Starting phenix.real_space_refine on Mon Apr 28 00:57:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gfx_29987/04_2025/8gfx_29987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gfx_29987/04_2025/8gfx_29987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gfx_29987/04_2025/8gfx_29987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gfx_29987/04_2025/8gfx_29987.map" model { file = "/net/cci-nas-00/data/ceres_data/8gfx_29987/04_2025/8gfx_29987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gfx_29987/04_2025/8gfx_29987.cif" } resolution = 3.0 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= 0.036 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 P 3 5.49 5 S 43 5.16 5 C 4314 2.51 5 N 1151 2.21 5 O 1214 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-5669/modules/chem_data/mon_lib" Total number of atoms: 6725 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1743 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 8, 'PHE:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2443 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 86 Chain: "G" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 348 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2143 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.09, per 1000 atoms: 0.76 Number of scatterers: 6725 At special positions: 0 Unit cell: (85.0346, 133.626, 100.653, 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 43 16.00 P 3 15.00 O 1214 8.00 N 1151 7.00 C 4314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 48.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.601A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 238 removed outlier: 4.151A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.693A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.504A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.651A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.953A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.854A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.716A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.765A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.639A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 61 removed outlier: 3.623A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 removed outlier: 3.700A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.084A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.859A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.608A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.667A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.818A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 238 removed outlier: 3.533A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.702A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.251A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.924A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.392A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.624A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.975A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.167A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.027A 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: 6.826A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.251A 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: 6.771A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.624A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.853A 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: 3.806A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1102 1.32 - 1.44: 1913 1.44 - 1.57: 3792 1.57 - 1.69: 5 1.69 - 1.81: 60 Bond restraints: 6872 Sorted by residual: bond pdb=" CA PHE R 332 " pdb=" C PHE R 332 " ideal model delta sigma weight residual 1.524 1.469 0.054 1.29e-02 6.01e+03 1.78e+01 bond pdb=" CA ARG R 239 " pdb=" C ARG R 239 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.40e-02 5.10e+03 1.50e+01 bond pdb=" C ARG R 239 " pdb=" N PHE R 240 " ideal model delta sigma weight residual 1.335 1.290 0.045 1.36e-02 5.41e+03 1.10e+01 bond pdb=" C PHE R 332 " pdb=" O PHE R 332 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" CA ALA R 335 " pdb=" CB ALA R 335 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.56e-02 4.11e+03 9.26e+00 ... (remaining 6867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 9158 1.38 - 2.75: 180 2.75 - 4.13: 28 4.13 - 5.50: 15 5.50 - 6.88: 4 Bond angle restraints: 9385 Sorted by residual: angle pdb=" N PHE R 332 " pdb=" CA PHE R 332 " pdb=" C PHE R 332 " ideal model delta sigma weight residual 111.36 104.48 6.88 1.09e+00 8.42e-01 3.98e+01 angle pdb=" C ILE R 334 " pdb=" CA ILE R 334 " pdb=" CB ILE R 334 " ideal model delta sigma weight residual 112.14 105.83 6.31 1.35e+00 5.49e-01 2.19e+01 angle pdb=" N GLN R 337 " pdb=" CA GLN R 337 " pdb=" C GLN R 337 " ideal model delta sigma weight residual 111.28 116.00 -4.72 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ARG R 239 " pdb=" CA ARG R 239 " pdb=" C ARG R 239 " ideal model delta sigma weight residual 112.54 116.90 -4.36 1.22e+00 6.72e-01 1.27e+01 angle pdb=" N ARG R 239 " pdb=" CA ARG R 239 " pdb=" CB ARG R 239 " ideal model delta sigma weight residual 110.39 105.00 5.39 1.66e+00 3.63e-01 1.05e+01 ... (remaining 9380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 3937 33.75 - 67.49: 