Starting phenix.real_space_refine on Sat Jun 7 02:48:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wq4_32699/06_2025/7wq4_32699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wq4_32699/06_2025/7wq4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wq4_32699/06_2025/7wq4_32699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wq4_32699/06_2025/7wq4_32699.map" model { file = "/net/cci-nas-00/data/ceres_data/7wq4_32699/06_2025/7wq4_32699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wq4_32699/06_2025/7wq4_32699.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.27, per 1000 atoms: 0.64 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.06 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: 2.36 Time building geometry restraints manager: 2.53 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: 4849 12.16 - 24.32: 191 24.32 - 36.47: 60 36.47 - 48.63: 26 48.63 - 60.79: 9 Dihedral angle restraints: 5135 sinusoidal: 2094 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 5132 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: 0.710 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 : 8.519 60.788 3162 Min Nonbonded Distance : 1.399 Molprobity Statistics. All-atom Clashscore : 6.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS A 209 PHE 0.010 0.001 PHE R 103 TYR 0.005 0.001 TYR N 60 ARG 0.001 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.12329 ( 430) hydrogen bonds : angle 5.57269 ( 1212) SS BOND : bond 0.00085 ( 3) SS BOND : angle 0.48101 ( 6) covalent geometry : bond 0.00736 ( 8467) covalent geometry : angle 0.61460 (11489) *********************** 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 : 0.924 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: 1.2283 time to fit residues: 331.5769 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 : 1.022 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.0370 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 GLN R 82 GLN R 253 HIS A 52 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN B 35 ASN B 91 HIS B 176 GLN B 220 GLN B 259 GLN N 77 ASN G 11 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131739 restraints weight = 8850.529| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.84 r_work: 0.3429 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8470 Z= 0.131 Angle : 0.520 7.319 11495 Z= 0.272 Chirality : 0.042 0.142 1306 Planarity : 0.004 0.028 1450 Dihedral : 5.145 55.945 1286 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.27 % Allowed : 13.85 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1032 helix: 1.56 (0.26), residues: 384 sheet: -0.18 (0.32), residues: 231 loop : -0.78 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 332 HIS 0.015 0.002 HIS R 176 PHE 0.023 0.002 PHE A 108 TYR 0.013 0.001 TYR A 243 ARG 0.006 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 430) hydrogen bonds : angle 4.16632 ( 1212) SS BOND : bond 0.00180 ( 3) SS BOND : angle 0.73744 ( 6) covalent geometry : bond 0.00298 ( 8467) covalent geometry : angle 0.51956 (11489) *********************** 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 202 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: R 88 LEU cc_start: 0.6820 (mt) cc_final: 0.6426 (mt) REVERT: R 96 LEU cc_start: 0.6322 (pt) cc_final: 0.5710 (tp) REVERT: R 166 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: A 8 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6652 (mm-30) REVERT: A 15 ARG cc_start: 0.7269 (ttt90) cc_final: 0.7054 (ttm-80) REVERT: A 73 LYS cc_start: 0.8894 (mttp) cc_final: 0.8656 (mttt) REVERT: A 78 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8039 (mmtt) REVERT: A 208 ARG cc_start: 0.7286 (mtm-85) cc_final: 0.6618 (tpt90) REVERT: A 222 GLU cc_start: 0.7554 (pm20) cc_final: 0.7086 (pt0) REVERT: B 57 LYS cc_start: 0.8996 (pttm) cc_final: 0.8755 (pttt) REVERT: B 135 VAL cc_start: 0.8358 (t) cc_final: 0.8150 (t) REVERT: B 186 ASP cc_start: 0.8452 (m-30) cc_final: 0.8114 (m-30) REVERT: B 188 MET cc_start: 0.8881 (mmm) cc_final: 0.8505 (mmm) REVERT: B 197 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7465 (mtp85) REVERT: B 212 ASP cc_start: 0.7862 (t0) cc_final: 0.7634 (t70) REVERT: B 214 ARG cc_start: 0.7543 (mmt180) cc_final: 0.7222 (mmt180) REVERT: B 234 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: B 263 THR cc_start: 0.8387 (t) cc_final: 