Starting phenix.real_space_refine on Thu Jan 16 01:42:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwk_37891/01_2025/8wwk_37891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwk_37891/01_2025/8wwk_37891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwk_37891/01_2025/8wwk_37891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwk_37891/01_2025/8wwk_37891.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwk_37891/01_2025/8wwk_37891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwk_37891/01_2025/8wwk_37891.cif" } resolution = 2.61 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= 0.001 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5712 2.51 5 N 1519 2.21 5 O 1668 1.98 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-5571/modules/chem_data/mon_lib" Total number of atoms: 8967 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2242 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 139 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.54, per 1000 atoms: 0.62 Number of scatterers: 8967 At special positions: 0 Unit cell: (88.81, 117.7, 120.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1668 8.00 N 1519 7.00 C 5712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 38.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.572A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.289A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.920A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.663A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.317A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 108 through 138 removed outlier: 3.573A pdb=" N MET R 112 " --> pdb=" O ILE R 108 " (cutoff:3.500A) Proline residue: R 113 - end of helix removed outlier: 3.819A pdb=" N SER R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 164 Processing helix chain 'R' and resid 164 through 174 removed outlier: 5.108A pdb=" N GLN R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU R 172 " --> pdb=" O MET R 168 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY R 174 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 216 removed outlier: 3.892A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.725A pdb=" N LYS R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.824A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 302 Processing helix chain 'R' and resid 313 through 348 Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.027A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.317A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.804A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.570A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.797A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.170A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.873A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.095A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.759A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.796A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.164A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.545A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.505A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.141A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 251 through 255 Processing sheet with id=AB7, first strand: chain 'L' and resid 8 through 9 485 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2888 1.34 - 1.46: 2186 1.46 - 1.58: 3985 1.58 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 9158 Sorted by residual: bond pdb=" N GLY B 116 " pdb=" CA GLY B 116 " ideal model delta sigma weight residual 1.458 1.447 0.010 9.20e-03 1.18e+04 1.30e+00 bond pdb=" C LEU A 39 " pdb=" N GLY A 40 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.70e-01 bond pdb=" C GLY B 116 " pdb=" O GLY B 116 " ideal model delta sigma weight residual 1.239 1.234 0.005 8.50e-03 1.38e+04 3.64e-01 bond pdb=" C MET R 165 " pdb=" N PRO R 166 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.18e-01 bond pdb=" CB PHE B 292 " pdb=" CG PHE B 292 " ideal model delta sigma weight residual 1.502 1.515 -0.013 2.30e-02 1.89e+03 3.12e-01 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 12233 1.17 - 2.33: 148 2.33 - 3.50: 34 3.50 - 4.67: 7 4.67 - 5.84: 5 Bond angle restraints: 12427 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.88e+00 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 109.34 112.83 -3.49 2.08e+00 2.31e-01 2.82e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 122.14 -5.84 3.50e+00 8.16e-02 2.78e+00 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.16 114.03 -2.87 1.76e+00 3.23e-01 2.65e+00 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 124.82 127.34 -2.52 1.78e+00 3.16e-01 2.01e+00 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 5228 16.13 - 32.25: 166 32.25 - 48.38: 28 48.38 - 64.50: 6 64.50 - 80.63: 1 Dihedral angle restraints: 5429 sinusoidal: 2063 harmonic: 3366 Sorted by residual: dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LYS R 139 " pdb=" C LYS R 139 " pdb=" N LEU