Starting phenix.real_space_refine on Sun Jun 15 11:43:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8l_38148/06_2025/8x8l_38148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8l_38148/06_2025/8x8l_38148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x8l_38148/06_2025/8x8l_38148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8l_38148/06_2025/8x8l_38148.map" model { file = "/net/cci-nas-00/data/ceres_data/8x8l_38148/06_2025/8x8l_38148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8l_38148/06_2025/8x8l_38148.cif" } resolution = 2.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 59 5.16 5 C 5641 2.51 5 N 1531 2.21 5 O 1620 1.98 5 H 8704 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17555 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "B" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 4996 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 200 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "E" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3385 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 834 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 4286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4286 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Time building chain proxies: 8.51, per 1000 atoms: 0.48 Number of scatterers: 17555 At special positions: 0 Unit cell: (123.6, 93.936, 129.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 O 1620 8.00 N 1531 7.00 C 5641 6.00 H 8704 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 186 " 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: 4.57 Conformation dependent library (CDL) restraints added in 1.6 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 39.2% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.518A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.715A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.625A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.506A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 removed outlier: 4.092A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.627A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.608A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.792A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.540A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.571A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'R' and resid 43 through 67 Processing helix chain 'R' and resid 73 through 91 Processing helix chain 'R' and resid 92 through 102 removed outlier: 3.578A pdb=" N ALA R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 143 removed outlier: 4.346A pdb=" N LEU R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU R 114 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET R 116 " --> pdb=" O CYS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 178 Proline residue: R 173 - end of helix Processing helix chain 'R' and resid 180 through 184 removed outlier: 4.438A pdb=" N GLY R 183 " --> pdb=" O VAL R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 210 through 235 Processing helix chain 'R' and resid 241 through 274 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 282 through 304 removed outlier: 4.188A pdb=" N TYR R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE R 287 " --> pdb=" O ALA R 283 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 316 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.662A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 57 removed outlier: 6.037A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.644A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.618A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.871A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.643A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 206 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 214 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.542A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.054A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.566A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.952A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.573A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.519A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.519A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1278 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: 