0.7946 (m) outliers start: 29 outliers final: 11 residues processed: 188 average time/residue: 1.2272 time to fit residues: 244.7431 Evaluate side-chains 156 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 166 GLN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE 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 100 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122474 restraints weight = 8978.842| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.86 r_work: 0.3286 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8470 Z= 0.153 Angle : 0.553 6.570 11495 Z= 0.292 Chirality : 0.043 0.138 1306 Planarity : 0.004 0.033 1450 Dihedral : 5.003 56.236 1282 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.50 % Allowed : 15.32 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1032 helix: 1.46 (0.27), residues: 397 sheet: 0.17 (0.33), residues: 223 loop : -0.71 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 332 HIS 0.012 0.001 HIS A 209 PHE 0.015 0.002 PHE B 151 TYR 0.010 0.002 TYR R 86 ARG 0.006 0.001 ARG R 137 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 430) hydrogen bonds : angle 4.37186 ( 1212) SS BOND : bond 0.00320 ( 3) SS BOND : angle 0.93724 ( 6) covalent geometry : bond 0.00356 ( 8467) covalent geometry : angle 0.55288 (11489) *********************** 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 187 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7270 (mt) REVERT: R 96 LEU cc_start: 0.6347 (pt) cc_final: 0.5764 (tp) REVERT: R 136 LEU cc_start: 0.7852 (tt) cc_final: 0.7562 (tp) REVERT: R 166 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: R 298 HIS cc_start: 0.6954 (t70) cc_final: 0.6537 (m-70) REVERT: A 15 ARG cc_start: 0.7277 (ttt90) cc_final: 0.6926 (ttm-80) REVERT: A 20 GLU cc_start: 0.7588 (tp30) cc_final: 0.7312 (tp30) REVERT: A 73 LYS cc_start: 0.9000 (mttp) cc_final: 0.8606 (mttt) REVERT: A 78 LYS cc_start: 0.8925 (mmtp) cc_final: 0.8189 (mptt) REVERT: A 82 HIS cc_start: 0.8408 (m170) cc_final: 0.8177 (m170) REVERT: A 208 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.6825 (mmm-85) REVERT: A 222 GLU cc_start: 0.7771 (pm20) cc_final: 0.7427 (pt0) REVERT: A 238 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8200 (mtt) REVERT: B 29 THR cc_start: 0.7227 (OUTLIER) cc_final: 0.6468 (p) REVERT: B 57 LYS cc_start: 0.9010 (pttm) cc_final: 0.8720 (pttt) REVERT: B 186 ASP cc_start: 0.8518 (m-30) cc_final: 0.8224 (m-30) REVERT: B 188 MET cc_start: 0.8848 (mmm) cc_final: 0.8463 (mmm) REVERT: B 197 ARG cc_start: 0.8030 (mtm180) cc_final: 0.7491 (mtp85) REVERT: B 212 ASP cc_start: 0.8246 (t0) cc_final: 0.8024 (t70) REVERT: B 214 ARG cc_start: 0.7782 (mmt180) cc_final: 0.7493 (mpp-170) REVERT: B 220 GLN cc_start: 0.8147 (tt0) cc_final: 0.7821 (tt0) REVERT: B 234 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: B 263 THR cc_start: 0.8756 (t) cc_final: 0.8231 (m) REVERT: G 37 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8089 (mp) REVERT: G 42 GLU cc_start: 0.7887 (pp20) cc_final: 0.7273 (mm-30) outliers start: 40 outliers final: 18 residues processed: 172 average time/residue: 1.3086 time to fit residues: 237.9994 Evaluate side-chains 147 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 A residue 162 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN 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 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 18 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 82 HIS B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121971 restraints weight = 8956.001| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.95 r_work: 0.3312 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8470 Z= 0.117 Angle : 0.499 7.492 11495 Z= 0.263 Chirality : 0.041 0.131 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.769 56.077 1282 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.05 % Allowed : 18.