Starting phenix.real_space_refine on Fri Oct 10 16:38:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ww2_37881/10_2025/8ww2_37881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ww2_37881/10_2025/8ww2_37881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ww2_37881/10_2025/8ww2_37881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ww2_37881/10_2025/8ww2_37881.map" model { file = "/net/cci-nas-00/data/ceres_data/8ww2_37881/10_2025/8ww2_37881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ww2_37881/10_2025/8ww2_37881.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.164 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 55 5.16 5 C 4950 2.51 5 N 1331 2.21 5 O 1456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7792 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2565 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 406 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 965 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1973 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {'OLA': 1, 'PLM': 1, 'Y01': 1} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Time building chain proxies: 1.97, per 1000 atoms: 0.25 Number of scatterers: 7792 At special positions: 0 Unit cell: (78.1, 101.2, 134.2, 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 55 16.00 O 1456 8.00 N 1331 7.00 C 4950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 177 " - pdb=" SG CYS R 184 " 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: 0.51 Conformation dependent library (CDL) restraints added in 342.8 milliseconds Enol-peptide restraints added in 1.4 microseconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 39.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.658A pdb=" N LYS A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.662A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.777A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.797A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.641A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.747A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.509A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.555A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.985A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.627A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.592A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.514A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.548A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 67 removed outlier: 3.811A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 92 Processing helix chain 'R' and resid 106 through 140 Processing helix chain 'R' and resid 141 through 144 removed outlier: 3.816A pdb=" N TYR R 144 " --> pdb=" O ALA R 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 146 through 167 removed outlier: 3.883A pdb=" N VAL R 150 " --> pdb=" O SER R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 230 removed outlier: 4.156A pdb=" N GLN R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 270 removed outlier: 4.020A pdb=" N PHE R 256 " --> pdb=" O VAL R 252 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) Proline residue: R 262 - end of helix removed outlier: 3.684A pdb=" N LEU R 268 " --> pdb=" O THR R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 283 removed outlier: 4.257A pdb=" N THR R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 298 removed outlier: 4.381A pdb=" N SER R 290 " --> pdb=" O ALA R 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET R 291 " --> pdb=" O THR R 287 " (cutoff:3.500A) Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.341A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.870A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.593A 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: 7.081A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.919A 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: 6.865A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.156A 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 153 removed outlier: 6.727A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.037A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.420A 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: 6.878A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.950A 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: 3.869A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.032A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1059 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: 1.28 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2365 1.34 - 1.46: 1302 1.46 - 