6.94 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8678 1.02 - 1.22: 46 1.22 - 1.42: 3825 1.42 - 1.62: 5112 1.62 - 1.82: 84 Bond restraints: 17745 Sorted by residual: bond pdb=" SG CYS R 260 " pdb=" HG CYS R 260 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" ND2 ASN R 310 " pdb="HD22 ASN R 310 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" ND2 ASN R 310 " pdb="HD21 ASN R 310 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" NE ARG R 312 " pdb=" HE ARG R 312 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG A 309 " pdb=" HE ARG A 309 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 17740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.78: 31897 7.78 - 15.56: 4 15.56 - 23.33: 0 23.33 - 31.11: 1 31.11 - 38.89: 2 Bond angle restraints: 31904 Sorted by residual: angle pdb=" C PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 109.00 70.11 38.89 3.00e+00 1.11e-01 1.68e+02 angle pdb=" N PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 110.00 74.57 35.43 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 109.00 78.81 30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" N VAL R 207 " pdb=" CA VAL R 207 " pdb=" C VAL R 207 " ideal model delta sigma weight residual 110.30 117.07 -6.77 9.70e-01 1.06e+00 4.87e+01 angle pdb=" N SER A 228 " pdb=" CA SER A 228 " pdb=" C SER A 228 " ideal model delta sigma weight residual 111.82 119.15 -7.33 1.16e+00 7.43e-01 3.99e+01 ... (remaining 31899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7798 17.74 - 35.49: 395 35.49 - 53.23: 168 53.23 - 70.97: 47 70.97 - 88.72: 9 Dihedral angle restraints: 8417 sinusoidal: 4475 harmonic: 3942 Sorted by residual: dihedral pdb=" CB CYS R 112 " pdb=" SG CYS R 112 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -137.94 51.94 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" C PHE R 211 " pdb=" N PHE R 211 " pdb=" CA PHE R 211 " pdb=" CB PHE R 211 " ideal model delta harmonic sigma weight residual -122.60 -134.21 11.61 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" N PRO G 54 " pdb=" C PRO G 54 " pdb=" CA PRO G 54 " pdb=" CB PRO G 54 " ideal model delta harmonic sigma weight residual 115.10 124.31 -9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 8414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1299 0.095 - 0.190: 87 0.190 - 0.286: 7 0.286 - 0.381: 1 0.381 - 0.476: 3 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA PRO G 54 " pdb=" N PRO G 54 " pdb=" C PRO G 54 " pdb=" CB PRO G 54 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA PHE R 211 " pdb=" N PHE R 211 " pdb=" C PHE R 211 " pdb=" CB PHE R 211 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA CYS R 260 " pdb=" N CYS R 260 " pdb=" C CYS R 260 " pdb=" CB CYS R 260 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 1394 not shown) Planarity restraints: 2649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 313 " -0.112 2.00e-02 2.50e+03 1.24e-01 2.31e+02 pdb=" CD GLN R 313 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN R 313 " 0.110 2.00e-02 2.50e+03 pdb=" NE2 GLN R 313 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN R 313 " 0.184 2.00e-02 2.50e+03 pdb="HE22 GLN R 313 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 310 " -0.053 2.00e-02 2.50e+03 5.25e-02 4.14e+01 pdb=" CG ASN R 310 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN R 310 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN R 310 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN R 310 " 0.074 2.00e-02 2.50e+03 pdb="HD22 ASN R 310 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 316 " -0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" N LYS R 317 " 0.056 2.00e-02 2.50e+03 pdb=" CA LYS R 317 " -0.014 2.00e-02 2.50e+03 pdb=" H LYS R 317 " -0.024 2.00e-02 2.50e+03 ... (remaining 2646 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 945 2.19 - 2.79: 35777 2.79 - 3.40: 48855 3.40 - 4.00: 63338 4.00 - 4.60: 97911 Nonbonded interactions: 246826 Sorted by model distance: nonbonded pdb=" O LYS G 19 " pdb="HD21 ASN G 23 " model vdw 1.590 2.450 nonbonded pdb="HH22 ARG A 208 " pdb=" OD1 ASP A 239 " model vdw 1.626 2.450 nonbonded pdb=" OE2 GLU A 8 " pdb=" HH TYR E 175 " model vdw 1.637 2.450 nonbonded pdb=" O ILE E 138 " pdb=" HG1 THR E 238 " model vdw 1.638 2.450 nonbonded pdb="HH12 ARG E 202 " pdb=" OD2 ASP E 223 " model vdw 1.640 2.450 ... (remaining 246821 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: 1.240 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: 0.300 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.004 0.068 9045 Z= 0.312 Angle : 0.603 9.479 12277 Z= 0.377 Chirality : 0.050 0.476 1397 Planarity : 0.003 0.034 1557 Dihedral : 9.651 75.047 3215 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.89 % Allowed : 3.68 % Favored : 94.43 % Cbeta Deviations : 0.09 % 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: 2.09 (0.26), residues: 1122 helix: 2.97 (0.27), residues: 385 sheet: 1.24 (0.32), residues: 268 loop : 0.15 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 261 HIS 0.002 0.001 HIS A 329 PHE 0.015 0.001 PHE R 315 TYR 0.009 0.001 TYR R 89 ARG 0.004 0.000 ARG R 67 Details of bonding type rmsd hydrogen bonds : bond 0.20308 ( 449) hydrogen bonds : angle 6.67040 ( 1278) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.84928 ( 8) covalent geometry : bond 0.00436 ( 9041) covalent geometry : angle 0.60270 (12269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 353 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 PHE cc_start: 0.5863 (t80) cc_final: 0.5513 (t80) REVERT: R 288 PHE cc_start: 0.7375 (t80) cc_final: 0.7130 (t80) REVERT: R 315 PHE cc_start: 0.7383 (t80) cc_final: 0.7085 (t80) outliers start: 18 outliers final: 5 residues processed: 363 average time/residue: 2.4160 time to fit residues: 938.1781 Evaluate side-chains 181 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 300 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.0000 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 204 GLN A 213 GLN A 234 GLN B 49 GLN B 225 GLN B 264 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.145655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117824 restraints weight = 38586.159| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.15 r_work: 0.3461 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9045 Z= 0.130 Angle : 0.543 8.626 12277 Z= 0.286 Chirality : 0.043 0.474 1397 Planarity : 0.005 0.062 1557 Dihedral : 5.039 74.997 1249 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.41 % Allowed : 18.91 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.26), residues: 1122 helix: 3.15 (0.26), residues: 385 sheet: 0.90 (0.31), residues: 255 loop : 0.31 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 302 HIS 0.004 0.001 HIS B 59 PHE 0.012 0.001 PHE E 203 TYR 0.015 0.001 TYR R 63 ARG 0.006 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 449) hydrogen bonds : angle 5.00197 ( 1278) SS BOND : bond 0.00906 ( 4) SS BOND : angle 3.04818 ( 8) covalent geometry : bond 0.00283 ( 9041) covalent geometry : angle 0.53784 (12269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.7351 (m-40) cc_final: 0.7110 (m-40) REVERT: B 50 MET cc_start: 0.8297 (mtm) cc_final: 0.8013 (mtm) REVERT: B 242 ASN cc_start: 0.7913 (p0) cc_final: 0.7283 (t160) REVERT: E 18 ARG cc_start: 0.7711 (tpp80) cc_final: 0.7434 (tpt-90) REVERT: E 87 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6877 (mtt90) REVERT: R 104 PHE cc_start: 0.6184 (t80) cc_final: 0.5629 (t80) REVERT: R 288 PHE cc_start: 0.7596 (t80) cc_final: 0.7151 (t80) REVERT: R 315 PHE cc_start: 0.7366 (t80) cc_final: 0.7102 (t80) outliers start: 42 outliers final: 15 residues processed: 211 average time/residue: 2.2358 time to fit residues: 508.4882 Evaluate side-chains 177 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 99 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 180 GLN B 181 GLN B 264 GLN E 77 ASN G 17 GLN R 100 ASN R 296 ASN R 313 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107702 restraints weight = 38615.692| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.13 r_work: 0.3316 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9045 Z= 0.190 Angle : 0.570 7.285 12277 Z= 0.309 Chirality : 0.044 0.432 1397 Planarity : 0.005 0.044 1557 Dihedral : 4.676 52.495 1245 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.10 % Allowed : 18.59 % Favored : 77.31 % 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: 1.62 (0.26), residues: 1122 helix: 2.81 (0.25), residues: 386 sheet: 0.56 (0.31), residues: 250 loop : -0.03 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 36 HIS 0.005 0.002 HIS B 230 PHE 0.019 0.002 PHE R 124 TYR 0.016 0.002 TYR R 294 ARG 0.005 