R 140 " pdb=" CA LEU R 140 " ideal model delta harmonic sigma weight residual 180.00 164.93 15.07 0 5.00e+00 4.00e-02 9.08e+00 dihedral pdb=" N LYS A 312 " pdb=" CA LYS A 312 " pdb=" CB LYS A 312 " pdb=" CG LYS A 312 " ideal model delta sinusoidal sigma weight residual 180.00 -127.96 -52.04 3 1.50e+01 4.44e-03 9.08e+00 ... (remaining 5426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 875 0.026 - 0.051: 316 0.051 - 0.077: 136 0.077 - 0.102: 63 0.102 - 0.128: 36 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1423 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO B 236 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO E 107 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO B 194 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.016 5.00e-02 4.00e+02 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 782 2.74 - 3.28: 8784 3.28 - 3.82: 15448 3.82 - 4.36: 19349 4.36 - 4.90: 32640 Nonbonded interactions: 77003 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.242 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.283 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.291 3.040 ... (remaining 76998 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.002 0.017 9158 Z= 0.100 Angle : 0.392 5.837 12427 Z= 0.207 Chirality : 0.039 0.128 1426 Planarity : 0.003 0.050 1570 Dihedral : 8.406 80.627 3245 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.72 % Allowed : 2.58 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1144 helix: 1.16 (0.25), residues: 394 sheet: 0.97 (0.30), residues: 288 loop : 0.36 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.002 0.001 HIS B 62 PHE 0.009 0.001 PHE B 199 TYR 0.010 0.001 TYR E 190 ARG 0.001 0.000 ARG R 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.983 Fit side-chains REVERT: A 8 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8499 (mt-10) REVERT: A 10 LYS cc_start: 0.8813 (mttt) cc_final: 0.8530 (mtmp) REVERT: A 29 LYS cc_start: 0.8064 (tttt) cc_final: 0.7657 (ttpp) REVERT: B 25 CYS cc_start: 0.7906 (p) cc_final: 0.6766 (m) REVERT: B 130 GLU cc_start: 0.8313 (mp0) cc_final: 0.8105 (mp0) REVERT: C 21 MET cc_start: 0.7082 (mmm) cc_final: 0.6469 (tmt) REVERT: C 47 GLU cc_start: 0.7999 (pt0) cc_final: 0.7741 (mp0) REVERT: E 43 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8073 (mtmt) REVERT: E 77 ASN cc_start: 0.8277 (m-40) cc_final: 0.7925 (m-40) REVERT: E 223 ASP cc_start: 0.8634 (m-30) cc_final: 0.8395 (m-30) REVERT: R 142 TRP cc_start: 0.6869 (m-90) cc_final: 0.5954 (m100) REVERT: R 252 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6406 (mpp-170) outliers start: 7 outliers final: 5 residues processed: 190 average time/residue: 1.3305 time to fit residues: 269.1989 Evaluate side-chains 147 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 220 GLN B 259 GLN R 194 ASN R 281 GLN R 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.167001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129036 restraints weight = 8704.177| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.70 r_work: 0.3033 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9158 Z= 0.195 Angle : 0.527 5.653 12427 Z= 0.286 Chirality : 0.042 0.137 1426 Planarity : 0.004 0.054 1570 Dihedral : 5.106 55.884 1267 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.79 % Allowed : 7.84 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.47 (0.25), residues: 1144 helix: 2.26 (0.25), residues: 394 sheet: 0.59 (0.29), residues: 279 loop : 0.20 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.013 0.002 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.006 0.001 ARG R 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.949 Fit side-chains REVERT: A 8 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8409 (mt-10) REVERT: A 28 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: A 29 LYS cc_start: 0.8164 (tttt) cc_final: 0.7661 (ttpp) REVERT: A 33 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: B 130 GLU cc_start: 0.8469 (mp0) cc_final: 0.8118 (mp0) REVERT: B 217 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8367 (pmm) REVERT: E 43 LYS cc_start: 0.8623 (mmtm) cc_final: 0.7880 (mtmt) REVERT: E 77 ASN cc_start: 0.8303 (m-40) cc_final: 0.7840 (m-40) REVERT: E 160 ARG cc_start: 0.7567 (mtp-110) cc_final: 0.7265 (ttm170) REVERT: R 142 TRP cc_start: 0.6896 (m-90) cc_final: 0.5784 (m100) REVERT: R 165 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8009 (ttt) REVERT: R 187 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7141 (mm) REVERT: R 235 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7783 (mp) REVERT: R 252 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.5895 (mpp-170) REVERT: R 345 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7569 (tp40) outliers start: 27 outliers final: 10 residues processed: 161 average time/residue: 1.4032 time to fit residues: 239.3750 Evaluate side-chains 163 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 322 HIS B 156 GLN B 259 