Starting phenix.real_space_refine on Wed Feb 12 22:05:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wq4_32699/02_2025/7wq4_32699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wq4_32699/02_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_32699/02_2025/7wq4_32699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wq4_32699/02_2025/7wq4_32699.map" model { file = "/net/cci-nas-00/data/ceres_data/7wq4_32699/02_2025/7wq4_32699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wq4_32699/02_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-5592/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: 5.07, per 1000 atoms: 0.61 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: 2.32 Conformation dependent library (CDL) restraints added in 962.3 milliseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 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: 2.55 Time building geometry restraints manager: 2.79 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: 0.010 Normalize map: mean=0, sd=1: 1.000 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.330 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.620 ------------------------------------------------------------------------------- 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 8467 Z= 0.442 Angle : 0.615 13.533 11489 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 *********************** 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 : 0.912 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: 1.2883 time to fit residues: 347.5493 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 = 0.131740 restraints weight = 8850.530| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.84 r_work: 0.3427 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- 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 8467 Z= 0.196 Angle : 0.520 7.319 11489 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 *********************** 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 : 0.888 Fit side-chains revert: symmetry clash REVERT: R 88 LEU cc_start: 0.6825 (mt) cc_final: 0.6431 (mt) REVERT: R 96 LEU cc_start: 0.6325 (pt) cc_final: 0.5713 (tp) REVERT: R 166 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: A 8 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 15 ARG cc_start: 0.7272 (ttt90) cc_final: 0.7057 (ttm-80) REVERT: A 73 LYS cc_start: 0.8898 (mttp) cc_final: 0.8660 (mttt) REVERT: A 78 LYS cc_start: 0.8735 (mmtp) cc_final: 0.8040 (mmtt) REVERT: A 208 ARG cc_start: 0.7292 (mtm-85) cc_final: 0.6613 (tpt90) REVERT: A 222 GLU cc_start: 0.7559 (pm20) cc_final: 0.7088 (pt0) REVERT: B 57 LYS cc_start: 0.8997 (pttm) cc_final: 0.8756 (pttt) REVERT: B 135 VAL cc_start: 0.8357 (t) cc_final: 0.8149 (t) REVERT: B 186 ASP cc_start: 0.8452 (m-30) cc_final: 0.8113 (m-30) REVERT: B 188 MET cc_start: 0.8880 (mmm) cc_final: 0.8504 (mmm) REVERT: B 197 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7463 (mtp85) REVERT: B 212 ASP cc_start: 0.7864 (t0) cc_final: 0.7636 (t70) REVERT: B 214 ARG cc_start: 0.7541 (mmt180) cc_final: 0.7220 (mmt180) REVERT: B 234 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: B 263 THR cc_start: 0.8387 (t) cc_final: 0.7944 (m) outliers start: 29 outliers final: 11 residues processed: 188 average time/residue: 1.3155 time to fit residues: 261.9022 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 : 0.897 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.154787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121353 restraints weight = 8995.129| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.81 r_work: 0.3279 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8467 Z= 0.283 Angle : 0.588 6.902 11489 Z= 0.312 Chirality : 0.044 0.168 1306 Planarity : 0.004 0.031 1450 Dihedral : 5.212 57.291 1282 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.62 % Allowed : 15.09 % Favored : 80.29 % 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: 0.35 (0.26), residues: 1032 helix: 1.34 (0.27), residues: 396 sheet: 0.19 (0.33), residues: 222 loop : -0.78 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.012 0.002 HIS A 209 PHE 0.016 0.002 PHE B 151 TYR 0.012 0.002 TYR R 86 ARG 0.005 0.001 ARG R 137 *********************** 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 188 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7199 (mt) REVERT: R 136 LEU cc_start: 0.7792 (tt) cc_final: 0.7505 (tp) REVERT: R 166 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: R 298 HIS cc_start: 0.7032 (t70) cc_final: 0.6606 (m-70) REVERT: A 15 ARG cc_start: 0.7343 (ttt90) cc_final: 0.6962 (ttm-80) REVERT: A 51 LYS cc_start: 0.7477 (pptt) cc_final: 0.7213 (mmmt) REVERT: A 73 LYS cc_start: 0.9012 (mttp) cc_final: 0.8628 (mttt) REVERT: A 78 LYS cc_start: 0.8921 (mmtp) cc_final: 0.8203 (mptt) REVERT: A 208 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.6838 (mmm-85) REVERT: A 222 GLU cc_start: 0.7803 (pm20) cc_final: 0.7462 (pt0) REVERT: A 238 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8229 (mtt) REVERT: B 57 LYS cc_start: 0.8990 (pttm) cc_final: 0.8702 (pttt) REVERT: B 186 ASP cc_start: 0.8586 (m-30) cc_final: 0.8293 (m-30) REVERT: B 188 MET cc_start: 0.8845 (mmm) cc_final: 0.8494 (mmm) REVERT: B 197 ARG cc_start: 0.8070 (mtm180) cc_final: 0.7550 (mtp85) REVERT: B 214 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7493 (mpp-170) REVERT: B 220 GLN cc_start: 0.8136 (tt0) cc_final: 0.7811 (tt0) REVERT: B 263 THR cc_start: 0.8786 (t) cc_final: 0.8256 (m) REVERT: G 37 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8075 (mp) REVERT: G 42 GLU cc_start: 0.7861 (pp20) cc_final: 0.7272 (mm-30) outliers start: 41 outliers final: 14 residues processed: 174 average time/residue: 1.3720 time to fit residues: 251.9463 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 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: 2.9990 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 100 optimal weight: 0.0170 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120029 restraints weight = 8979.051| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.92 r_work: 0.3294 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8467 Z= 0.195 Angle : 0.518 5.873 11489 Z= 0.274 Chirality : 0.042 0.140 1306 Planarity : 0.003 0.029 1450 Dihedral : 4.700 56.565 1280 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.83 % Allowed : 18.81 % 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: 0.71 (0.26), residues: 1032 helix: 1.75 (0.27), residues: 391 sheet: 0.33 (0.32), residues: 230 loop : -0.66 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 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 0.006 0.000 ARG B 134 *********************** 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 173 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.901 Fit side-chains REVERT: R 35 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7316 (mt) REVERT: R 136 LEU cc_start: 0.7883 (tt) cc_final: 0.7605 (tp) REVERT: R 166 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: R 298 HIS cc_start: 0.7086 (t70) cc_final: 0.6557 (m-70) REVERT: A 8 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6413 (mm-30) REVERT: A 15 ARG cc_start: 0.7451 (ttt90) cc_final: 0.7115 (ttm-80) REVERT: A 51 LYS cc_start: 0.7533 (pptt) cc_final: 0.7302 (mmmt) REVERT: A 78 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8167 (mptt) REVERT: A 208 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.6829 (mmm-85) REVERT: A 238 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8167 (mtt) REVERT: A 242 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7243 (tt0) REVERT: B 57 LYS cc_start: 0.8942 (pttm) cc_final: 0.8672 (pttt) REVERT: B 59 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8411 (t80) REVERT: B 134 ARG cc_start: 0.7351 (ptm-80) cc_final: 0.6533 (tpp-160) REVERT: B 186 ASP cc_start: 0.8526 (m-30) cc_final: 0.8274 (m-30) REVERT: B 188 MET cc_start: 0.8884 (mmm) cc_final: 0.8515 (mmm) REVERT: B 197 ARG cc_start: 0.8182 (mtm180) cc_final: 0.7633 (mtp85) REVERT: B 214 ARG cc_start: 0.7873 (mmt180) cc_final: 0.7516 (mpp-170) REVERT: B 220 GLN cc_start: 0.8073 (tt0) cc_final: 0.7668 (tt0) REVERT: B 234 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: B 258 ASP cc_start: 0.7167 (t0) cc_final: 0.6866 (t70) REVERT: B 263 THR cc_start: 0.8773 (t) cc_final: 0.8232 (m) REVERT: G 37 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8081 (mp) REVERT: G 42 GLU cc_start: 0.7848 (pp20) cc_final: 0.7336 (mm-30) outliers start: 34 outliers final: 18 residues processed: 163 average time/residue: 1.3822 time to fit residues: 238.0077 Evaluate side-chains 155 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 32 GLN B 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121552 restraints weight = 8830.645| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.91 