0.001 ARG R 149 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 449) hydrogen bonds : angle 4.88567 ( 1278) SS BOND : bond 0.01711 ( 4) SS BOND : angle 1.47407 ( 8) covalent geometry : bond 0.00428 ( 9041) covalent geometry : angle 0.56921 (12269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7316 (t0) cc_final: 0.7045 (t0) REVERT: A 231 ASN cc_start: 0.7882 (m-40) cc_final: 0.7634 (m110) REVERT: B 38 ILE cc_start: 0.8155 (tp) cc_final: 0.7840 (mm) REVERT: B 48 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7884 (mp) REVERT: B 139 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7540 (ppt-90) REVERT: B 261 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6631 (mtp85) REVERT: B 298 ASN cc_start: 0.8172 (p0) cc_final: 0.7968 (p0) REVERT: B 345 ASN cc_start: 0.7389 (t160) cc_final: 0.7156 (t0) REVERT: E 18 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7280 (tpt-90) REVERT: E 87 ARG cc_start: 0.7187 (mtm-85) cc_final: 0.6819 (mtt90) REVERT: R 315 PHE cc_start: 0.7495 (t80) cc_final: 0.7165 (t80) outliers start: 39 outliers final: 20 residues processed: 192 average time/residue: 2.1718 time to fit residues: 450.6355 Evaluate side-chains 172 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 345 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105898 restraints weight = 38953.710| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.12 r_work: 0.3280 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9045 Z= 0.190 Angle : 0.563 8.274 12277 Z= 0.301 Chirality : 0.044 0.428 1397 Planarity : 0.004 0.043 1557 Dihedral : 4.703 51.427 1243 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.31 % Allowed : 18.38 % Favored : 77.31 % 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: 1.37 (0.25), residues: 1122 helix: 2.71 (0.25), residues: 387 sheet: 0.34 (0.32), residues: 255 loop : -0.25 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.006 0.002 HIS A 324 PHE 0.013 0.002 PHE B 297 TYR 0.014 0.002 TYR R 294 ARG 0.003 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 449) hydrogen bonds : angle 4.82391 ( 1278) SS BOND : bond 0.01473 ( 4) SS BOND : angle 1.11558 ( 8) covalent geometry : bond 0.00431 ( 9041) covalent geometry : angle 0.56290 (12269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7336 (t0) cc_final: 0.7072 (t0) REVERT: A 284 ARG cc_start: 0.7303 (ptp90) cc_final: 0.7060 (ptt-90) REVERT: B 38 ILE cc_start: 0.8187 (tp) cc_final: 0.7911 (mm) REVERT: B 48 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7959 (mp) REVERT: B 50 MET cc_start: 0.8369 (mtm) cc_final: 0.8017 (mtm) REVERT: B 139 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7589 (ppt-90) REVERT: B 261 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6612 (mtp85) REVERT: B 263 ASP cc_start: 0.7613 (t0) cc_final: 0.7360 (t0) REVERT: B 298 ASN cc_start: 0.8227 (p0) cc_final: 0.8023 (p0) REVERT: C 7 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7198 (m-40) REVERT: E 18 ARG cc_start: 0.7471 (tpp80) cc_final: 0.7096 (tpt-90) REVERT: E 43 LYS cc_start: 0.8523 (mppt) cc_final: 0.8282 (mmtp) REVERT: G 37 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8057 (ttp) REVERT: R 315 PHE cc_start: 0.7553 (t80) cc_final: 0.7189 (t80) outliers start: 41 outliers final: 18 residues processed: 182 average time/residue: 2.3605 time to fit residues: 464.2961 Evaluate side-chains 163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105377 restraints weight = 39302.352| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.15 r_work: 0.3276 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9045 Z= 0.162 Angle : 0.547 8.149 12277 Z= 0.291 Chirality : 0.043 0.430 1397 Planarity : 0.004 0.047 1557 Dihedral : 4.556 50.342 1242 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.68 % Allowed : 19.12 % Favored : 77.21 % 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: 1.29 (0.25), residues: 1122 helix: 2.70 (0.25), residues: 387 sheet: 0.24 (0.32), residues: 255 loop : -0.31 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.004 0.001 HIS B 230 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR R 294 ARG 0.005 0.000 ARG R 113 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 449) hydrogen bonds : angle 4.75166 ( 1278) SS BOND : bond 0.01273 ( 4) SS BOND : angle 1.06984 ( 8) covalent geometry : bond 0.00363 ( 9041) covalent geometry : angle 0.54628 (12269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: A 229 ASP cc_start: 0.7286 (t0) cc_final: 0.7046 (t0) REVERT: A 284 ARG cc_start: 0.7288 (ptp90) cc_final: 0.7059 (ptt-90) REVERT: B 38 ILE cc_start: 0.8214 (tp) cc_final: 0.7935 (mm) REVERT: B 48 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8021 (mp) REVERT: B 50 MET cc_start: 0.8443 (mtm) cc_final: 0.8098 (mtm) REVERT: B 139 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7680 (ppt-90) REVERT: B 239 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: B 261 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6655 (mtp85) REVERT: B 263 ASP cc_start: 0.7669 (t0) cc_final: 0.7386 (t0) REVERT: B 298 ASN cc_start: 0.8244 (p0) cc_final: 0.8043 (p0) REVERT: E 18 ARG cc_start: 0.7475 (tpp80) cc_final: 0.7071 (tpt-90) REVERT: E 43 LYS cc_start: 0.8497 (mppt) cc_final: 0.8231 (mmtp) REVERT: G 37 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7972 (ttp) REVERT: R 58 ASN cc_start: 0.8469 (m-40) cc_final: 0.8052 (m110) REVERT: R 315 PHE cc_start: 0.7666 (t80) cc_final: 0.7317 (t80) REVERT: R 317 LYS cc_start: 0.5059 (mttt) cc_final: 0.4595 (mtmm) outliers start: 35 outliers final: 20 residues processed: 176 average time/residue: 2.2960 time to fit residues: 436.4960 Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 18 GLN B 49 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.103664 restraints weight = 39380.445| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.09 r_work: 0.3246 rms_B_bonded: 2.39 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: 0.8412 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9045 Z= 0.228 Angle : 0.596 9.451 12277 Z= 0.321 Chirality : 0.044 0.418 1397 Planarity : 0.005 0.050 1557 Dihedral : 4.829 49.345 1242 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.15 % Allowed : 18.28 % 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: 0.87 (0.25), residues: 1122 helix: 2.27 (0.25), residues: 393 sheet: -0.02 (0.31), residues: 269 loop : -0.50 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 211 HIS 0.006 0.002 HIS B 230 PHE 0.015 0.002 PHE B 156 TYR 0.017 0.002 TYR R 204 ARG 0.004 0.001 ARG R 113 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 449) hydrogen bonds : angle 4.90475 ( 1278) SS BOND : bond 0.01920 ( 4) SS BOND : angle 0.94946 ( 8) covalent geometry : bond 0.00517 ( 9041) covalent geometry : angle 0.59533 (12269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: B 38 ILE cc_start: 0.8219 (tp) cc_final: 0.7882 (mm) REVERT: B 48 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 139 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7665 (ppt-90) REVERT: B 219 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7523 (mtt180) REVERT: B 261 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6650 (mtp85) REVERT: B 263 ASP cc_start: 0.7748 (t0) cc_final: 0.7449 (t0) REVERT: E 18 ARG cc_start: 0.7486 (tpp80) cc_final: 0.7082 (tpt-90) REVERT: E 43 LYS cc_start: 0.8562 (mppt) cc_final: 0.8262 (mmtp) REVERT: R 125 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8508 (t) REVERT: R 249 MET cc_start: 0.8052 (tpp) cc_final: 0.7778 (tpp) REVERT: R 315 PHE cc_start: 0.7573 (t80) cc_final: 0.7206 (t80) REVERT: R 317 LYS cc_start: 0.4852 (mttt) cc_final: 0.4573 (mtmm) outliers start: 49 outliers final: 29 residues processed: 179 average time/residue: 2.2054 time to fit residues: 426.1540 Evaluate side-chains 161 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 49 GLN R 100 ASN R 143 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103973 restraints weight = 38870.557| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.14 r_work: 0.3258 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9045 Z= 0.174 Angle : 0.563 8.605 12277 Z= 0.301 Chirality : 0.043 0.423 1397 Planarity : 0.005 0.049 1557 Dihedral : 4.798 48.536 1242 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.20 % Allowed : 19.54 % Favored : 76.26 % 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: 1.02 (0.25), residues: 1122 helix: 2.50 (0.25), residues: 387 sheet: 0.13 (0.32), residues: 257 loop : -0.52 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.006 0.001 HIS B 230 PHE 0.011 0.001 PHE R 287 TYR 0.012 0.001 TYR R 286 ARG 0.002 0.000 ARG R 113 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 449) hydrogen bonds : angle 4.80683 ( 1278) SS