GLN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.165416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127706 restraints weight = 8833.220| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.73 r_work: 0.3026 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9158 Z= 0.243 Angle : 0.536 6.314 12427 Z= 0.290 Chirality : 0.043 0.174 1426 Planarity : 0.004 0.057 1570 Dihedral : 5.323 57.980 1267 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.30 % Allowed : 9.49 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.39 (0.25), residues: 1144 helix: 2.43 (0.25), residues: 393 sheet: 0.36 (0.29), residues: 276 loop : 0.05 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.015 0.002 PHE B 151 TYR 0.015 0.002 TYR R 341 ARG 0.005 0.001 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: A 29 LYS cc_start: 0.8134 (tttt) cc_final: 0.7614 (ttpp) REVERT: A 33 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: B 217 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8427 (pmm) REVERT: E 23 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7867 (p) REVERT: E 43 LYS cc_start: 0.8627 (mmtm) cc_final: 0.7875 (mtmt) REVERT: E 77 ASN cc_start: 0.8399 (m-40) cc_final: 0.7944 (m-40) REVERT: E 160 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.7298 (ttm170) REVERT: E 234 GLU cc_start: 0.8889 (pt0) cc_final: 0.8649 (pt0) REVERT: R 142 TRP cc_start: 0.6879 (m-90) cc_final: 0.5781 (m100) REVERT: R 165 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7769 (ttt) REVERT: R 235 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7806 (mp) REVERT: R 250 TYR cc_start: 0.8188 (m-80) cc_final: 0.7920 (m-10) REVERT: R 252 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6792 (mpt90) outliers start: 32 outliers final: 16 residues processed: 157 average time/residue: 1.4278 time to fit residues: 237.6517 Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 322 HIS B 156 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130275 restraints weight = 8680.184| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.78 r_work: 0.3020 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9158 Z= 0.214 Angle : 0.511 5.948 12427 Z= 0.276 Chirality : 0.042 0.151 1426 Planarity : 0.004 0.058 1570 Dihedral : 5.341 59.636 1267 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.61 % Allowed : 9.80 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.39 (0.25), residues: 1144 helix: 2.55 (0.25), residues: 393 sheet: 0.20 (0.29), residues: 282 loop : 0.05 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8401 (mt-10) REVERT: A 28 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: A 29 LYS cc_start: 0.8120 (tttt) cc_final: 0.7624 (ttpp) REVERT: A 33 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: B 217 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8418 (pmm) REVERT: C 58 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: E 43 LYS cc_start: 0.8631 (mmtm) cc_final: 0.7837 (mtmt) REVERT: E 77 ASN cc_start: 0.8392 (m-40) cc_final: 0.7957 (m-40) REVERT: E 160 ARG cc_start: 0.7540 (mtp-110) cc_final: 0.6785 (mmm160) REVERT: E 234 GLU cc_start: 0.8905 (pt0) cc_final: 0.8652 (pt0) REVERT: R 142 TRP cc_start: 0.6951 (m-90) cc_final: 0.5695 (m100) REVERT: R 250 TYR cc_start: 0.8171 (m-80) cc_final: 0.7905 (m-10) REVERT: R 252 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6806 (mpt90) REVERT: R 356 LEU cc_start: 0.7990 (mm) cc_final: 0.7702 (mm) outliers start: 35 outliers final: 19 residues processed: 162 average time/residue: 1.4170 time to fit residues: 243.3694 Evaluate side-chains 163 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.166072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128600 restraints weight = 8669.629| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.73 r_work: 0.2991 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9158 Z= 0.307 Angle : 0.568 7.322 12427 Z= 0.305 Chirality : 0.044 0.205 1426 Planarity : 0.004 0.061 1570 Dihedral : 5.564 59.043 1267 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.72 % Allowed : 10.11 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1144 helix: 2.41 (0.25), residues: 394 sheet: 0.24 (0.28), residues: 297 loop : -0.10 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.017 0.002 PHE B 151 TYR 0.014 0.002 TYR R 341 ARG 0.004 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.999 Fit side-chains REVERT: A 28 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: A 29 LYS cc_start: 0.8187 (tttt) cc_final: 0.7677 (ttpp) REVERT: A 33 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: B 42 ARG cc_start: 0.6988 (tpt170) cc_final: 0.6239 (tpt170) REVERT: B 217 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8288 (pmm) REVERT: C 58 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: E 43 LYS cc_start: 0.8629 (mmtm) cc_final: 0.7818 (mtmt) REVERT: E 65 LYS cc_start: 0.8005 (tttt) cc_final: 0.7602 (ttmm) REVERT: E 160 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.6813 (mmm160) REVERT: E 234 GLU cc_start: 0.8909 (pt0) cc_final: 0.8687 (pt0) REVERT: R 142 TRP