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1032 helix: 1.85 (0.27), residues: 392 sheet: 0.28 (0.32), residues: 223 loop : -0.48 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS A 209 PHE 0.011 0.001 PHE B 151 TYR 0.011 0.001 TYR R 129 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 430) hydrogen bonds : angle 4.20223 ( 1212) SS BOND : bond 0.00216 ( 3) SS BOND : angle 1.16657 ( 6) covalent geometry : bond 0.00261 ( 8467) covalent geometry : angle 0.49871 (11489) *********************** 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 169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7242 (mt) REVERT: R 136 LEU cc_start: 0.7866 (tt) cc_final: 0.7608 (tp) REVERT: R 166 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: R 298 HIS cc_start: 0.7004 (t70) cc_final: 0.6533 (m-70) REVERT: A 15 ARG cc_start: 0.7465 (ttt90) cc_final: 0.7125 (ttm-80) REVERT: A 20 GLU cc_start: 0.7622 (tp30) cc_final: 0.7386 (tp30) REVERT: A 51 LYS cc_start: 0.7465 (pptt) cc_final: 0.7249 (mmmt) REVERT: A 78 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8157 (mptt) REVERT: A 208 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.6801 (mmm-85) REVERT: A 238 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8173 (mtt) REVERT: B 57 LYS cc_start: 0.8937 (pttm) cc_final: 0.8669 (pttt) REVERT: B 186 ASP cc_start: 0.8434 (m-30) cc_final: 0.8159 (m-30) REVERT: B 188 MET cc_start: 0.8873 (mmm) cc_final: 0.8537 (mmm) REVERT: B 197 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7554 (mtp85) REVERT: B 212 ASP cc_start: 0.8221 (t0) cc_final: 0.7979 (t70) REVERT: B 214 ARG cc_start: 0.7717 (mmt180) cc_final: 0.7435 (mpp-170) REVERT: B 220 GLN cc_start: 0.8085 (tt0) cc_final: 0.7756 (tt0) REVERT: B 234 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: B 263 THR cc_start: 0.8731 (t) cc_final: 0.8194 (m) REVERT: G 37 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8026 (mp) REVERT: G 42 GLU cc_start: 0.7860 (pp20) cc_final: 0.7329 (mm-30) outliers start: 36 outliers final: 15 residues processed: 156 average time/residue: 1.3543 time to fit residues: 223.1345 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 135 GLU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 154 LEU 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 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 99 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 76 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 70 optimal weight: 0.0040 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 32 GLN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123641 restraints weight = 8851.122| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.93 r_work: 0.3337 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8470 Z= 0.096 Angle : 0.468 8.132 11495 Z= 0.246 Chirality : 0.041 0.141 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.571 55.639 1282 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.72 % Allowed : 18.24 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1032 helix: 2.11 (0.27), residues: 391 sheet: 0.47 (0.32), residues: 230 loop : -0.45 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.010 0.001 PHE B 151 TYR 0.012 0.001 TYR R 129 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 430) hydrogen bonds : angle 4.03016 ( 1212) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.77322 ( 6) covalent geometry : bond 0.00204 ( 8467) covalent geometry : angle 0.46739 (11489) *********************** 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 188 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7342 (mt) REVERT: R 136 LEU cc_start: 0.7781 (tt) cc_final: 0.7543 (tp) REVERT: R 166 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: R 298 HIS cc_start: 0.7293 (t70) cc_final: 0.6464 (m-70) REVERT: A 15 ARG cc_start: 0.7402 (ttt90) cc_final: 0.7088 (ttm-80) REVERT: A 20 GLU cc_start: 0.7618 (tp30) cc_final: 0.7390 (tp30) REVERT: A 51 LYS cc_start: 0.7514 (pptt) cc_final: 0.7300 (mmmt) REVERT: A 78 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8114 (mptt) REVERT: A 208 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.6796 (mmm-85) REVERT: A 222 GLU cc_start: 0.7702 (pm20) cc_final: 0.7397 (pt0) REVERT: A 238 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8129 (mtt) REVERT: A 242 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7296 (tt0) REVERT: B 57 LYS cc_start: 0.8916 (pttm) cc_final: 0.8704 (pttt) REVERT: B 134 ARG cc_start: 0.7305 (ptm-80) cc_final: 0.6529 (tpm170) REVERT: B 186 ASP cc_start: 0.8387 (m-30) cc_final: 0.8112 (m-30) REVERT: B 188 MET cc_start: 0.8857 (mmm) cc_final: 0.8477 (mmm) REVERT: B 197 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7660 (mtp85) REVERT: B 212 ASP cc_start: 0.8229 (t0) cc_final: 0.7918 (t0) REVERT: B 214 ARG cc_start: 0.7717 (mmt180) cc_final: 0.7473 (mpp-170) REVERT: B 234 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: B 263 THR cc_start: 0.8710 (t) cc_final: 0.8212 (m) REVERT: G 37 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8038 (mp) REVERT: G 42 GLU cc_start: 0.7822 (pp20) cc_final: 0.7349 (mm-30) REVERT: G 50 LEU cc_start: 0.8381 (mt) cc_final: 0.8172 (mp) outliers start: 33 outliers final: 17 residues processed: 174 average time/residue: 1.2613 time to fit residues: 232.5536 Evaluate side-chains 161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 122 ASP Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 43 ILE 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 99 CYS 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 87 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 55 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123539 restraints weight = 8933.970| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.92 r_work: 0.3337 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8470 Z= 0.095 Angle : 0.468 8.842 11495 Z= 0.245 Chirality : 0.041 0.140 1306 Planarity : 0.003 0.027 1450 Dihedral : 4.494 55.397 1282 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.15 % Allowed : 19.93 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1032 helix: 2.27 (0.27), residues: 390 sheet: 0.41 (0.32), residues: 239 loop : -0.35 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.011 0.001 PHE A 74 TYR 0.016 0.001 TYR B 124 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 430) hydrogen bonds : angle 3.96251 ( 1212) SS BOND : bond 0.00215 ( 3) SS BOND : angle 0.71525 ( 6) covalent geometry : bond 0.00202 ( 8467) covalent geometry : angle 0.46745 (11489) *********************** 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 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7279 (mt) REVERT: R 136 LEU cc_start: 0.7737 (tt) cc_final: 0.7530 (tp) REVERT: R 166 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: R 298 HIS cc_start: 0.7301 (t70) cc_final: 0.6451 (m-70) REVERT: A 20 GLU cc_start: 0.7626 (tp30) cc_final: 0.7392 (tp30) REVERT: A 78 LYS cc_start: 0.8769 (mmtp) cc_final: 0.8098 (mptt) REVERT: A 208 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.6836 (mmm-85) REVERT: A 222 GLU cc_start: 0.7690 (pm20) cc_final: 0.7386 (pt0) REVERT: A 242 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7400 (tt0) REVERT: B 57 LYS cc_start: 0.8928 (pttm) cc_final: 0.8581 (ptpt) REVERT: B 134 ARG cc_start: 0.7388 (ptm-80) cc_final: 0.6614 (tpm170) REVERT: B 186 ASP cc_start: 0.8362 (m-30) cc_final: 0.8069 (m-30) REVERT: B 188 MET cc_start: 0.8829 (mmm) cc_final: 0.8490 (mmm) REVERT: B 197 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7687 (mtp85) REVERT: B 212 ASP cc_start: 0.8247 (t0) cc_final: 0.7937 (t0) REVERT: B 214 ARG cc_start: 0.7736 (mmt180) cc_final: 0.7424 (mpp-170) REVERT: B 220 GLN cc_start: 0.8021 (tt0) cc_final: 0.7730 (tt0) REVERT: B 234 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: B 263 THR cc_start: 0.8718 (t) cc_final: 0.8198 (m) REVERT: G 37 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7988 (mp) REVERT: G 42 GLU cc_start: 0.7897 (pp20) cc_final: 0.7384 (mm-30) REVERT: G 50 LEU cc_start: 0.8301 (mt) cc_final: 0.8086 (mp) outliers start: 28 outliers final: 18 residues processed: 163 average time/residue: 1.3671 time to fit residues: 235.6308 Evaluate side-chains 162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE 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 122 ASP Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 43 ILE 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 99 CYS 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 23 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120276 restraints weight = 8884.790| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.92 r_work: 0.3286 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8470 Z= 0.127 Angle : 0.520 13.199 11495 Z= 0.271 Chirality : 0.042 0.164 1306 Planarity : 0.003 0.033 1450 Dihedral : 4.784 58.291 1282 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.60 % Allowed : 19.93 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1032 helix: 2.15 (0.27), residues: 390 sheet: 0.49 (0.32), residues: 221 loop : -0.42 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 209 PHE 0.012 0.002 PHE B 151 TYR 0.012 