Planarity : 0.003 0.036 1450 Dihedral : 4.727 57.436 1168 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.59 % Allowed : 21.51 % Favored : 75.90 % 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: 1.13 (0.26), residues: 1032 helix: 2.28 (0.26), residues: 390 sheet: 0.55 (0.33), residues: 219 loop : -0.60 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 15 TYR 0.013 0.001 TYR R 129 PHE 0.011 0.001 PHE B 199 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8467) covalent geometry : angle 0.51429 / 0.27 (11489) SS BOND : bond 0.00301 / 0.15 ( 3) SS BOND : angle 1.90370 / 1.69 ( 6) hydrogen bonds : bond 0.03572 / 2.45 ( 430) hydrogen bonds : angle 4.11079 / 2.95 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7697 (tt) cc_final: 0.7454 (tp) REVERT: R 166 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: R 200 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7876 (p) REVERT: R 298 HIS cc_start: 0.7450 (t70) cc_final: 0.6470 (m-70) REVERT: A 20 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7228 (tp30) REVERT: A 73 LYS cc_start: 0.9032 (mttp) cc_final: 0.8783 (mttt) REVERT: A 82 HIS cc_start: 0.8274 (m170) cc_final: 0.8043 (m170) REVERT: A 208 ARG cc_start: 0.7817 (mtm110) cc_final: 0.6909 (mmm-85) REVERT: A 222 GLU cc_start: 0.7825 (pm20) cc_final: 0.7441 (pt0) REVERT: A 242 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7238 (mt-10) REVERT: B 57 LYS cc_start: 0.8908 (pttm) cc_final: 0.8533 (ptpt) REVERT: B 59 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8113 (t80) REVERT: B 134 ARG cc_start: 0.7356 (ptm-80) cc_final: 0.6577 (tpp-160) REVERT: B 197 ARG cc_start: 0.7950 (mtm180) cc_final: 0.7643 (mtp85) REVERT: B 220 GLN cc_start: 0.8026 (tt0) cc_final: 0.7673 (tt0) REVERT: B 234 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: B 263 THR cc_start: 0.8776 (t) cc_final: 0.8169 (m) REVERT: G 37 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8033 (mp) REVERT: G 42 GLU cc_start: 0.7882 (pp20) cc_final: 0.7402 (mm-30) outliers start: 23 outliers final: 12 residues processed: 152 average time/residue: 0.6278 time to fit residues: 100.8238 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 61 ASN A 75 GLN B 32 GLN B 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119045 restraints weight = 8963.844| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.95 r_work: 0.3279 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8470 Z= 0.136 Angle : 0.553 14.614 11495 Z= 0.287 Chirality : 0.043 0.220 1306 Planarity : 0.004 0.038 1450 Dihedral : 4.856 57.604 1168 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.03 % Allowed : 22.07 % Favored : 75.90 % 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: 1.06 (0.26), residues: 1032 helix: 2.19 (0.26), residues: 390 sheet: 0.58 (0.33), residues: 219 loop : -0.64 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 15 TYR 0.013 0.001 TYR R 129 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8467) covalent geometry : angle 0.55157 / 0.29 (11489) SS BOND : bond 0.00332 / 0.16 ( 3) SS BOND : angle 2.06452 / 1.77 ( 6) hydrogen bonds : bond 0.04045 / 2.78 ( 430) hydrogen bonds : angle 4.23428 / 3.04 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7701 (tt) cc_final: 0.7446 (tp) REVERT: R 166 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: R 200 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7839 (p) REVERT: R 298 HIS cc_start: 0.7481 (t70) cc_final: 0.6512 (m-70) REVERT: A 73 LYS cc_start: 0.9066 (mttp) cc_final: 0.8809 (mttt) REVERT: A 82 HIS cc_start: 0.8278 (m170) cc_final: 0.8031 (m170) REVERT: A 222 GLU cc_start: 0.7898 (pm20) cc_final: 0.7497 (pt0) REVERT: B 57 LYS cc_start: 0.8942 (pttm) cc_final: 0.8578 (pttt) REVERT: B 59 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8426 (t80) REVERT: B 134 ARG cc_start: 0.7364 (ptm-80) cc_final: 0.6581 (tpp-160) REVERT: B 197 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7740 (mtp85) REVERT: B 220 GLN cc_start: 0.8142 (tt0) cc_final: 0.7776 (tt0) REVERT: B 234 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: B 263 THR cc_start: 0.8793 (t) cc_final: 0.8184 (m) REVERT: G 37 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8010 (mp) REVERT: G 42 GLU cc_start: 0.7893 (pp20) cc_final: 0.7420 (mm-30) outliers start: 18 outliers final: 13 residues processed: 142 average time/residue: 0.6438 time to fit residues: 96.4839 Evaluate side-chains 140 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 61 ASN A 75 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.154031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119266 restraints weight = 8980.702| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.93 r_work: 0.3285 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8470 Z= 0.132 Angle : 0.550 14.575 11495 Z= 0.285 Chirality : 0.042 0.141 1306 Planarity : 0.004 0.064 1450 Dihedral : 4.827 55.282 1168 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.48 % Allowed : 21.85 % Favored : 75.68 % 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: 1.08 (0.26), residues: 1032 helix: 2.22 (0.26), residues: 390 sheet: 0.58 (0.33), residues: 219 loop : -0.64 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 208 TYR 0.013 0.001 TYR R 129 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8467) covalent geometry : angle 0.54796 / 0.28 (11489) SS BOND : bond 0.00339 / 0.17 ( 3) SS BOND : angle 2.07385 / 1.79 ( 6) hydrogen bonds : bond 0.03980 / 2.72 ( 430) hydrogen bonds : angle 4.21856 / 3.03 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3618.81 seconds wall clock time: 62 minutes 20.40 seconds (3740.40 seconds total)