r_work: 0.3311 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8467 Z= 0.160 Angle : 0.486 7.765 11489 Z= 0.257 Chirality : 0.041 0.143 1306 Planarity : 0.003 0.027 1450 Dihedral : 4.509 57.188 1280 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.60 % Allowed : 19.37 % Favored : 77.03 % 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: 0.95 (0.26), residues: 1032 helix: 2.00 (0.27), residues: 391 sheet: 0.45 (0.32), residues: 231 loop : -0.58 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS A 209 PHE 0.011 0.001 PHE B 151 TYR 0.012 0.001 TYR R 129 ARG 0.005 0.000 ARG B 134 *********************** 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 178 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7297 (mt) REVERT: R 136 LEU cc_start: 0.7797 (tt) cc_final: 0.7560 (tp) REVERT: R 166 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: R 298 HIS cc_start: 0.7342 (t70) cc_final: 0.6492 (m-70) REVERT: A 8 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6376 (mm-30) REVERT: A 15 ARG cc_start: 0.7437 (ttt90) cc_final: 0.7093 (ttm-80) REVERT: A 20 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7143 (tp30) REVERT: A 51 LYS cc_start: 0.7496 (pptt) cc_final: 0.7279 (mmmt) REVERT: A 73 LYS cc_start: 0.9026 (mttp) cc_final: 0.8764 (mttt) REVERT: A 78 LYS cc_start: 0.8822 (mmtp) cc_final: 0.8143 (mptt) REVERT: A 92 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: A 208 ARG cc_start: 0.7533 (mtm-85) cc_final: 0.6805 (mmm-85) REVERT: A 222 GLU cc_start: 0.7751 (pm20) cc_final: 0.7429 (pt0) REVERT: A 242 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7315 (tt0) REVERT: B 57 LYS cc_start: 0.8922 (pttm) cc_final: 0.8693 (pttt) REVERT: B 186 ASP cc_start: 0.8410 (m-30) cc_final: 0.8110 (m-30) REVERT: B 188 MET cc_start: 0.8853 (mmm) cc_final: 0.8477 (mmm) REVERT: B 197 ARG cc_start: 0.8240 (mtm180) cc_final: 0.7674 (mtp85) REVERT: B 214 ARG cc_start: 0.7866 (mmt180) cc_final: 0.7587 (mpp-170) REVERT: B 234 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8184 (m-80) REVERT: B 263 THR cc_start: 0.8770 (t) cc_final: 0.8208 (m) REVERT: G 37 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8016 (mp) REVERT: G 42 GLU cc_start: 0.7778 (pp20) cc_final: 0.7320 (mm-30) outliers start: 32 outliers final: 15 residues processed: 167 average time/residue: 1.3641 time to fit residues: 240.9015 Evaluate side-chains 161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 166 GLN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 92 GLU 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 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 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: 0.9980 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 0.0030 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN A 75 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121708 restraints weight = 8952.799| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.92 r_work: 0.3315 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8467 Z= 0.150 Angle : 0.482 8.831 11489 Z= 0.255 Chirality : 0.041 0.143 1306 Planarity : 0.003 0.030 1450 Dihedral : 4.439 58.356 1280 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.83 % Allowed : 19.14 % Favored : 77.03 % 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: 1.11 (0.26), residues: 1032 helix: 2.17 (0.27), residues: 390 sheet: 0.45 (0.32), residues: 230 loop : -0.47 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.011 0.001 PHE A 74 TYR 0.013 0.001 TYR R 129 ARG 0.007 0.000 ARG B 134 *********************** 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 179 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7233 (mt) REVERT: R 136 LEU cc_start: 0.7747 (tt) cc_final: 0.7518 (tp) REVERT: R 166 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: R 200 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7857 (p) REVERT: R 298 HIS cc_start: 0.7348 (t70) cc_final: 0.6476 (m-70) REVERT: A 8 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6358 (mm-30) REVERT: A 20 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7232 (tp30) REVERT: A 73 LYS cc_start: 0.9042 (mttp) cc_final: 0.8635 (mttt) REVERT: A 78 LYS cc_start: 0.8808 (mmtp) cc_final: 0.8141 (mptt) REVERT: A 82 HIS cc_start: 0.8364 (m170) cc_final: 0.8068 (m170) REVERT: A 92 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: A 208 ARG cc_start: 0.7546 (mtm-85) cc_final: 0.6824 (mmm-85) REVERT: A 222 GLU cc_start: 0.7724 (pm20) cc_final: 0.7397 (pt0) REVERT: A 242 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7386 (tt0) REVERT: B 57 LYS cc_start: 0.8941 (pttm) cc_final: 0.8568 (ptpt) REVERT: B 134 ARG cc_start: 0.7363 (ptm-80) cc_final: 0.6573 (tpm170) REVERT: B 186 ASP cc_start: 0.8421 (m-30) cc_final: 0.8152 (m-30) REVERT: B 188 MET cc_start: 0.8864 (mmm) cc_final: 0.8528 (mmm) REVERT: B 197 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7670 (mtp85) REVERT: B 214 ARG cc_start: 0.7805 (mmt180) cc_final: 0.7489 (mpp-170) REVERT: B 220 GLN cc_start: 0.8029 (tt0) cc_final: 0.7732 (tt0) REVERT: B 234 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: B 263 THR cc_start: 0.8775 (t) cc_final: 0.8191 (m) REVERT: G 37 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8017 (mp) REVERT: G 42 GLU cc_start: 0.7896 (pp20) cc_final: 0.7393 (mm-30) outliers start: 34 outliers final: 19 residues processed: 167 average time/residue: 1.3874 time to fit residues: 244.5965 Evaluate side-chains 162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 166 GLN Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 92 GLU 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 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 28 THR Chi-restraints excluded: chain N residue 63 SER 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=2.50 ------------------------------------------------------------------------------- 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: 6.9990 chunk 44 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 34 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN A 75 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121383 restraints weight = 8880.529| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.92 r_work: 0.3312 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8467 Z= 0.158 Angle : 0.495 13.288 11489 Z= 0.258 Chirality : 0.041 0.171 1306 Planarity : 0.003 0.032 1450 Dihedral : 4.450 59.919 1280 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.94 % Allowed : 19.48 % Favored : 76.58 % 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: 2.22 (0.27), residues: 390 sheet: 0.44 (0.32), residues: 223 loop : -0.45 (0.29), residues: 419 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 B 151 TYR 0.010 0.001 TYR R 213 ARG 0.007 0.000 ARG A 15 *********************** 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 176 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7350 (mt) REVERT: R 136 LEU cc_start: 0.7753 (tt) cc_final: 0.7531 (tp) REVERT: R 166 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7109 (tt0) REVERT: R 200 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7853 (p) REVERT: R 298 HIS cc_start: 0.7376 (t70) cc_final: 0.6483 (m-70) REVERT: A 78 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8134 (mptt) REVERT: A 92 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: A 208 ARG cc_start: 0.7581 (mtm-85) cc_final: 0.6833 (mmm-85) REVERT: A 242 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7336 (tt0) REVERT: B 35 ASN cc_start: 0.7799 (t0) cc_final: 0.7421 (t0) REVERT: B 57 LYS cc_start: 0.8940 (pttm) cc_final: 0.8564 (ptpt) REVERT: B 134 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.6586 (tpm170) REVERT: B 186 ASP cc_start: 0.8443 (m-30) cc_final: 0.8190 (m-30) REVERT: B 188 MET cc_start: 0.8862 (mmm) cc_final: 0.8541 (mmm) REVERT: B 197 ARG cc_start: 0.8028 (mtm180) cc_final: 0.7619 (mtp85) REVERT: B 214 ARG cc_start: 0.7766 (mmt180) cc_final: 0.7529 (mpp-170) REVERT: B 220 GLN cc_start: 0.8049 (tt0) cc_final: 0.7777 (tt0) REVERT: B 234 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: B 263 THR cc_start: 0.8787 (t) cc_final: 0.8201 (m) REVERT: G 37 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8025 (mp) REVERT: G 42 GLU cc_start: 0.7878 (pp20) cc_final: 0.7390 (mm-30) outliers start: 35 outliers final: 21 residues processed: 166 average time/residue: 1.3714 time to fit residues: 240.5513 Evaluate side-chains 163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 297 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 92 GLU 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 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 28 THR Chi-restraints excluded: chain N residue 63 SER 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: 2.