0.001 TYR R 129 ARG 0.007 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 430) hydrogen bonds : angle 4.15023 ( 1212) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.84179 ( 6) covalent geometry : bond 0.00290 ( 8467) covalent geometry : angle 0.52022 (11489) *********************** 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 171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7313 (mt) REVERT: R 136 LEU cc_start: 0.7752 (tt) cc_final: 0.7546 (tp) REVERT: R 166 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: R 196 TYR cc_start: 0.8735 (t80) cc_final: 0.8498 (t80) REVERT: R 200 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7875 (p) REVERT: R 298 HIS cc_start: 0.7407 (t70) cc_final: 0.6559 (m-70) REVERT: A 20 GLU cc_start: 0.7632 (tp30) cc_final: 0.7381 (tp30) REVERT: A 78 LYS cc_start: 0.8836 (mmtp) cc_final: 0.8163 (mptt) REVERT: A 208 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.6876 (mmm-85) REVERT: A 222 GLU cc_start: 0.7817 (pm20) cc_final: 0.7463 (pt0) REVERT: A 242 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7441 (tt0) REVERT: B 57 LYS cc_start: 0.8961 (pttm) cc_final: 0.8690 (pttt) REVERT: B 59 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8413 (t80) REVERT: B 186 ASP cc_start: 0.8454 (m-30) cc_final: 0.8194 (m-30) REVERT: B 188 MET cc_start: 0.8901 (mmm) cc_final: 0.8585 (mmm) REVERT: B 197 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7673 (mtp85) REVERT: B 212 ASP cc_start: 0.8304 (t0) cc_final: 0.8088 (t70) REVERT: B 214 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7490 (mpp-170) REVERT: B 220 GLN cc_start: 0.8122 (tt0) cc_final: 0.7776 (tt0) REVERT: B 234 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: B 263 THR cc_start: 0.8798 (t) cc_final: 0.8208 (m) REVERT: G 37 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8029 (mp) REVERT: G 42 GLU cc_start: 0.7921 (pp20) cc_final: 0.7418 (mm-30) REVERT: G 50 LEU cc_start: 0.8430 (mt) cc_final: 0.8215 (mp) outliers start: 32 outliers final: 20 residues processed: 159 average time/residue: 1.3370 time to fit residues: 224.7618 Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE 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 247 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 204 SER 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 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 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 168 GLN A 75 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119795 restraints weight = 9021.562| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.94 r_work: 0.3293 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8470 Z= 0.131 Angle : 0.533 14.085 11495 Z= 0.276 Chirality : 0.042 0.181 1306 Planarity : 0.004 0.042 1450 Dihedral : 4.868 57.808 1282 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.83 % Allowed : 19.26 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1032 helix: 2.15 (0.26), residues: 390 sheet: 0.60 (0.33), residues: 214 loop : -0.46 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS A 209 PHE 0.012 0.002 PHE B 151 TYR 0.012 0.001 TYR A 243 ARG 0.009 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 430) hydrogen bonds : angle 4.15882 ( 1212) SS BOND : bond 0.00294 ( 3) SS BOND : angle 0.87104 ( 6) covalent geometry : bond 0.00302 ( 8467) covalent geometry : angle 0.53285 (11489) *********************** 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 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7249 (mt) REVERT: R 136 LEU cc_start: 0.7769 (tt) cc_final: 0.7546 (tp) REVERT: R 166 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: R 200 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7900 (p) REVERT: R 298 HIS cc_start: 0.7424 (t70) cc_final: 0.6489 (m-70) REVERT: A 20 GLU cc_start: 0.7658 (tp30) cc_final: 0.7412 (tp30) REVERT: A 78 LYS cc_start: 0.8853 (mmtp) cc_final: 0.8182 (mptt) REVERT: A 208 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.6839 (mmm-85) REVERT: A 242 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7405 (tt0) REVERT: B 57 LYS cc_start: 0.8944 (pttm) cc_final: 0.8683 (pttt) REVERT: B 59 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8334 (t80) REVERT: B 134 ARG cc_start: 0.7430 (ptm-80) cc_final: 0.6640 (tpm170) REVERT: B 186 ASP cc_start: 0.8497 (m-30) cc_final: 0.8272 (m-30) REVERT: B 188 MET cc_start: 0.8884 (mmm) cc_final: 0.8610 (mmm) REVERT: B 197 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7676 (mtp85) REVERT: B 212 ASP cc_start: 0.8340 (t0) cc_final: 0.8131 (t70) REVERT: B 214 ARG cc_start: 0.7821 (mmt180) cc_final: 0.7534 (mpp-170) REVERT: B 220 GLN cc_start: 0.8107 (tt0) cc_final: 0.7805 (tt0) REVERT: B 234 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: B 263 THR cc_start: 0.8824 (t) cc_final: 0.8217 (m) REVERT: G 37 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8038 (mp) REVERT: G 42 GLU cc_start: 0.7903 (pp20) cc_final: 0.7416 (mm-30) REVERT: G 50 LEU cc_start: 0.8393 (mt) cc_final: 0.8173 (mp) outliers start: 34 outliers final: 25 residues processed: 160 average time/residue: 1.3850 time to fit residues: 235.3646 Evaluate side-chains 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 122 ASP Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 204 SER 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 65 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 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 168 GLN 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 = 0.3811 r_free = 0.3811 target = 0.153375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118515 restraints weight = 9030.445| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.93 r_work: 0.3273 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8470 Z= 0.150 Angle : 0.558 14.534 11495 Z= 0.289 Chirality : 0.043 0.207 1306 Planarity : 0.004 0.033 1450 Dihedral : 4.994 54.247 1282 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.60 % Allowed : 20.05 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1032 helix: 2.05 (0.26), residues: 390 sheet: 0.61 (0.33), residues: 214 loop : -0.52 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 96 HIS 0.008 0.001 HIS A 209 PHE 0.013 0.002 PHE B 151 TYR 0.013 0.002 TYR A 243 ARG 0.008 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 430) hydrogen bonds : angle 4.27389 ( 1212) SS BOND : bond 0.00330 ( 3) SS BOND : angle 0.93184 ( 6) covalent geometry : bond 0.00352 ( 8467) covalent geometry : angle 0.55733 (11489) *********************** 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 166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7243 (mt) REVERT: R 136 LEU cc_start: 0.7772 (tt) cc_final: 0.7537 (tp) REVERT: R 166 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: R 200 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7900 (p) REVERT: R 298 HIS cc_start: 0.7505 (t70) cc_final: 0.6546 (m-70) REVERT: A 20 GLU cc_start: 0.7703 (tp30) cc_final: 0.7473 (tp30) REVERT: A 73 LYS cc_start: 0.9015 (mttp) cc_final: 0.8781 (mttt) REVERT: A 78 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8184 (mptt) REVERT: A 208 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.6845 (mmm-85) REVERT: A 222 GLU cc_start: 0.7897 (pm20) cc_final: 0.7499 (pt0) REVERT: A 242 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7378 (mt-10) REVERT: B 57 LYS cc_start: 0.8952 (pttm) cc_final: 0.8717 (pttt) REVERT: B 59 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8488 (t80) REVERT: B 134 ARG cc_start: 0.7428 (ptm-80) cc_final: 0.6624 (tpp-160) REVERT: B 186 ASP cc_start: 0.8548 (m-30) cc_final: 0.8328 (m-30) REVERT: B 188 MET cc_start: 0.8911 (mmm) cc_final: 0.8648 (mmm) REVERT: B 197 ARG cc_start: 0.8060 (mtm180) cc_final: 0.7692 (mtp85) REVERT: B 214 ARG cc_start: 0.7832 (mmt180) cc_final: 0.7612 (mpp-170) REVERT: B 220 GLN cc_start: 0.8141 (tt0) cc_final: 0.7822 (tt0) REVERT: B 234 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: B 263 THR cc_start: 0.8817 (t) cc_final: 0.8201 (m) REVERT: G 37 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8078 (mp) REVERT: G 42 GLU cc_start: 0.7909 (pp20) cc_final: 0.7427 (mm-30) REVERT: G 50 LEU cc_start: 0.8440 (mt) cc_final: 0.8220 (mp) outliers start: 32 outliers final: 21 residues processed: 154 average time/residue: 1.3339 time to fit residues: 217.3837 Evaluate side-chains 158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE 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 246 CYS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 154 LEU 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 65 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 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 VAL 