47 67.49 - 101.24: 7 101.24 - 134.98: 0 134.98 - 168.73: 2 Dihedral angle restraints: 3993 sinusoidal: 1381 harmonic: 2612 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -122.00 -168.73 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -62.25 166.84 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual -56.21 -127.50 71.29 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 3990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 784 0.041 - 0.082: 253 0.082 - 0.123: 65 0.123 - 0.164: 7 0.164 - 0.205: 1 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA PHE R 240 " pdb=" N PHE R 240 " pdb=" C PHE R 240 " pdb=" CB PHE R 240 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1107 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 239 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ARG R 239 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG R 239 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE R 240 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C ILE R 205 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 335 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C ALA R 335 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA R 335 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE R 336 " 0.009 2.00e-02 2.50e+03 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1447 2.78 - 3.31: 5965 3.31 - 3.84: 10439 3.84 - 4.37: 12024 4.37 - 4.90: 22245 Nonbonded interactions: 52120 Sorted by model distance: nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.302 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.368 3.120 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE1 GLU G 22 " model vdw 2.368 3.120 ... (remaining 52115 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: 2.260 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 0.054 6873 Z= 0.228 Angle : 0.529 6.875 9387 Z= 0.303 Chirality : 0.042 0.205 1110 Planarity : 0.003 0.031 1175 Dihedral : 13.466 168.728 2294 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.67 (0.29), residues: 880 helix: 1.37 (0.27), residues: 398 sheet: 0.35 (0.42), residues: 171 loop : -0.65 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.006 0.001 HIS B 183 PHE 0.017 0.001 PHE B 234 TYR 0.016 0.001 TYR B 59 ARG 0.002 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.20123 ( 353) hydrogen bonds : angle 6.42747 ( 1035) SS BOND : bond 0.00205 ( 1) SS BOND : angle 1.39676 ( 2) covalent geometry : bond 0.00412 ( 6872) covalent geometry : angle 0.52836 ( 9385) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.726 Fit side-chains REVERT: A 364 THR cc_start: 0.9101 (m) cc_final: 0.8854 (m) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 1.0615 time to fit residues: 114.7968 Evaluate side-chains 79 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 220 HIS A 227 GLN B 75 GLN R 241 HIS R 296 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108517 restraints weight = 8406.657| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.12 r_work: 0.3190 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6873 Z= 0.131 Angle : 0.494 6.392 9387 Z= 0.267 Chirality : 0.041 0.142 1110 Planarity : 0.003 0.033 1175 Dihedral : 9.456 171.478 983 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.30 % Allowed : 9.80 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 880 helix: 1.81 (0.27), residues: 399 sheet: 0.62 (0.42), residues: 169 loop : -0.72 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE A 212 TYR 0.015 0.001 TYR B 59 ARG 0.003 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.05501 ( 353) hydrogen bonds : angle 4.66820 ( 1035) SS BOND : bond 0.00283 ( 1) SS BOND : angle 1.35391 ( 2) covalent geometry : bond 0.00290 ( 6872) covalent geometry : angle 0.49353 ( 9385) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.780 Fit side-chains REVERT: B 262 MET cc_start: 0.8985 (ttm) cc_final: 0.8755 (ttm) REVERT: R 195 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9018 (t) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 1.2241 time to fit residues: 112.2778 Evaluate side-chains 80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 85 optimal weight: 0.0020 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110513 restraints weight = 8472.224| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.14 r_work: 0.3229 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6873 Z= 0.098 Angle : 0.450 6.454 9387 Z= 0.243 Chirality : 0.040 0.137 1110 Planarity : 0.003 0.030 1175 Dihedral : 9.360 172.966 983 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.30 % Allowed : 11.79 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 880 helix: 2.01 (0.28), residues: 400 sheet: 0.56 (0.41), residues: 175 loop : -0.54 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.008 0.001 PHE B 241 TYR 0.009 0.001 TYR R 209 ARG 0.003 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 353) hydrogen bonds : angle 4.30277 ( 1035) SS BOND : bond 0.00263 ( 1) SS BOND : angle 1.17975 ( 2) covalent geometry : bond 0.00197 ( 6872) covalent geometry : angle 0.44960 ( 9385) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.845 Fit side-chains REVERT: R 195 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.9015 (t) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 1.1495 time to fit residues: 106.0333 Evaluate