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.157239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122486 restraints weight = 8984.052| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.94 r_work: 0.3327 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8467 Z= 0.142 Angle : 0.489 13.959 11489 Z= 0.254 Chirality : 0.041 0.192 1306 Planarity : 0.003 0.040 1450 Dihedral : 4.366 58.483 1280 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.38 % Allowed : 20.05 % Favored : 76.58 % 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: 1.20 (0.26), residues: 1032 helix: 2.30 (0.26), residues: 390 sheet: 0.42 (0.33), residues: 223 loop : -0.40 (0.30), residues: 419 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 A 74 TYR 0.010 0.001 TYR A 243 ARG 0.010 0.000 ARG A 15 *********************** 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 171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7285 (mt) REVERT: R 136 LEU cc_start: 0.7732 (tt) cc_final: 0.7503 (tp) REVERT: R 166 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: R 200 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7873 (p) REVERT: R 298 HIS cc_start: 0.7344 (t70) cc_final: 0.6380 (m-70) REVERT: A 20 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7249 (tp30) REVERT: A 73 LYS cc_start: 0.9012 (mttp) cc_final: 0.8734 (mttt) REVERT: A 78 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8124 (mptt) REVERT: A 208 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.6833 (mmm-85) REVERT: A 222 GLU cc_start: 0.7689 (pm20) cc_final: 0.7416 (pt0) REVERT: A 242 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7279 (tt0) REVERT: B 35 ASN cc_start: 0.7746 (t0) cc_final: 0.7364 (t0) REVERT: B 57 LYS cc_start: 0.8929 (pttm) cc_final: 0.8559 (ptpt) REVERT: B 134 ARG cc_start: 0.7397 (ptm-80) cc_final: 0.6626 (tpm170) REVERT: B 186 ASP cc_start: 0.8398 (m-30) cc_final: 0.8107 (m-30) REVERT: B 188 MET cc_start: 0.8853 (mmm) cc_final: 0.8522 (mmm) REVERT: B 197 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7638 (mtp85) REVERT: B 214 ARG cc_start: 0.7791 (mmt180) cc_final: 0.7570 (mpp-170) REVERT: B 220 GLN cc_start: 0.8053 (tt0) cc_final: 0.7774 (tt0) REVERT: B 234 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: B 263 THR cc_start: 0.8756 (t) cc_final: 0.8216 (m) REVERT: G 37 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7998 (mp) REVERT: G 42 GLU cc_start: 0.7875 (pp20) cc_final: 0.7392 (mm-30) outliers start: 30 outliers final: 18 residues processed: 161 average time/residue: 1.3821 time to fit residues: 234.7039 Evaluate side-chains 155 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 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 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 46 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN A 75 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120598 restraints weight = 9004.172| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.93 r_work: 0.3301 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8467 Z= 0.177 Angle : 0.525 14.484 11489 Z= 0.270 Chirality : 0.042 0.202 1306 Planarity : 0.003 0.036 1450 Dihedral : 4.487 55.283 1280 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.15 % Allowed : 20.50 % 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: 1.19 (0.26), residues: 1032 helix: 2.25 (0.26), residues: 390 sheet: 0.50 (0.32), residues: 221 loop : -0.43 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.012 0.001 PHE B 151 TYR 0.016 0.001 TYR B 124 ARG 0.009 0.000 ARG A 15 *********************** 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 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7345 (mt) REVERT: R 136 LEU cc_start: 0.7740 (tt) cc_final: 0.7504 (tp) REVERT: R 166 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: R 200 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7861 (p) REVERT: R 298 HIS cc_start: 0.7366 (t70) cc_final: 0.6387 (m-70) REVERT: A 20 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7312 (tp30) REVERT: A 73 LYS cc_start: 0.9030 (mttp) cc_final: 0.8759 (mttt) REVERT: A 78 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8143 (mptt) REVERT: A 208 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.6854 (mmm-85) REVERT: A 222 GLU cc_start: 0.7733 (pm20) cc_final: 0.7441 (pt0) REVERT: A 242 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7237 (mt-10) REVERT: B 35 ASN cc_start: 0.7737 (t0) cc_final: 0.7340 (t0) REVERT: B 57 LYS cc_start: 0.8965 (pttm) cc_final: 