1.58: 4196 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 7940 Sorted by residual: bond pdb=" N VAL R 94 " pdb=" CA VAL R 94 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.35e-02 5.49e+03 7.32e+00 bond pdb=" N LEU R 95 " pdb=" CA LEU R 95 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.26e+00 bond pdb=" N LEU R 93 " pdb=" CA LEU R 93 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.05e+00 bond pdb=" N HIS R 96 " pdb=" CA HIS R 96 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.42e-02 4.96e+03 5.87e+00 bond pdb=" N THR R 279 " pdb=" CA THR R 279 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.60e+00 ... (remaining 7935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10390 1.68 - 3.35: 341 3.35 - 5.03: 46 5.03 - 6.71: 13 6.71 - 8.38: 3 Bond angle restraints: 10793 Sorted by residual: angle pdb=" N VAL R 100 " pdb=" CA VAL R 100 " pdb=" C VAL R 100 " ideal model delta sigma weight residual 113.10 108.68 4.42 9.70e-01 1.06e+00 2.07e+01 angle pdb=" N ILE R 103 " pdb=" CA ILE R 103 " pdb=" C ILE R 103 " ideal model delta sigma weight residual 113.71 110.13 3.58 9.50e-01 1.11e+00 1.42e+01 angle pdb=" N VAL R 94 " pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 112.29 108.87 3.42 9.40e-01 1.13e+00 1.32e+01 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 121.98 116.53 5.45 1.53e+00 4.27e-01 1.27e+01 angle pdb=" N PHE R 97 " pdb=" CA PHE R 97 " pdb=" C PHE R 97 " ideal model delta sigma weight residual 113.55 109.28 4.27 1.26e+00 6.30e-01 1.15e+01 ... (remaining 10788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 4266 16.43 - 32.86: 385 32.86 - 49.29: 71 49.29 - 65.72: 20 65.72 - 82.15: 14 Dihedral angle restraints: 4756 sinusoidal: 1808 harmonic: 2948 Sorted by residual: dihedral pdb=" CB CYS R 177 " pdb=" SG CYS R 177 " pdb=" SG CYS R 184 " pdb=" CB CYS R 184 " ideal model delta sinusoidal sigma weight residual -86.00 -153.70 67.70 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CA LYS B 127 " pdb=" C LYS B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LEU B 139 " pdb=" C LEU B 139 " pdb=" N ALA B 140 " pdb=" CA ALA B 140 " ideal model delta harmonic sigma weight residual 180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1011 0.057 - 0.115: 212 0.115 - 0.172: 31 0.172 - 0.229: 1 0.229 - 0.287: 2 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CBG Y01 R 602 " pdb=" CAQ Y01 R 602 " pdb=" CBD Y01 R 602 " pdb=" CBI Y01 R 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.62 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CBF Y01 R 602 " pdb=" CAS Y01 R 602 " pdb=" CBD Y01 R 602 " pdb=" CBH Y01 R 602 " both_signs ideal model delta sigma weight residual False -2.45 -2.68 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CBE Y01 R 602 " pdb=" CAP Y01 R 602 " pdb=" CBB Y01 R 602 " pdb=" CBI Y01 R 602 " both_signs ideal model delta sigma weight residual False 2.57 2.77 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1254 not shown) Planarity restraints: 1375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA R 601 " -0.039 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C11 OLA R 601 " 0.017 2.00e-02 2.50e+03 pdb=" C8 OLA R 601 " -0.017 2.00e-02 2.50e+03 pdb=" C9 OLA R 601 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO G 60 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 236 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 ... (remaining 1372 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 9 2.43 - 3.05: 4501 3.05 - 3.66: 10444 3.66 - 4.28: 15904 4.28 - 4.90: 27810 Nonbonded interactions: 58668 Sorted by model distance: nonbonded pdb=" O LEU R 95 " pdb=" CD1 LEU R 112 " model vdw 1.809 3.460 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASN A 239 " pdb=" NZ LYS B 57 " model vdw 2.287 3.120 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.301 3.120 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.332 3.040 ... (remaining 58663 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: 1.570 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 0.045 7943 Z= 0.206 Angle : 0.714 8.383 10799 Z= 0.409 Chirality : 0.048 0.287 1257 Planarity : 0.005 0.051 1375 Dihedral : 13.756 82.154 2845 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.26), residues: 1004 helix: 1.59 (0.28), residues: 360 sheet: 0.52 (0.35), residues: 232 loop : -1.66 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.020 0.002 TYR B 59 PHE 0.022 0.002 PHE N 108 TRP 0.031 0.002 TRP B 82 HIS 0.012 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7940) covalent geometry : angle 0.71400 (10793) SS BOND : bond 0.00635 ( 3) SS BOND : angle 1.08834 ( 6) hydrogen bonds : bond 0.12793 ( 368) hydrogen bonds : angle 5.48110 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.305 Fit side-chains REVERT: B 134 ARG cc_start: 0.6840 (ptp-110) cc_final: 0.6583 (pmt170) REVERT: R 118 MET cc_start: 0.6560 (ttp) cc_final: 0.6210 (ttm) outliers start: 0 outliers final: 1 residues processed: 105 average time/residue: 0.6589 time to fit residues: 72.6494 Evaluate side-chains 94 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.174073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131086 restraints weight = 7798.552| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.07 r_work: 0.3201 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7943 Z= 0.130 Angle : 0.538 10.850 10799 Z= 0.292 Chirality : 0.043 0.175 1257 Planarity : 0.005 0.058 1375 Dihedral : 6.679 59.561 1201 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.24 % Allowed : 7.43 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.27), residues: 1004 helix: 1.98 (0.28), residues: 362 sheet: 0.76 (0.36), residues: 227 loop : -1.49 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 197 TYR 0.012 0.001 TYR R 139 PHE 0.016 0.001 PHE N 108 TRP 0.024 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7940) covalent geometry : angle 0.53806 (10793) SS BOND : bond 0.00504 ( 3) SS BOND : angle 0.79581 ( 6) hydrogen bonds : bond 0.06527 ( 368) hydrogen bonds : angle 4.29215 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.304 Fit side-chains REVERT: A 314 GLU cc_start: 0.6697 (pm20) cc_final: 0.6205 (pm20) REVERT: A 356 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7357 (mtm180) REVERT: B 134 ARG cc_start: 0.7522 (ptp-110) cc_final: 0.6474 (pmt170) REVERT: B 214 ARG cc_start: 0.7971 (mmt180) cc_final: 0.7768 (mtm-85) REVERT: N 35 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8118 (OUTLIER) REVERT: R 118 MET cc_start: 0.6369 (ttp) cc_final: 0.5977 (ttm) REVERT: R 283 LEU cc_start: 0.7231 (tp) cc_final: 0.6912 (tm) outliers start: 10 outliers final: 5 residues processed: 102 average time/residue: 0.7103 time to fit residues: 76.0786 Evaluate side-chains 100 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 269 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN R 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.175027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131975 restraints weight = 7742.811| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.88 r_work: 0.3266 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7943 Z= 0.112 Angle : 0.484 6.631 10799 Z= 0.264 Chirality : 0.042 0.140 1257 Planarity : 0.004 0.054 1375 Dihedral : 6.405 59.491 1199 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.61 % Allowed : 9.65 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.27), residues: 1004 helix: 2.27 (0.28), residues: 362 sheet: 0.87 (0.36), residues: 227 loop : -1.25 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.009 0.001 TYR R 213 PHE 0.013 0.001 PHE A 212 TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7940) covalent geometry : angle 0.48383 (10793) SS BOND : bond 0.00482 ( 3) SS BOND : angle 0.63990 ( 6) hydrogen bonds : bond 0.05673 ( 368) hydrogen bonds : angle 3.99842 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.190 Fit side-chains REVERT: A 28 ARG cc_start: 0.7768 (ptp-110) cc_final: 0.6959 (mtm-85) REVERT: A 229 ASP cc_start: 0.6447 (t0) cc_final: 0.5965 (t70) REVERT: A 314 GLU cc_start: 0.6711 (pm20) cc_final: 0.6509 (pm20) REVERT: A 356 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7373 (mtm180) REVERT: B 59 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8231 (t80) REVERT: B 134 ARG cc_start: 0.7512 (ptp-110) cc_final: 0.6468 (pmt170) REVERT: B 137 ARG cc_start: 0.8000 (tpt170) cc_final: 0.7721 (tpp-160) REVERT: B 217 MET cc_start: 0.8551 (pmm) cc_final: 0.8292 (pmt) REVERT: N 35 ASN cc_start: 0.8706 (p0) cc_final: 0.8223 (p0) REVERT: R 118 MET cc_start: 0.6475 (ttp) cc_final: 0.6085 (ttm) REVERT: R 283 LEU cc_start: 0.7251 (tp) cc_final: 0.6912 (tm) outliers start: 13 outliers final: 6 residues processed: 105 average time/residue: 0.6517 time to fit residues: 72.0413 Evaluate side-chains 100 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.175096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130956 restraints weight = 7872.264| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.07 r_work: 0.3199 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7943 Z= 0.117 Angle : 0.489 5.527 10799 Z= 0.267 Chirality : 0.042 0.136 1257 Planarity : 0.004 0.054 1375 Dihedral : 6.228 58.402 1199 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.49 % Allowed : 11.39 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.27), residues: 1004 helix: 2.41 (0.28), residues: 362 sheet: 0.79 (0.36), residues: 226 loop : -1.09 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.011 0.001 TYR R 139 PHE 0.017 0.001 PHE N 108 TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 7940) covalent geometry : angle 0.48890 (10793) SS BOND : bond 0.00548 ( 3) SS BOND : angle 0.69852 ( 6) hydrogen bonds : bond 0.05779 ( 368) hydrogen bonds : angle 3.93018 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.308 Fit side-chains REVERT: A 28 ARG cc_start: 0.7678 (ptp-110) cc_final: 0.6957 (mtm-85) REVERT: A 314 GLU cc_start: 0.6720 (pm20) cc_final: 0.6487 (pm20) REVERT: A 356 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7389 (mtm180) REVERT: B 59 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8337 (t80) REVERT: B 134 ARG cc_start: 0.7556 (ptp-110) cc_final: 0.6470 (pmt170) REVERT: B 186 ASP cc_start: 0.8257 (m-30) cc_final: 0.8044 (m-30) REVERT: N 35 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8231 (p0) REVERT: R 118 MET cc_start: 0.6413 (ttp) cc_final: 0.6012 (ttm) outliers start: 12 outliers final: 9 residues processed: 102 average time/residue: 0.6877 time to fit residues: 73.7418 Evaluate side-chains 107 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.175058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131059 restraints weight = 7697.799| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.05 r_work: 0.3196 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7943 Z= 0.116 Angle : 0.482 5.535 10799 Z= 0.263 Chirality : 0.042 0.137 1257 Planarity : 0.004 0.054 1375 Dihedral : 6.038 56.738 1199 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.98 % Allowed : 12.62 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.27), residues: 1004 helix: 2.45 (0.28), residues: 368 sheet: 0.84 (0.36), residues: 229 loop : -1.00 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.010 0.001 TYR R 213 PHE 0.015 0.001 PHE N 108 TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7940) covalent geometry : angle 0.48155 (10793) SS BOND : bond 0.00551 ( 3) SS BOND : angle 0.67062 ( 6) hydrogen bonds : bond 0.05686 ( 368) hydrogen bonds : angle 3.86454 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.298 Fit side-chains REVERT: A 28 ARG cc_start: 0.7789 (ptp-110) cc_final: 0.7048 (mtm-85) REVERT: A 314 GLU cc_start: 0.6751 (pm20) cc_final: 0.6501 (pm20) REVERT: A 356 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7354 (mtm180) REVERT: B 19 ARG cc_start: 0.7124 (ttp-170) cc_final: 0.6921 (ttp-170) REVERT: B 59 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 186 ASP cc_start: 0.8245 (m-30) cc_final: 0.8028 (m-30) REVERT: B 214 ARG cc_start: 0.7873 (mtp-110) cc_final: 0.7434 (mmt180) REVERT: B 217 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7607 (ppp) REVERT: N 35 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8254 (OUTLIER) REVERT: N 80 TYR cc_start: 0.8218 (m-80) cc_final: 0.7841 (m-80) REVERT: R 118 MET cc_start: 0.6416 (ttp) cc_final: 0.6009 (ttm) outliers start: 16 outliers final: 10 residues processed: 106 average time/residue: 0.6289 time to fit residues: 70.3055 Evaluate side-chains 105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 0.0020 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.171048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125450 restraints weight = 7757.257| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.90 r_work: 0.3177 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7943 Z= 0.179 Angle : 0.590 8.748 10799 Z= 0.318 Chirality : 0.045 0.167 1257 Planarity : 0.005 0.053 1375 Dihedral : 6.370 57.677 1199 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.98 % Allowed : 13.49 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.27), residues: 1004 helix: 2.30 (0.28), residues: 366 sheet: 0.67 (0.35), residues: 236 loop : -1.10 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.016 0.002 TYR R 213 PHE 0.026 0.002 PHE N 108 TRP 0.018 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7940) covalent geometry : angle 0.58998 (10793) SS BOND : bond 0.00837 ( 3) SS BOND : angle 1.05712 ( 6) hydrogen bonds : bond 0.07394 ( 368) hydrogen bonds : angle 4.13375 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.178 Fit side-chains REVERT: A 28 ARG cc_start: 0.7892 (ptp-110) cc_final: 0.7058 (mtm-85) REVERT: A 314 GLU cc_start: 0.6776 (pm20) cc_final: 0.6570 (pm20) REVERT: A 356 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7503 (mtm180) REVERT: B 59 