side-chains 83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 85 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.095110 restraints weight = 8921.556| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.06 r_work: 0.2876 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6873 Z= 0.098 Angle : 0.444 6.481 9387 Z= 0.238 Chirality : 0.039 0.136 1110 Planarity : 0.003 0.030 1175 Dihedral : 9.334 175.478 983 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.45 % Allowed : 12.56 % Favored : 84.99 % 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: 1.33 (0.29), residues: 880 helix: 2.12 (0.27), residues: 401 sheet: 0.59 (0.42), residues: 172 loop : -0.60 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE A 212 TYR 0.009 0.001 TYR R 209 ARG 0.004 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 353) hydrogen bonds : angle 4.09417 ( 1035) SS BOND : bond 0.00252 ( 1) SS BOND : angle 1.05974 ( 2) covalent geometry : bond 0.00206 ( 6872) covalent geometry : angle 0.44336 ( 9385) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.821 Fit side-chains REVERT: R 195 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.9023 (t) outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 1.1593 time to fit residues: 105.6398 Evaluate side-chains 84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.138801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110165 restraints weight = 8498.060| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.13 r_work: 0.3203 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6873 Z= 0.113 Angle : 0.460 6.455 9387 Z= 0.245 Chirality : 0.040 0.137 1110 Planarity : 0.003 0.032 1175 Dihedral : 9.386 177.705 983 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.91 % Allowed : 13.02 % Favored : 84.07 % 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: 1.34 (0.29), residues: 880 helix: 2.13 (0.27), residues: 401 sheet: 0.59 (0.42), residues: 172 loop : -0.59 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 211 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE B 241 TYR 0.010 0.001 TYR R 209 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 353) hydrogen bonds : angle 4.06729 ( 1035) SS BOND : bond 0.00258 ( 1) SS BOND : angle 1.08118 ( 2) covalent geometry : bond 0.00255 ( 6872) covalent geometry : angle 0.45987 ( 9385) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.832 Fit side-chains REVERT: B 153 ASP cc_start: 0.7924 (t0) cc_final: 0.7682 (t70) REVERT: R 195 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9077 (t) outliers start: 19 outliers final: 14 residues processed: 89 average time/residue: 1.1092 time to fit residues: 104.7734 Evaluate side-chains 90 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107374 restraints weight = 8552.343| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.12 r_work: 0.3162 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6873 Z= 0.154 Angle : 0.507 6.343 9387 Z= 0.271 Chirality : 0.042 0.146 1110 Planarity : 0.003 0.035 1175 Dihedral : 9.503 178.806 983 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.98 % Allowed : 13.02 % Favored : 83.00 % 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 (0.29), residues: 880 helix: 2.10 (0.28), residues: 396 sheet: 0.62 (0.41), residues: 172 loop : -0.63 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.005 0.001 HIS B 183 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR R 132 ARG 0.005 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 353) hydrogen bonds : angle 4.19140 ( 1035) SS BOND : bond 0.00285 ( 1) SS BOND : angle 1.19918 ( 2) covalent geometry : bond 0.00373 ( 6872) covalent geometry : angle 0.50724 ( 9385) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.730 Fit side-chains REVERT: R 195 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9074 (t) outliers start: 26 outliers final: 16 residues processed: 91 average time/residue: 1.0910 time to fit residues: 105.2534 Evaluate side-chains 89 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108457 restraints weight = 8525.295| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.14 r_work: 0.3184 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6873 Z= 0.118 Angle : 0.476 6.327 9387 Z= 0.255 Chirality : 0.040 0.141 1110 Planarity : 0.003 0.031 1175 Dihedral : 9.401 176.619 983 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.06 % Allowed : 14.70 % Favored : 82.24 % 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 (0.29), residues: 880 helix: 2.16 (0.27), residues: 395 sheet: 0.60 (0.41), residues: 173 loop : -0.64 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.009 0.001 TYR R 132 ARG 0.005 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 353) hydrogen bonds : angle 4.09545 ( 1035) SS BOND : bond 0.00303 ( 1) SS BOND : angle 1.26284 ( 2) covalent geometry : bond 0.00269 ( 6872) covalent geometry : angle 0.47524 ( 9385) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.679 Fit side-chains REVERT: B 35 ASN cc_start: 0.8413 (t160) cc_final: 0.8021 (t0) outliers start: 20 outliers final: 18 residues processed: 89 average time/residue: 1.0304 time to fit residues: 97.5727 Evaluate side-chains 92 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 3 optimal weight: 4.9990 chunk 57 optimal weight: 0.0470 chunk 21 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 