cc_start: 0.6873 (m-90) cc_final: 0.5573 (m100) REVERT: R 165 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7993 (ttt) REVERT: R 250 TYR cc_start: 0.8242 (m-80) cc_final: 0.8003 (m-10) outliers start: 36 outliers final: 20 residues processed: 161 average time/residue: 1.5256 time to fit residues: 260.3929 Evaluate side-chains 166 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.165489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127886 restraints weight = 8737.707| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.65 r_work: 0.3003 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9158 Z= 0.213 Angle : 0.514 6.127 12427 Z= 0.278 Chirality : 0.042 0.139 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.041 43.883 1262 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.72 % Allowed : 11.04 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.25), residues: 1144 helix: 2.55 (0.25), residues: 394 sheet: 0.12 (0.29), residues: 284 loop : -0.03 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.015 0.002 PHE B 151 TYR 0.013 0.001 TYR R 341 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.084 Fit side-chains REVERT: A 28 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: A 29 LYS cc_start: 0.8131 (tttt) cc_final: 0.7637 (ttpp) REVERT: A 33 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: A 270 LYS cc_start: 0.8483 (mttt) cc_final: 0.7933 (mttp) REVERT: B 42 ARG cc_start: 0.7043 (tpt170) cc_final: 0.6308 (tpt170) REVERT: C 58 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: E 43 LYS cc_start: 0.8640 (mmtm) cc_final: 0.7869 (mtmt) REVERT: E 65 LYS cc_start: 0.7979 (tttt) cc_final: 0.7587 (ttmm) REVERT: E 77 ASN cc_start: 0.8579 (m-40) cc_final: 0.8039 (m-40) REVERT: E 160 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7254 (ttm170) REVERT: E 192 MET cc_start: 0.7977 (ttp) cc_final: 0.7758 (tmm) REVERT: E 234 GLU cc_start: 0.8931 (pt0) cc_final: 0.8687 (pt0) REVERT: R 142 TRP cc_start: 0.6933 (m-90) cc_final: 0.5657 (m100) REVERT: R 165 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7876 (ttt) REVERT: R 250 TYR cc_start: 0.8206 (m-80) cc_final: 0.7963 (m-10) outliers start: 36 outliers final: 21 residues processed: 161 average time/residue: 1.5044 time to fit residues: 256.0706 Evaluate side-chains 163 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.166373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128386 restraints weight = 8856.380| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.69 r_work: 0.3017 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9158 Z= 0.187 Angle : 0.499 5.954 12427 Z= 0.269 Chirality : 0.042 0.182 1426 Planarity : 0.004 0.060 1570 Dihedral : 4.937 43.648 1262 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.10 % Allowed : 11.76 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.39 (0.25), residues: 1144 helix: 2.65 (0.25), residues: 396 sheet: 0.17 (0.29), residues: 277 loop : -0.05 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.014 0.001 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.947 Fit side-chains REVERT: A 8 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 28 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: A 29 LYS cc_start: 0.8125 (tttt) cc_final: 0.7627 (ttpp) REVERT: A 33 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: A 270 LYS cc_start: 0.8497 (mttt) cc_final: 0.8044 (mttp) REVERT: C 58 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: E 43 LYS cc_start: 0.8650 (mmtm) cc_final: 0.7805 (mtpt) REVERT: E 77 ASN cc_start: 0.8561 (m-40) cc_final: 0.8053 (m-40) REVERT: E 160 ARG cc_start: 0.7560 (mtp-110) cc_final: 0.7265 (ttm170) REVERT: R 142 TRP cc_start: 0.6896 (m-90) cc_final: 0.5618 (m100) REVERT: R 252 ARG cc_start: 0.6945 (mpt90) cc_final: 0.5809 (mpp-170) outliers start: 30 outliers final: 20 residues processed: 159 average time/residue: 1.4784 time to fit residues: 248.6424 Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 5.9990 chunk 66 optimal weight: 0.0170 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.167117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129636 restraints weight = 8932.503| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.69 r_work: 0.3142 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9158 Z= 0.165 Angle : 0.487 6.496 12427 Z= 0.262 Chirality : 0.041 0.135 1426 Planarity : 0.004 0.060 1570 Dihedral : 4.821 43.065 1262 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.10 % Allowed : 11.46 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.45 (0.25), residues: 1144 helix: 2.73 (0.25), residues: 396 sheet: 0.17 (0.29), residues: 278 loop : -0.00 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG R 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.054 Fit side-chains REVERT: A 17 LYS cc_start: 0.8350 (mttt) cc_final: 0.7989 (mtpt) REVERT: A 28 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: A 29 LYS cc_start: 0.8146 (tttt) cc_final: 0.7683 (ttpp) REVERT: A 33 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: A 243 MET cc_start: 0.8552 (tpp) cc_final: 0.8333 (ttm) REVERT: A 270 LYS cc_start: 0.8531 (mttt) cc_final: 0.8087 (mttp) REVERT: C 58 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: E 43 LYS cc_start: 0.8627 (mmtm) cc_final: 0.7881 (mtpt) REVERT: E 77 ASN cc_start: 0.8572 (m-40) cc_final: 0.8069 (m-40) REVERT: R 142 TRP cc_start: 0.6940 (m-90) cc_final: 0.5719 (m100) REVERT: R 345 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7038 (mm-40) outliers start: 30 outliers final: 18 residues processed: 158 average time/residue: 1.4857 time to fit residues: 248.6344 Evaluate side-chains 160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN R 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128379 restraints weight = 8752.826| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.66 r_work: 0.2991 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9158 Z= 0.342 Angle : 0.606 8.239 12427 Z= 0.323 Chirality : 0.046 0.262 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.246 43.318 1262 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.10 % Allowed : 11.66 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1144 helix: 2.47 (0.25), residues: 394 sheet: 0.07 (0.28), residues: 300 loop : -0.13 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.005 0.001 HIS B 183 PHE 0.015 0.002 PHE A 196 TYR 0.015 0.002 TYR R 341 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.007 Fit side-chains REVERT: A 28 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: A 29 LYS cc_start: 0.8092 (tttt) cc_final: 0.7587 (ttpp) REVERT: A 33 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: A 270 LYS cc_start: 0.8487 (mttt) cc_final: 0.8022 (mttp) REVERT: B 42 ARG cc_start: 0.7077 (tpt170) cc_final: 0.6330 (tpt170) REVERT: E 43 LYS cc_start: 0.8605 (mmtm) cc_final: 0.7721 (mtpt) REVERT: E 65 LYS cc_start: 0.7988 (tttt) cc_final: 0.7583 (ttmm) REVERT: E 160 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.6803 (mmm160) REVERT: R 142 TRP cc_start: 0.6921 (m-90) cc_final: 0.5623 (m100) REVERT: R 165 MET cc_start: 0.8299 (ttm) cc_final: 0.7911 (ttt) REVERT: R 345 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.6995 (mm-40) outliers start: 30 outliers final: 20 residues processed: 152 average time/residue: 1.5989 time to fit residues: 256.6500 Evaluate side-chains 159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128904 restraints weight = 8765.666| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.72 r_work: 0.3003 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9158 Z= 0.265 Angle : 0.561 7.353 12427 Z= 0.301 Chirality : 0.044 0.203 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.191 43.472 1262 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.68 % Allowed : 12.49 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.24 (0.25), residues: 1144 helix: 2.51 (0.25), residues: 394 sheet: 0.10 (0.28), residues: 297 loop : -0.12 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 248 HIS 0.004 0.001 HIS A 188 PHE 0.014 0.002 PHE B 151 TYR 0.012 0.002 TYR R 341 ARG 0.009 0.001 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.062 Fit side-chains REVERT: A 28 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: A 29 LYS cc_start: 0.8106 (tttt) cc_final: 0.7608 (ttpp) REVERT: A 33 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: A 270 LYS cc_start: 0.8493 (mttt) cc_final: 0.8029 (mttp) REVERT: B 42 ARG cc_start: 0.7065 (tpt170) cc_final: 0.6331 (tpt170) REVERT: E 43 LYS cc_start: 0.8637 (mmtm) cc_final: 0.7797 (mtpt) REVERT: E 65 LYS cc_start: 0.7981 (tttt) cc_final: 0.7588 (ttmm) REVERT: E 77 ASN cc_start: 0.8592 (m-40) cc_final: 0.8046 (m-40) REVERT: E 160 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7269 (ttm170) REVERT: R 142 TRP cc_start: 0.6924 (m-90) cc_final: 0.5619 (m100) REVERT: R 165 MET cc_start: 0.8273 (ttm) cc_final: 0.7892 (ttt) REVERT: R 345 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6968 (mm110) outliers start: 26 outliers final: 21 residues processed: 156 average time/residue: 1.5584 time to fit residues: 256.8211 Evaluate side-chains 163 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 41 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.168158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131091 restraints weight = 8827.523| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.63 r_work: 0.3053 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9158 Z= 0.162 Angle : 0.504 7.385 12427 Z= 0.271 Chirality : 0.042 0.200 1426 Planarity : 0.004 0.061 1570 Dihedral : 4.944 43.914 1262 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.58 % Allowed : 12.69 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1144 helix: 2.67 (0.26), residues: 396 sheet: 0.12 (0.29), residues: 278 loop : -0.06 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.013 0.001 PHE R 283 TYR 0.012 0.001 TYR E 190 ARG 0.009 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8072.00 seconds wall clock time: 143 minutes 10.53 seconds (8590.53 seconds total)