Starting phenix.real_space_refine on Wed Feb 4 06:37:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kt7_62558/02_2026/9kt7_62558.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kt7_62558/02_2026/9kt7_62558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kt7_62558/02_2026/9kt7_62558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kt7_62558/02_2026/9kt7_62558.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kt7_62558/02_2026/9kt7_62558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kt7_62558/02_2026/9kt7_62558.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 5798 2.51 5 N 1551 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9094 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2393 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain: "A" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1830 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.25 Number of scatterers: 9094 At special positions: 0 Unit cell: (92.759, 117.438, 135.309, 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 70 16.00 O 1675 8.00 N 1551 7.00 C 5798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.04 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 323.4 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 36.6% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'R' and resid 24 through 54 Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.902A pdb=" N LEU R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 131 removed outlier: 3.672A pdb=" N ARG R 101 " --> pdb=" O ASP R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 138 Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 165 removed outlier: 3.793A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS R 165 " --> pdb=" O LEU R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 165' Processing helix chain 'R' and resid 187 through 218 removed outlier: 4.437A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 225 through 261 removed outlier: 3.798A pdb=" N ALA R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 266 through 280 Processing helix chain 'R' and resid 282 through 295 removed outlier: 4.061A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.625A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.683A pdb=" N ASP A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 348 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.992A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.239A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.748A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 12 through 13 removed outlier: 3.534A pdb=" N GLU R 12 " --> pdb=" O CYS R 18 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS R 18 " --> pdb=" O GLU R 12 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE R 182 " --> pdb=" O CYS R 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 169 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.969A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.579A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.849A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.926A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.730A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.752A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.666A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.847A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.897A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.897A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.802A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.580A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2521 1.33 - 1.46: 2032 1.46 - 1.58: 4636 1.58 - 1.70: 1 1.70 - 1.83: 103 Bond restraints: 9293 Sorted by residual: bond pdb=" C02 FI7 R 401 " pdb=" C17 FI7 R 401 " ideal model delta sigma weight residual 1.545 1.716 -0.171 2.00e-02 2.50e+03 7.35e+01 bond pdb=" C07 FI7 R 401 " pdb=" C08 FI7 R 401 " ideal model delta sigma weight residual 1.466 1.563 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C20 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.396 1.489 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C07 FI7 R 401 " pdb=" N06 FI7 R 401 " ideal model delta sigma weight residual 1.364 1.452 -0.088 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C04 FI7 R 401 " pdb=" C05 FI7 R 401 " ideal model delta sigma weight residual 1.483 1.569 -0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 9288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 12436 2.61 - 5.22: 121 5.22 - 7.83: 13 7.83 - 10.44: 3 10.44 - 13.05: 1 Bond angle restraints: 12574 Sorted by residual: angle pdb=" C02 FI7 R 401 " pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 113.44 126.49 -13.05 3.00e+00 1.11e-01 1.89e+01 angle pdb=" C ASP