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 51 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 58 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122380 restraints weight = 8912.824| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.92 r_work: 0.3323 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4664 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= 0.101 Angle : 0.500 14.341 11495 Z= 0.258 Chirality : 0.041 0.143 1306 Planarity : 0.003 0.035 1450 Dihedral : 4.708 54.128 1282 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.27 % Allowed : 20.72 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1032 helix: 2.34 (0.26), residues: 390 sheet: 0.56 (0.33), residues: 219 loop : -0.43 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.011 0.001 PHE B 151 TYR 0.010 0.001 TYR R 129 ARG 0.008 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 430) hydrogen bonds : angle 4.04012 ( 1212) SS BOND : bond 0.00237 ( 3) SS BOND : angle 0.68127 ( 6) covalent geometry : bond 0.00218 ( 8467) covalent geometry : angle 0.50011 (11489) ********************** 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 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7205 (mt) REVERT: R 136 LEU cc_start: 0.7764 (tt) cc_final: 0.7535 (tp) REVERT: R 166 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: R 200 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7889 (p) REVERT: R 298 HIS cc_start: 0.7448 (t70) cc_final: 0.6452 (m-70) REVERT: A 20 GLU cc_start: 0.7596 (tp30) cc_final: 0.7354 (tp30) REVERT: A 78 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8144 (mptt) REVERT: A 208 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.6812 (mmm-85) REVERT: A 222 GLU cc_start: 0.7766 (pm20) cc_final: 0.7418 (pt0) REVERT: A 242 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7186 (mt-10) REVERT: B 35 ASN cc_start: 0.7840 (t0) cc_final: 0.7491 (t0) REVERT: B 57 LYS cc_start: 0.8932 (pttm) cc_final: 0.8577 (ptpt) REVERT: B 59 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8038 (t80) REVERT: B 134 ARG cc_start: 0.7386 (ptm-80) cc_final: 0.6613 (tpm170) REVERT: B 186 ASP cc_start: 0.8409 (m-30) cc_final: 0.8159 (m-30) REVERT: B 188 MET cc_start: 0.8832 (mmm) cc_final: 0.8556 (mmm) REVERT: B 197 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7697 (mtp85) REVERT: B 220 GLN cc_start: 0.8023 (tt0) cc_final: 0.7729 (tt0) REVERT: B 234 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: B 263 THR cc_start: 0.8749 (t) cc_final: 0.8145 (m) REVERT: G 37 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8001 (mp) REVERT: G 42 GLU cc_start: 0.7840 (pp20) cc_final: 0.7403 (mm-30) outliers start: 29 outliers final: 17 residues processed: 156 average time/residue: 1.3514 time to fit residues: 223.1897 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 : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE 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 246 CYS Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 86 VAL 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 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 99 CYS Chi-restraints excluded: chain N residue 110 VAL 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 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 168 GLN A 75 GLN B 32 GLN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120905 restraints weight = 9010.647| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.93 r_work: 0.3308 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4732 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= 0.115 Angle : 0.521 14.900 11495 Z= 0.269 Chirality : 0.041 0.141 1306 Planarity : 0.003 0.037 1450 Dihedral : 4.762 53.452 1282 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.82 % Allowed : 21.40 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1032 helix: 2.32 (0.26), residues: 390 sheet: 0.63 (0.33), residues: 214 loop : -0.42 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR R 129 ARG 0.008 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 430) hydrogen bonds : angle 4.09003 ( 1212) SS BOND : bond 0.00264 ( 3) SS BOND : angle 0.77924 ( 6) covalent geometry : bond 0.00257 ( 8467) covalent geometry : angle 0.52088 (11489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7739.91 seconds wall clock time: 133 minutes 32.44 seconds (8012.44 seconds total)