340 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110386 restraints weight = 8477.763| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.11 r_work: 0.3209 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6873 Z= 0.099 Angle : 0.458 6.338 9387 Z= 0.244 Chirality : 0.039 0.137 1110 Planarity : 0.003 0.030 1175 Dihedral : 9.305 174.285 983 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.91 % Allowed : 15.16 % Favored : 81.93 % 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: 1.34 (0.29), residues: 880 helix: 2.20 (0.27), residues: 397 sheet: 0.47 (0.41), residues: 177 loop : -0.60 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.008 0.001 TYR A 311 ARG 0.004 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 353) hydrogen bonds : angle 4.00039 ( 1035) SS BOND : bond 0.00264 ( 1) SS BOND : angle 1.16934 ( 2) covalent geometry : bond 0.00211 ( 6872) covalent geometry : angle 0.45760 ( 9385) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.735 Fit side-chains REVERT: B 35 ASN cc_start: 0.8404 (t160) cc_final: 0.8008 (t0) outliers start: 19 outliers final: 12 residues processed: 84 average time/residue: 1.0737 time to fit residues: 96.0185 Evaluate side-chains 84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 189 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 340 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110577 restraints weight = 8577.069| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.14 r_work: 0.3212 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6873 Z= 0.097 Angle : 0.453 6.416 9387 Z= 0.241 Chirality : 0.039 0.135 1110 Planarity : 0.003 0.030 1175 Dihedral : 9.190 170.950 983 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.60 % Allowed : 15.77 % Favored : 81.62 % 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: 1.38 (0.29), residues: 880 helix: 2.27 (0.27), residues: 397 sheet: 0.57 (0.41), residues: 175 loop : -0.67 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.009 0.001 PHE A 376 TYR 0.008 0.001 TYR R 209 ARG 0.004 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 353) hydrogen bonds : angle 3.95153 ( 1035) SS BOND : bond 0.00261 ( 1) SS BOND : angle 1.03731 ( 2) covalent geometry : bond 0.00206 ( 6872) covalent geometry : angle 0.45233 ( 9385) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.771 Fit side-chains REVERT: A 25 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7728 (ttpp) REVERT: B 35 ASN cc_start: 0.8407 (t160) cc_final: 0.8010 (t0) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 1.0973 time to fit residues: 99.3592 Evaluate side-chains 86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 38 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 220 HIS B 340 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108877 restraints weight = 8702.133| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.04 r_work: 0.3183 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6873 Z= 0.142 Angle : 0.501 6.704 9387 Z= 0.268 Chirality : 0.041 0.141 1110 Planarity : 0.003 0.034 1175 Dihedral : 9.231 168.266 983 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.91 % Allowed : 15.93 % Favored : 81.16 % 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: 1.26 (0.29), residues: 880 helix: 2.12 (0.27), residues: 397 sheet: 0.56 (0.41), residues: 174 loop : -0.69 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.006 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.011 0.001 TYR R 132 ARG 0.006 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 353) hydrogen bonds : angle 4.11067 ( 1035) SS BOND : bond 0.00218 ( 1) SS BOND : angle 1.00866 ( 2) covalent geometry : bond 0.00340 ( 6872) covalent geometry : angle 0.50107 ( 9385) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.811 Fit side-chains REVERT: A 25 LYS cc_start: 0.8251 (ttmm) cc_final: 0.7870 (ttpp) REVERT: B 35 ASN cc_start: 0.8500 (t160) cc_final: 0.8105 (t0) outliers start: 19 outliers final: 16 residues processed: 83 average time/residue: 1.0630 time to fit residues: 93.7815 Evaluate side-chains 88 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 26 optimal weight: 0.0870 chunk 74 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 340 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111403 restraints weight = 8589.762| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.14 r_work: 0.3224 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6873 Z= 0.091 Angle : 0.449 6.256 9387 Z= 0.240 Chirality : 0.039 0.134 1110 Planarity : 0.003 0.030 1175 Dihedral : 9.068 165.546 983 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.45 % Allowed : 16.08 % Favored : 81.47 % 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: 1.39 (0.29), residues: 880 helix: 2.23 (0.27), residues: 402 sheet: 0.58 (0.41), residues: 175 loop : -0.67 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.010 0.001 PHE A 222 TYR 0.008 0.001 TYR R 209 ARG 0.005 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 353) hydrogen bonds : angle 3.99595 ( 1035) SS BOND : bond 0.00225 ( 1) SS BOND : angle 1.02386 ( 2) covalent geometry : bond 0.00186 ( 6872) covalent geometry : angle 0.44899 ( 9385) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4949.06 seconds wall clock time: 84 minutes 58.38 seconds (5098.38 seconds total)