0.8691 (pttt) REVERT: B 59 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8339 (t80) REVERT: B 134 ARG cc_start: 0.7417 (ptm-80) cc_final: 0.6626 (tpm170) REVERT: B 186 ASP cc_start: 0.8468 (m-30) cc_final: 0.8228 (m-30) REVERT: B 188 MET cc_start: 0.8882 (mmm) cc_final: 0.8566 (mmm) REVERT: B 197 ARG cc_start: 0.8031 (mtm180) cc_final: 0.7682 (mtp85) REVERT: B 214 ARG cc_start: 0.7811 (mmt180) cc_final: 0.7588 (mpp-170) REVERT: B 220 GLN cc_start: 0.8077 (tt0) cc_final: 0.7778 (tt0) REVERT: B 234 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: B 263 THR cc_start: 0.8766 (t) cc_final: 0.8144 (m) REVERT: G 37 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8050 (mp) REVERT: G 42 GLU cc_start: 0.7894 (pp20) cc_final: 0.7407 (mm-30) outliers start: 28 outliers final: 19 residues processed: 155 average time/residue: 1.4329 time to fit residues: 234.4692 Evaluate side-chains 152 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 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 113 THR 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: 0.7980 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN A 75 GLN B 32 GLN B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119182 restraints weight = 8906.959| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.86 r_work: 0.3271 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8467 Z= 0.221 Angle : 0.557 14.964 11489 Z= 0.288 Chirality : 0.043 0.200 1306 Planarity : 0.004 0.037 1450 Dihedral : 4.693 50.768 1280 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.27 % Allowed : 20.61 % Favored : 76.13 % 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: 2.13 (0.26), residues: 390 sheet: 0.57 (0.33), residues: 214 loop : -0.50 (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 0.014 0.002 TYR A 243 ARG 0.008 0.000 ARG A 15 ********************** 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 164 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7224 (mt) REVERT: R 136 LEU cc_start: 0.7755 (tt) cc_final: 0.7502 (tp) REVERT: R 166 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: R 200 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7792 (p) REVERT: R 298 HIS cc_start: 0.7467 (t70) cc_final: 0.6541 (m-70) REVERT: A 73 LYS cc_start: 0.9078 (mttp) cc_final: 0.8819 (mttt) REVERT: A 78 LYS cc_start: 0.8868 (mmtp) cc_final: 0.8189 (mptt) REVERT: A 208 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.6896 (mmm-85) REVERT: A 222 GLU cc_start: 0.7868 (pm20) cc_final: 0.7498 (pt0) REVERT: B 35 ASN cc_start: 0.7765 (t0) cc_final: 0.7375 (t0) REVERT: B 57 LYS cc_start: 0.8956 (pttm) cc_final: 0.8682 (pttt) REVERT: B 59 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8347 (t80) REVERT: B 134 ARG cc_start: 0.7435 (ptm-80) cc_final: 0.6605 (tpp-160) REVERT: B 154 ASP cc_start: 0.8251 (m-30) cc_final: 0.8012 (m-30) REVERT: B 188 MET cc_start: 0.8823 (mmm) cc_final: 0.8476 (mmm) REVERT: B 197 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7694 (mtp85) REVERT: B 214 ARG cc_start: 0.7843 (mmt180) cc_final: 0.7605 (mpp-170) REVERT: B 220 GLN cc_start: 0.8146 (tt0) cc_final: 0.7845 (tt0) REVERT: B 234 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: B 263 THR cc_start: 0.8825 (t) cc_final: 0.8223 (m) REVERT: G 37 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8069 (mp) REVERT: G 42 GLU cc_start: 0.7886 (pp20) cc_final: 0.7410 (mm-30) outliers start: 29 outliers final: 19 residues processed: 154 average time/residue: 1.3803 time to fit residues: 224.7708 Evaluate side-chains 151 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN A 75 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120859 restraints weight = 9000.475| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.86 r_work: 0.3296 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8467 Z= 0.173 Angle : 0.523 14.667 11489 Z= 0.270 Chirality : 0.041 0.142 1306 Planarity : 0.003 0.036 1450 Dihedral : 4.544 48.391 1280 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.82 % Allowed : 21.06 % Favored : 76.13 % 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: 1.18 (0.26), residues: 1032 helix: 2.28 (0.26), residues: 390 sheet: 0.58 (0.33), residues: 214 loop : -0.50 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR N 95 ARG 0.008 0.000 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7337.36 seconds wall clock time: 130 minutes 1.77 seconds (7801.77 seconds total)