R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta sigma weight residual 120.24 122.96 -2.72 6.30e-01 2.52e+00 1.86e+01 angle pdb=" C VAL R 29 " pdb=" N LEU R 30 " pdb=" CA LEU R 30 " ideal model delta sigma weight residual 120.09 124.95 -4.86 1.25e+00 6.40e-01 1.51e+01 angle pdb=" C ILE R 98 " pdb=" CA ILE R 98 " pdb=" CB ILE R 98 " ideal model delta sigma weight residual 114.35 110.82 3.53 1.06e+00 8.90e-01 1.11e+01 angle pdb=" C02 FI7 R 401 " pdb=" C17 FI7 R 401 " pdb=" O18 FI7 R 401 " ideal model delta sigma weight residual 121.40 111.96 9.44 3.00e+00 1.11e-01 9.90e+00 ... (remaining 12569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 5031 17.68 - 35.36: 405 35.36 - 53.04: 69 53.04 - 70.72: 12 70.72 - 88.40: 8 Dihedral angle restraints: 5525 sinusoidal: 2193 harmonic: 3332 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual 93.00 167.41 -74.41 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual -86.00 -149.95 63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CA VAL R 88 " pdb=" C VAL R 88 " pdb=" N ARG R 89 " pdb=" CA ARG R 89 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 5522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1068 0.048 - 0.095: 261 0.095 - 0.143: 77 0.143 - 0.191: 0 0.191 - 0.238: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA ASP R 290 " pdb=" N ASP R 290 " pdb=" C ASP R 290 " pdb=" CB ASP R 290 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR C 52 " pdb=" CA THR C 52 " pdb=" OG1 THR C 52 " pdb=" CG2 THR C 52 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1405 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO E 75 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO R 32 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO C 53 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.019 5.00e-02 4.00e+02 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 85 2.66 - 3.22: 8122 3.22 - 3.78: 13447 3.78 - 4.34: 18944 4.34 - 4.90: 32040 Nonbonded interactions: 72638 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" OE1 GLU A 298 " model vdw 2.094 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR R 284 " pdb=" O23 FI7 R 401 " model vdw 2.302 3.040 nonbonded pdb=" OE2 GLU R 190 " pdb=" NH2 ARG R 251 " model vdw 2.311 3.120 nonbonded pdb=" NH2 ARG R 218 " pdb=" OD1 ASP A 341 " model vdw 2.312 3.120 ... (remaining 72633 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.050 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.005 0.171 9297 Z= 0.230 Angle : 0.694 13.052 12582 Z= 0.380 Chirality : 0.045 0.238 1408 Planarity : 0.004 0.064 1588 Dihedral : 13.321 88.401 3359 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1136 helix: 1.41 (0.27), residues: 374 sheet: 0.43 (0.31), residues: 272 loop : -0.78 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.012 0.002 TYR E 190 PHE 0.016 0.002 PHE B 199 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9293) covalent geometry : angle 0.69184 (12574) SS BOND : bond 0.00746 ( 4) SS BOND : angle 2.33919 ( 8) hydrogen bonds : bond 0.16324 ( 435) hydrogen bonds : angle 6.02676 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.373 Fit side-chains REVERT: R 106 MET cc_start: 0.6299 (mmm) cc_final: 0.5827 (mmm) REVERT: R 154 ILE cc_start: 0.5165 (mt) cc_final: 0.4946 (mt) REVERT: R 167 MET cc_start: 0.4212 (mmp) cc_final: 0.3674 (ptp) REVERT: R 192 MET cc_start: 0.5948 (mmp) cc_final: 0.5449 (mmt) REVERT: A 24 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6649 (ttp80) REVERT: B 258 ASP cc_start: 0.7128 (t70) cc_final: 0.6837 (t0) REVERT: E 3 GLN cc_start: 0.7758 (tt0) cc_final: 0.7378 (tt0) REVERT: E 73 ASP cc_start: 0.8034 (t0) cc_final: 0.7527 (t70) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.7829 time to fit residues: 113.4453 Evaluate side-chains 105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN R 137 ASN A 52 GLN A 256 ASN A 331 ASN C 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.163406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102007 restraints weight = 9849.573| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.04 r_work: 0.2792 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9297 Z= 0.185 Angle : 0.644 8.600 12582 Z= 0.345 Chirality : 0.047 0.241 1408 Planarity : 0.004 0.046 1588 Dihedral : 5.422 36.396 1268 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 1.61 % Allowed : 8.95 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1136 helix: 1.31 (0.27), residues: 387 sheet: 0.61 (0.30), residues: 270 loop : -0.96 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 89 TYR 0.015 0.002 TYR E 190 PHE 0.016 0.002 PHE A 189 TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9293) covalent geometry : angle 0.64254 (12574) SS BOND : bond 0.00825 ( 4) SS BOND : angle 1.63332 ( 