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8525 (t80) REVERT: B 217 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7738 (ppp) REVERT: R 118 MET cc_start: 0.6550 (ttp) cc_final: 0.6133 (ttm) REVERT: R 231 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6664 (mpp80) REVERT: R 249 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7439 (mp) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.6446 time to fit residues: 69.0704 Evaluate side-chains 109 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 231 ARG Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 79 optimal weight: 0.0060 chunk 16 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.176042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131976 restraints weight = 7794.626| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.03 r_work: 0.3213 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7943 Z= 0.103 Angle : 0.457 4.991 10799 Z= 0.252 Chirality : 0.041 0.140 1257 Planarity : 0.004 0.054 1375 Dihedral : 5.892 56.273 1199 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.49 % Allowed : 14.60 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.27), residues: 1004 helix: 2.66 (0.28), residues: 360 sheet: 0.77 (0.35), residues: 236 loop : -0.96 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.008 0.001 TYR R 213 PHE 0.012 0.001 PHE A 212 TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 7940) covalent geometry : angle 0.45649 (10793) SS BOND : bond 0.00455 ( 3) SS BOND : angle 0.54105 ( 6) hydrogen bonds : bond 0.05293 ( 368) hydrogen bonds : angle 3.78776 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.286 Fit side-chains REVERT: A 28 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7016 (mtm-85) REVERT: A 314 GLU cc_start: 0.6769 (pm20) cc_final: 0.6506 (pm20) REVERT: A 356 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7350 (mtm180) REVERT: B 59 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8277 (t80) REVERT: B 186 ASP cc_start: 0.8198 (m-30) cc_final: 0.7878 (m-30) REVERT: N 35 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.7975 (p0) REVERT: N 80 TYR cc_start: 0.8168 (m-80) cc_final: 0.7840 (m-80) REVERT: R 118 MET cc_start: 0.6267 (ttp) cc_final: 0.5878 (ttm) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 0.6283 time to fit residues: 68.3235 Evaluate side-chains 104 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN B 32 GLN R 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.169054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125394 restraints weight = 7757.487| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.97 r_work: 0.3164 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7943 Z= 0.230 Angle : 0.673 11.129 10799 Z= 0.360 Chirality : 0.047 0.161 1257 Planarity : 0.005 0.073 1375 Dihedral : 6.558 59.667 1199 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.10 % Allowed : 14.60 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.26), residues: 1004 helix: 2.13 (0.27), residues: 363 sheet: 0.76 (0.35), residues: 231 loop : -1.12 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.018 0.002 TYR R 213 PHE 0.029 0.003 PHE N 108 TRP 0.017 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 7940) covalent geometry : angle 0.67233 (10793) SS BOND : bond 0.01054 ( 3) SS BOND : angle 1.18344 ( 6) hydrogen bonds : bond 0.08428 ( 368) hydrogen bonds : angle 4.25823 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.250 Fit side-chains REVERT: A 229 ASP cc_start: 0.6837 (t0) cc_final: 0.6605 (t0) REVERT: A 314 GLU cc_start: 0.6818 (pm20) cc_final: 0.6614 (pm20) REVERT: A 356 ARG cc_start: 0.8404 (mtp180) cc_final: 0.7675 (mtm180) REVERT: B 59 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8522 (t80) REVERT: B 165 THR cc_start: 0.9040 (m) cc_final: 0.8597 (t) REVERT: N 35 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8420 (p0) REVERT: R 118 MET cc_start: 0.6693 (ttp) cc_final: 0.6260 (ttm) REVERT: R 231 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6654 (mpp80) REVERT: R 249 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7404 (mp) outliers start: 17 outliers final: 10 residues processed: 105 average time/residue: 0.6366 time to fit residues: 70.3422 Evaluate side-chains 108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 231 ARG Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN B 32 GLN R 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.173325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129352 restraints weight = 7657.306| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.03 r_work: 0.3172 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7943 