BOND : bond 0.01477 ( 4) SS BOND : angle 1.31057 ( 8) covalent geometry : bond 0.00390 ( 9041) covalent geometry : angle 0.56188 (12269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: B 38 ILE cc_start: 0.8239 (tp) cc_final: 0.7898 (mm) REVERT: B 48 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 49 GLN cc_start: 0.8125 (tt0) cc_final: 0.7898 (tt0) REVERT: B 50 MET cc_start: 0.8479 (mtm) cc_final: 0.8060 (mtm) REVERT: B 139 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7688 (ppt-90) REVERT: B 219 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7335 (mtt180) REVERT: B 261 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6629 (mtp85) REVERT: B 263 ASP cc_start: 0.7831 (t0) cc_final: 0.7548 (t0) REVERT: E 18 ARG cc_start: 0.7495 (tpp80) cc_final: 0.7067 (tpt-90) REVERT: E 43 LYS cc_start: 0.8536 (mppt) cc_final: 0.8216 (mmtp) REVERT: R 125 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8526 (t) REVERT: R 315 PHE cc_start: 0.7670 (t80) cc_final: 0.7314 (t80) REVERT: R 317 LYS cc_start: 0.4980 (mttt) cc_final: 0.4485 (mtmm) outliers start: 40 outliers final: 25 residues processed: 168 average time/residue: 2.2898 time to fit residues: 414.1700 Evaluate side-chains 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 100 ASN R 313 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.135073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105740 restraints weight = 38655.902| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.12 r_work: 0.3286 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9045 Z= 0.112 Angle : 0.524 7.197 12277 Z= 0.275 Chirality : 0.042 0.432 1397 Planarity : 0.004 0.048 1557 Dihedral : 4.548 47.099 1242 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.47 % Allowed : 20.38 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.26), residues: 1122 helix: 2.79 (0.26), residues: 387 sheet: 0.18 (0.32), residues: 259 loop : -0.39 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 211 HIS 0.004 0.001 HIS B 230 PHE 0.012 0.001 PHE R 287 TYR 0.012 0.001 TYR R 89 ARG 0.004 0.000 ARG E 87 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 449) hydrogen bonds : angle 4.61592 ( 1278) SS BOND : bond 0.01068 ( 4) SS BOND : angle 1.25049 ( 8) covalent geometry : bond 0.00246 ( 9041) covalent geometry : angle 0.52340 (12269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8221 (tp) cc_final: 0.7894 (mm) REVERT: B 48 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8046 (mp) REVERT: B 50 MET cc_start: 0.8459 (mtm) cc_final: 0.8036 (mtm) REVERT: B 239 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: B 261 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6647 (mtp85) REVERT: B 263 ASP cc_start: 0.7791 (t0) cc_final: 0.7557 (t0) REVERT: E 18 ARG cc_start: 0.7504 (tpp80) cc_final: 0.7078 (tpt-90) REVERT: E 43 LYS cc_start: 0.8481 (mppt) cc_final: 0.8166 (mmtp) REVERT: R 125 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8541 (t) REVERT: R 249 MET cc_start: 0.8048 (tpp) cc_final: 0.7812 (tpp) REVERT: R 315 PHE cc_start: 0.7655 (t80) cc_final: 0.7301 (t80) REVERT: R 317 LYS cc_start: 0.4951 (mttt) cc_final: 0.4453 (mtmm) outliers start: 33 outliers final: 19 residues processed: 163 average time/residue: 2.5904 time to fit residues: 456.5363 Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 274 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 108 optimal weight: 0.0970 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 49 GLN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105634 restraints weight = 39133.017| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.15 r_work: 0.3286 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9045 Z= 0.120 Angle : 0.526 7.325 12277 Z= 0.276 Chirality : 0.042 0.434 1397 Planarity : 0.004 0.063 1557 Dihedral : 4.483 45.670 1242 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.73 % Allowed : 20.80 % Favored : 76.47 % 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: 1.32 (0.26), residues: 1122 helix: 2.79 (0.25), residues: 387 sheet: 0.32 (0.32), residues: 260 loop : -0.40 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.005 0.001 HIS B 230 PHE 0.014 0.001 PHE R 287 TYR 0.009 0.001 TYR R 89 ARG 0.010 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 449) hydrogen bonds : angle 4.53925 ( 1278) SS BOND : bond 0.01068 ( 4) SS BOND : angle 