8) hydrogen bonds : bond 0.05606 ( 435) hydrogen bonds : angle 4.66253 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.368 Fit side-chains REVERT: R 77 ILE cc_start: 0.5277 (OUTLIER) cc_final: 0.5023 (tt) REVERT: R 106 MET cc_start: 0.6344 (mmm) cc_final: 0.5952 (mmm) REVERT: R 138 LYS cc_start: 0.7259 (mtmt) cc_final: 0.6883 (mtpt) REVERT: R 167 MET cc_start: 0.4390 (mmp) cc_final: 0.4048 (tpp) REVERT: A 53 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6354 (mpp) REVERT: B 46 ARG cc_start: 0.8322 (mtm180) cc_final: 0.7789 (mtp85) REVERT: B 258 ASP cc_start: 0.7574 (t70) cc_final: 0.7126 (t0) REVERT: B 262 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7980 (ptm) REVERT: E 3 GLN cc_start: 0.8256 (tt0) cc_final: 0.7932 (tt0) REVERT: E 73 ASP cc_start: 0.8246 (t0) cc_final: 0.7794 (t70) REVERT: E 89 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7641 (pp20) outliers start: 16 outliers final: 6 residues processed: 111 average time/residue: 0.7872 time to fit residues: 92.0464 Evaluate side-chains 113 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN R 286 ASN A 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.165285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104141 restraints weight = 9849.347| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.17 r_work: 0.2877 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9297 Z= 0.127 Angle : 0.553 8.239 12582 Z= 0.298 Chirality : 0.043 0.241 1408 Planarity : 0.004 0.039 1588 Dihedral : 5.056 35.965 1268 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.73 % Favored : 97.18 % Rotamer: Outliers : 2.11 % Allowed : 11.67 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1136 helix: 1.60 (0.27), residues: 384 sheet: 0.68 (0.30), residues: 271 loop : -0.84 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 89 TYR 0.014 0.001 TYR E 190 PHE 0.014 0.001 PHE A 189 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9293) covalent geometry : angle 0.55264 (12574) SS BOND : bond 0.00577 ( 4) SS BOND : angle 1.08784 ( 8) hydrogen bonds : bond 0.04664 ( 435) hydrogen bonds : angle 4.30676 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.369 Fit side-chains REVERT: R 77 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4976 (tt) REVERT: R 106 MET cc_start: 0.6212 (mmm) cc_final: 0.5784 (mmm) REVERT: R 138 LYS cc_start: 0.7171 (mtmt) cc_final: 0.6862 (mttt) REVERT: R 167 MET cc_start: 0.4400 (mmp) cc_final: 0.3216 (tpp) REVERT: R 192 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.5296 (mmt) REVERT: A 53 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6438 (mpp) REVERT: A 188 HIS cc_start: 0.8012 (t70) cc_final: 0.7802 (t-90) REVERT: B 46 ARG cc_start: 0.8340 (mtm180) cc_final: 0.7771 (mtp85) REVERT: B 170 ASP cc_start: 0.8436 (t70) cc_final: 0.8221 (t0) REVERT: B 258 ASP cc_start: 0.7592 (t70) cc_final: 0.7072 (t0) REVERT: B 262 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7980 (ptm) REVERT: E 3 GLN cc_start: 0.8298 (tt0) cc_final: 0.7946 (tt0) REVERT: E 73 ASP cc_start: 0.8268 (t0) cc_final: 0.7819 (t70) outliers start: 21 outliers final: 8 residues processed: 120 average time/residue: 0.7726 time to fit residues: 97.5263 Evaluate side-chains 115 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN R 161 HIS 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 = 0.163651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101618 restraints weight = 9950.284| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.23 r_work: 0.2863 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9297 Z= 0.158 Angle : 0.586 8.258 12582 Z= 0.316 Chirality : 0.045 0.239 1408 Planarity : 0.004 0.042 1588 Dihedral : 5.169 31.180 1268 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 2.41 % Allowed : 13.88 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1136 helix: 1.57 (0.27), residues: 384 sheet: 0.64 (0.30), residues: 277 loop : -0.87 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 89 TYR 0.014 0.002 TYR E 190 PHE 0.014 0.002 PHE A 189 TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9293) covalent geometry : angle 0.58581 (12574) SS BOND : bond 0.00678 ( 4) SS BOND : angle 1.24639 ( 8) hydrogen bonds : bond 0.05000 ( 435) hydrogen bonds : angle 4.35342 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.358 Fit side-chains REVERT: R 77 ILE cc_start: 0.5231 (OUTLIER) cc_final: 0.4970 (tt) REVERT: R 106 MET cc_start: 0.6238 (mmm) cc_final: 0.5816 (mmm) REVERT: R 138 LYS cc_start: 0.7168 (mtmt) cc_final: 0.6878 (mttt) REVERT: R 167 MET cc_start: 0.4272 (mmp) cc_final: 0.4023 (tpp) REVERT: R 192 MET cc_start: 0.5692 (OUTLIER) cc_final: 0.5459 (mmt) REVERT: A 53 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6327 (mpp) REVERT: A 243 MET cc_start: 0.8087 (tpp) cc_final: 