Z= 0.127 Angle : 0.509 5.826 10799 Z= 0.279 Chirality : 0.042 0.143 1257 Planarity : 0.004 0.052 1375 Dihedral : 6.140 57.680 1199 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.49 % Allowed : 15.35 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.27), residues: 1004 helix: 2.46 (0.28), residues: 360 sheet: 0.73 (0.35), residues: 236 loop : -1.05 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.012 0.001 TYR R 139 PHE 0.017 0.001 PHE N 108 TRP 0.022 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7940) covalent geometry : angle 0.50918 (10793) SS BOND : bond 0.00615 ( 3) SS BOND : angle 0.72260 ( 6) hydrogen bonds : bond 0.06318 ( 368) hydrogen bonds : angle 3.97218 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.317 Fit side-chains REVERT: A 314 GLU cc_start: 0.6756 (pm20) cc_final: 0.6491 (pm20) REVERT: A 356 ARG cc_start: 0.8226 (mtp180) cc_final: 0.7428 (mtm180) REVERT: B 59 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8358 (t80) REVERT: B 165 THR cc_start: 0.8962 (m) cc_final: 0.8412 (t) REVERT: B 188 MET cc_start: 0.9038 (mmp) cc_final: 0.8763 (mmm) REVERT: N 35 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8040 (p0) REVERT: R 118 MET cc_start: 0.6391 (ttp) cc_final: 0.6003 (ttm) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.6530 time to fit residues: 71.5457 Evaluate side-chains 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 0.3980 chunk 76 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 25 optimal weight: 0.0570 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 213 GLN R 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.177735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132941 restraints weight = 7715.795| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.90 r_work: 0.3255 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7943 Z= 0.098 Angle : 0.445 4.984 10799 Z= 0.244 Chirality : 0.041 0.141 1257 Planarity : 0.004 0.053 1375 Dihedral : 5.762 59.911 1199 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 15.72 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.27), residues: 1004 helix: 2.73 (0.28), residues: 360 sheet: 0.81 (0.35), residues: 236 loop : -0.88 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.014 0.001 TYR R 139 PHE 0.011 0.001 PHE A 212 TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 7940) covalent geometry : angle 0.44459 (10793) SS BOND : bond 0.00402 ( 3) SS BOND : angle 0.46907 ( 6) hydrogen bonds : bond 0.04849 ( 368) hydrogen bonds : angle 3.69494 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.299 Fit side-chains REVERT: A 314 GLU cc_start: 0.6760 (pm20) cc_final: 0.6492 (pm20) REVERT: A 356 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7244 (mtm180) REVERT: B 59 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8204 (t80) REVERT: B 186 ASP cc_start: 0.8108 (m-30) cc_final: 0.7857 (m-30) REVERT: B 214 ARG cc_start: 0.7647 (mtp-110) cc_final: 0.7047 (mpt-90) REVERT: N 35 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.7838 (p0) REVERT: N 80 TYR cc_start: 0.8142 (m-80) cc_final: 0.7833 (m-80) REVERT: R 118 MET cc_start: 0.6160 (ttp) cc_final: 0.5784 (ttm) REVERT: R 266 TYR cc_start: 0.7240 (t80) cc_final: 0.7040 (t80) outliers start: 9 outliers final: 7 residues processed: 106 average time/residue: 0.6426 time to fit residues: 71.7970 Evaluate side-chains 104 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 86 optimal weight: 0.0470 chunk 63 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN R 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.175835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132298 restraints weight = 7743.633| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.07 r_work: 0.3206 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7943 Z= 0.114 Angle : 0.477 5.646 10799 Z= 0.260 Chirality : 0.041 0.140 1257 Planarity : 0.004 0.052 1375 Dihedral : 5.801 59.876 1199 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.87 % Allowed : 16.09 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.27), residues: 1004 helix: 2.67 (0.27), residues: 366 sheet: 0.80 (0.35), residues: 236 loop : -0.83 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.009 0.001 TYR R 213 PHE 0.015 0.001 PHE N 108 TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7940) covalent geometry : angle 0.47714 (10793) SS BOND : bond 0.00542 ( 3) SS BOND : angle 0.59648 ( 6) hydrogen bonds : bond 0.05403 ( 368) hydrogen bonds : angle 3.74531 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3196.81 seconds wall clock time: 55 minutes 6.09 seconds (3306.09 seconds total)