1.09869 ( 8) covalent geometry : bond 0.00268 ( 9041) covalent geometry : angle 0.52546 (12269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7335 (t0) cc_final: 0.7027 (t0) REVERT: A 348 ASP cc_start: 0.8651 (t70) cc_final: 0.8411 (t0) REVERT: B 38 ILE cc_start: 0.8267 (tp) cc_final: 0.7942 (mm) REVERT: B 48 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 49 GLN cc_start: 0.8105 (tt0) cc_final: 0.7867 (tt0) REVERT: B 50 MET cc_start: 0.8452 (mtm) cc_final: 0.8044 (mtm) REVERT: B 239 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: B 263 ASP cc_start: 0.7810 (t0) cc_final: 0.7581 (t0) REVERT: B 267 MET cc_start: 0.7965 (ttm) cc_final: 0.7718 (mtp) REVERT: E 18 ARG cc_start: 0.7542 (tpp80) cc_final: 0.7142 (tpt-90) REVERT: E 43 LYS cc_start: 0.8478 (mppt) cc_final: 0.8170 (mmtp) REVERT: R 58 ASN cc_start: 0.8453 (m-40) cc_final: 0.8082 (m110) REVERT: R 125 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8545 (t) REVERT: R 315 PHE cc_start: 0.7652 (t80) cc_final: 0.7282 (t80) REVERT: R 317 LYS cc_start: 0.4949 (mttt) cc_final: 0.4215 (mtmp) outliers start: 26 outliers final: 18 residues processed: 155 average time/residue: 2.1377 time to fit residues: 358.2853 Evaluate side-chains 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.137039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107740 restraints weight = 38696.172| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.14 r_work: 0.3314 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9045 Z= 0.097 Angle : 0.504 6.908 12277 Z= 0.262 Chirality : 0.042 0.438 1397 Planarity : 0.004 0.051 1557 Dihedral : 4.292 43.660 1242 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.31 % Allowed : 21.85 % Favored : 75.84 % 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: 1.49 (0.26), residues: 1122 helix: 2.97 (0.26), residues: 387 sheet: 0.46 (0.33), residues: 255 loop : -0.37 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 302 HIS 0.003 0.001 HIS B 230 PHE 0.013 0.001 PHE R 287 TYR 0.008 0.001 TYR E 95 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 449) hydrogen bonds : angle 4.41026 ( 1278) SS BOND : bond 0.00832 ( 4) SS BOND : angle 1.01323 ( 8) covalent geometry : bond 0.00216 ( 9041) covalent geometry : angle 0.50383 (12269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7311 (t0) cc_final: 0.6982 (t0) REVERT: A 348 ASP cc_start: 0.8618 (t70) cc_final: 0.8381 (t0) REVERT: B 38 ILE cc_start: 0.8248 (tp) cc_final: 0.7920 (mm) REVERT: B 50 MET cc_start: 0.8391 (mtm) cc_final: 0.7999 (mtm) REVERT: B 170 THR cc_start: 0.8725 (p) cc_final: 0.8463 (p) REVERT: B 239 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: E 18 ARG cc_start: 0.7552 (tpp80) cc_final: 0.7134 (tpt-90) REVERT: E 43 LYS cc_start: 0.8467 (mppt) cc_final: 0.8170 (mmtp) REVERT: R 125 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8492 (t) REVERT: R 315 PHE cc_start: 0.7608 (t80) cc_final: 0.7249 (t80) REVERT: R 317 LYS cc_start: 0.4965 (mttt) cc_final: 0.4231 (mtmp) outliers start: 22 outliers final: 12 residues processed: 156 average time/residue: 2.1036 time to fit residues: 355.4156 Evaluate side-chains 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 274 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 108 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.105429 restraints weight = 38936.661| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.14 r_work: 0.3278 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9045 Z= 0.150 Angle : 0.539 8.087 12277 Z= 0.285 Chirality : 0.043 0.432 1397 Planarity : 0.005 0.055 1557 Dihedral : 4.468 42.399 1242 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.89 % Allowed : 22.06 % Favored : 76.05 % 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: 1.32 (0.26), residues: 1122 helix: 2.86 (0.25), residues: 387 sheet: 0.24 (0.32), residues: 254 loop : -0.42 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.006 0.001 HIS B 230 PHE 0.016 0.001 PHE R 287 TYR 0.011 0.001 TYR R 294 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 449) hydrogen bonds : angle 4.51783 ( 1278) SS BOND : bond 0.01290 ( 4) SS BOND : angle 1.11695 ( 8) covalent geometry : bond 0.00340 ( 9041) covalent geometry : angle 0.53851 (12269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15395.83 seconds wall clock time: 265 minutes 17.37 seconds (15917.37 seconds total)