0.7833 (ttm) REVERT: B 46 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7730 (mtp85) REVERT: B 258 ASP cc_start: 0.7668 (t70) cc_final: 0.7123 (t0) REVERT: B 262 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: C 28 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6060 (mp) REVERT: E 69 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8694 (m) REVERT: E 73 ASP cc_start: 0.8277 (t0) cc_final: 0.7823 (t70) outliers start: 24 outliers final: 10 residues processed: 120 average time/residue: 0.7861 time to fit residues: 99.1555 Evaluate side-chains 125 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN A 188 HIS A 333 GLN B 1 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.164829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102396 restraints weight = 9906.128| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.21 r_work: 0.2888 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9297 Z= 0.140 Angle : 0.560 8.228 12582 Z= 0.302 Chirality : 0.044 0.236 1408 Planarity : 0.004 0.040 1588 Dihedral : 5.060 31.837 1268 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 2.72 % Allowed : 14.29 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1136 helix: 1.67 (0.27), residues: 384 sheet: 0.67 (0.29), residues: 277 loop : -0.89 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 89 TYR 0.014 0.001 TYR E 190 PHE 0.014 0.001 PHE A 189 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9293) covalent geometry : angle 0.55942 (12574) SS BOND : bond 0.00618 ( 4) SS BOND : angle 1.17197 ( 8) hydrogen bonds : bond 0.04711 ( 435) hydrogen bonds : angle 4.24676 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.367 Fit side-chains REVERT: R 77 ILE cc_start: 0.5245 (OUTLIER) cc_final: 0.5005 (tt) REVERT: R 106 MET cc_start: 0.6157 (mmm) cc_final: 0.5748 (mmm) REVERT: R 138 LYS cc_start: 0.7188 (mtmt) cc_final: 0.6875 (mttt) REVERT: R 167 MET cc_start: 0.4216 (mmp) cc_final: 0.3079 (tpp) REVERT: R 192 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.5353 (mmt) REVERT: R 288 MET cc_start: 0.5603 (ptm) cc_final: 0.5369 (ppp) REVERT: A 53 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6372 (mpp) REVERT: B 46 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7699 (mtp85) REVERT: B 258 ASP cc_start: 0.7638 (t70) cc_final: 0.7055 (t0) REVERT: B 262 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8002 (ptm) REVERT: C 28 ILE cc_start: 0.6221 (OUTLIER) cc_final: 0.5975 (mp) REVERT: E 69 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8628 (m) REVERT: E 73 ASP cc_start: 0.8280 (t0) cc_final: 0.7798 (t70) outliers start: 27 outliers final: 12 residues processed: 121 average time/residue: 0.7589 time to fit residues: 96.6635 Evaluate side-chains 121 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN R 286 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.101493 restraints weight = 9865.237| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.17 r_work: 0.2824 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9297 Z= 0.216 Angle : 0.669 9.447 12582 Z= 0.358 Chirality : 0.047 0.233 1408 Planarity : 0.004 0.043 1588 Dihedral : 5.519 27.656 1268 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 2.62 % Allowed : 15.29 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1136 helix: 1.44 (0.27), residues: 383 sheet: 0.63 (0.29), residues: 277 loop : -1.01 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 202 TYR 0.014 0.002 TYR E 190 PHE 0.017 0.002 PHE A 189 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 9293) covalent geometry : angle 0.66285 (12574) SS BOND : bond 0.01112 ( 4) SS BOND : angle 3.58117 ( 8) hydrogen bonds : bond 0.05554 ( 435) hydrogen bonds : angle 4.51605 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.379 Fit side-chains REVERT: R 77 ILE cc_start: 0.5266 (OUTLIER) cc_final: 0.4993 (tt) REVERT: R 106 MET cc_start: 0.6316 (mmm) cc_final: 0.5930 (mmm) REVERT: R 138 LYS cc_start: 0.7312 (mtmt) cc_final: 0.7017 (mttt) REVERT: R 167 MET cc_start: 0.4163 (mmp) cc_final: 0.3341 (tpp) REVERT: R 192 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5423 (mmt) REVERT: A 53 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6426 (mpp) REVERT: B 46 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7753 (mtp85) REVERT: B 258 ASP cc_start: 0.7629 (t70) cc_final: 0.7058 (t0) REVERT: B 262 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8133 (ptm) REVERT: C 28 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.6175 (mp) REVERT: E 69 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8677 (m) REVERT: E 73 ASP cc_start: 0.8283 (t0) cc_final: 0.7833 (t70) outliers start: 26 outliers final: 13 residues processed: 117 average time/residue: 0.7670 time to fit residues: 94.6926 Evaluate side-chains 124 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104487 restraints weight = 9898.100| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.23 r_work: 0.2855 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9297 Z= 0.180 Angle : 0.626 8.269 12582 Z= 0.336 Chirality : 0.046 0.231 1408 Planarity : 0.004 0.042 1588 Dihedral : 5.421 28.750 1268 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.39 % Rotamer: Outliers : 2.72 % Allowed : 16.00 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1136 helix: 1.39 (0.27), residues: 388 sheet: 0.63 (0.29), residues: 277 loop : -1.10 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 202 TYR 0.014 0.002 TYR E 190 PHE 0.016 0.002 PHE A 189 TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9293) covalent geometry : angle 0.62155 (12574) SS BOND : bond 0.00940 ( 4) SS BOND : angle 2.94369 ( 8) hydrogen bonds : bond 0.05213 ( 435) hydrogen bonds : angle 4.44538 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.366 Fit side-chains REVERT: R 77 ILE cc_start: 0.5371 (OUTLIER) cc_final: 0.5099 (tt) REVERT: R 106 MET cc_start: 0.6317 (mmm) cc_final: 0.5926 (mmm) REVERT: R 138 LYS cc_start: 0.7293 (mtmt) cc_final: 0.7028 (mttt) REVERT: R 167 MET cc_start: 0.4106 (mmp) cc_final: 0.3350 (mmp) REVERT: R 192 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5433 (mmt) REVERT: A 53 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6419 (mpp) REVERT: B 46 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7732 (mtp85) REVERT: B 258 ASP cc_start: 0.7657 (t70) cc_final: 0.7088 (t0) REVERT: B 262 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8114 (ptm) REVERT: C 28 ILE cc_start: 0.6529 (OUTLIER) cc_final: 0.6259 (mp) REVERT: E 69 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8657 (m) REVERT: E 73 ASP cc_start: 0.8282 (t0) cc_final: 0.7823 (t70) outliers start: 27 outliers final: 13 residues processed: 118 average time/residue: 0.7624 time to fit residues: 94.8250 Evaluate side-chains 124 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.165651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.104611 restraints weight = 9839.046| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.15 r_work: 0.2921 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9297 Z= 0.116 Angle : 0.533 8.198 12582 Z= 0.287 Chirality : 0.043 0.230 1408 Planarity : 0.004 0.039 1588 Dihedral : 4.959 33.089 1268 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.27 % Rotamer: Outliers : 2.62 % Allowed : 16.40 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1136 helix: 1.76 (0.27), residues: 385 sheet: 0.67 (0.30), residues: 280 loop : -0.90 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 208 TYR 0.013 0.001 TYR E 190 PHE 0.014 0.001 PHE B 199 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9293) covalent geometry : angle 0.52944 (12574) SS BOND : bond 0.00727 ( 4) SS BOND : angle 2.41746 ( 8) hydrogen bonds : bond 0.04168 ( 435) hydrogen bonds : angle 4.13293 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.395 Fit side-chains REVERT: R 106 MET cc_start: 0.6274 (mmm) cc_final: 0.5936 (mmm) REVERT: R 138 LYS cc_start: 0.7178 (mtmt) cc_final: 0.6862 (mttt) REVERT: R 167 MET cc_start: 0.3758 (mmp) cc_final: 0.2927 (mmt) REVERT: R 192 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.5330 (mmt) REVERT: R 288 MET cc_start: 0.5609 (ptm) cc_final: 0.5325 (ppp) REVERT: A 53 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6460 (mpp) REVERT: B 46 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7703 (mtp85) REVERT: B 170 ASP cc_start: 0.8408 (t70) cc_final: 0.8139 (t0) REVERT: B 258 ASP cc_start: 0.7588 (t70) cc_final: 0.7080 (t0) REVERT: B 262 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8021 (ptm) REVERT: C 28 ILE cc_start: 0.6212 (OUTLIER) cc_final: 0.5984 (mp) REVERT: E 73 ASP cc_start: 0.8262 (t0) cc_final: 0.7795 (t70) outliers start: 26 outliers final: 12 residues processed: 125 average time/residue: 0.6968 time to fit residues: 91.9431 Evaluate side-chains 122 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN A 52 GLN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.164328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103527 restraints weight = 9799.544| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.02 r_work: 0.2879 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9297 Z= 0.169 Angle : 0.600 8.265 12582 Z= 0.323 Chirality : 0.045 0.230 1408 Planarity : 0.004 0.041 1588 Dihedral : 5.249 28.664 1268 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.31 % Allowed : 16.90 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1136 helix: 1.58 (0.27), residues: 389 sheet: 0.67 (0.29), residues: 277 loop : -1.04 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 251 TYR 0.013 0.002 TYR E 190 PHE 0.015 0.002 PHE A 189 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9293) covalent geometry : angle 0.59735 (12574) SS BOND : bond 0.00821 ( 4) SS BOND : angle 2.47473 ( 8) hydrogen bonds : bond 0.04994 ( 435) hydrogen bonds : angle 4.35980 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.359 Fit side-chains REVERT: R 106 MET cc_start: 0.6270 (mmm) cc_final: 0.5887 (mmm) REVERT: R 138 LYS cc_start: 0.7311 (mtmt) cc_final: 0.6994 (mttt) REVERT: R 167 MET cc_start: 0.3899 (mmp) cc_final: 0.3185 (mmp) REVERT: R 192 MET cc_start: 0.5839 (OUTLIER) cc_final: 0.5469 (mmt) REVERT: R 288 MET cc_start: 0.5656 (ptm) cc_final: 0.5368 (ppp) REVERT: A 35 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8307 (mtpt) REVERT: A 53 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6433 (mpp) REVERT: B 46 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7747 (mtp85) REVERT: B 258 ASP cc_start: 0.7635 (t70) cc_final: 0.7076 (t0) REVERT: B 262 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8085 (ptm) REVERT: C 28 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6195 (mp) REVERT: E 73 ASP cc_start: 0.8293 (t0) cc_final: 0.7822 (t70) outliers start: 23 outliers final: 13 residues processed: 119 average time/residue: 0.7442 time to fit residues: 93.4527 Evaluate side-chains 126 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 81 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN A 188 HIS E 3 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 = 0.162981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.099683 restraints weight = 9835.420| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.25 r_work: 0.2748 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9297 Z= 0.219 Angle : 0.671 8.324 12582 Z= 0.360 Chirality : 0.048 0.229 1408 Planarity : 0.004 0.042 1588 Dihedral : 5.555 25.805 1268 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 2.21 % Allowed : 17.00 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1136 helix: 1.33 (0.27), residues: 388 sheet: 0.61 (0.29), residues: 277 loop : -1.11 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 202 TYR 0.015 0.002 TYR E 190 PHE 0.016 0.002 PHE E 27 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9293) covalent geometry : angle 0.66800 (12574) SS BOND : bond 0.00960 ( 4) SS BOND : angle 2.65074 ( 8) hydrogen bonds : bond 0.05599 ( 435) hydrogen bonds : angle 4.54730 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.325 Fit side-chains REVERT: R 77 ILE cc_start: 0.5344 (OUTLIER) cc_final: 0.5006 (tt) REVERT: R 106 MET cc_start: 0.6262 (mmm) cc_final: 0.5898 (mmm) REVERT: R 138 LYS cc_start: 0.7303 (mtmt) cc_final: 0.7043 (mttt) REVERT: R 167 MET cc_start: 0.4014 (mmp) cc_final: 0.3467 (ptt) REVERT: R 192 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.5384 (mmt) REVERT: A 35 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8332 (mtpt) REVERT: A 53 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6397 (mpp) REVERT: B 46 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7737 (mtp85) REVERT: B 258 ASP cc_start: 0.7669 (t70) cc_final: 0.7068 (t0) REVERT: B 262 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8173 (ptm) REVERT: C 28 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6237 (mp) REVERT: E 73 ASP cc_start: 0.8243 (t0) cc_final: 0.7799 (t70) outliers start: 22 outliers final: 14 residues processed: 120 average time/residue: 0.6928 time to fit residues: 87.8652 Evaluate side-chains 127 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 45 optimal weight: 0.0060 chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN A 188 HIS A 333 GLN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.165733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102482 restraints weight = 9723.510| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.33 r_work: 0.2869 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9297 Z= 0.112 Angle : 0.528 8.197 12582 Z= 0.286 Chirality : 0.043 0.229 1408 Planarity : 0.003 0.039 1588 Dihedral : 4.966 33.386 1268 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.81 % Allowed : 17.81 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1136 helix: 1.68 (0.27), residues: 389 sheet: 0.73 (0.30), residues: 277 loop : -0.97 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 222 TYR 0.014 0.001 TYR E 190 PHE 0.014 0.001 PHE B 199 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9293) covalent geometry : angle 0.52599 (12574) SS BOND : bond 0.00656 ( 4) SS BOND : angle 2.02530 ( 8) hydrogen bonds : bond 0.04071 ( 435) hydrogen bonds : angle 4.12780 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4114.68 seconds wall clock time: 70 minutes 48.47 seconds (4248.47 seconds total)