Starting phenix.real_space_refine on Wed Mar 4 00:55:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lw5_63431/03_2026/9lw5_63431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lw5_63431/03_2026/9lw5_63431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lw5_63431/03_2026/9lw5_63431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lw5_63431/03_2026/9lw5_63431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lw5_63431/03_2026/9lw5_63431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lw5_63431/03_2026/9lw5_63431.map" } resolution = 2.87 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= 0.093 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 59 5.16 5 C 6017 2.51 5 N 1620 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9418 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1843 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2473 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "G" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 363 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "S" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "N" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 930 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2112 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 22 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 ALDP R 401 " occ=0.50 ... (20 atoms not shown) pdb=" O2 BLDP R 401 " occ=0.50 Time building chain proxies: 2.33, per 1000 atoms: 0.25 Number of scatterers: 9418 At special positions: 0 Unit cell: (87.6825, 123.405, 132.065, 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 59 16.00 O 1722 8.00 N 1620 7.00 C 6017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 0.67 Conformation dependent library (CDL) restraints added in 280.2 milliseconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.9% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 4.098A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.513A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.598A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.544A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.553A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.604A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.553A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.588A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.793A 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 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.054A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.606A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'R' and resid 34 through 62 removed outlier: 4.309A pdb=" N GLU R 62 " --> pdb=" O ILE R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 86 removed outlier: 4.023A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'R' and resid 101 through 137 removed outlier: 4.335A pdb=" N TRP R 105 " --> pdb=" O PHE R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix removed outlier: 3.788A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 186 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 234 removed outlier: 3.751A pdb=" N GLN R 229 " --> pdb=" O GLU R 225 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.757A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU R 310 " --> pdb=" O GLU R 306 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix 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: 6.004A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.245A 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: 6.546A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.677A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.956A 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: 6.740A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.688A 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: 3.728A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.723A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.480A 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 232 removed outlier: 6.573A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.712A 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: 3.725A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 6 removed outlier: 3.558A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 4.949A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 4.949A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.595A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.532A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.942A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1347 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: 1.55 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3037 1.35 - 1.46: 2477 1.46 - 1.58: 4022 1.58 - 1.70: 2 1.70 - 1.82: 83 Bond restraints: 9621 Sorted by residual: bond pdb=" C3 BLDP R 401 " pdb=" C4 BLDP R 401 " ideal model delta sigma weight residual 1.400 1.303 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C3 ALDP R 401 " pdb=" C4 ALDP R 401 " ideal model delta sigma weight residual 1.400 1.309 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C7 BLDP R 401 " pdb=" C8 BLDP R 401 " ideal model delta sigma weight residual 1.528 1.612 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C3 BLDP R 401 " pdb=" O1 BLDP R 401 " ideal model delta sigma weight residual 1.353 1.430 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C3 ALDP R 401 " pdb=" O1 ALDP R 401 " ideal model delta sigma weight residual 1.353 1.424 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 9616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 12873 1.59 - 3.18: 175 3.18 - 4.77: 33 4.77 - 6.36: 11 6.36 - 7.95: 2 Bond angle restraints: 13094 Sorted by residual: angle pdb=" N MET S 192 " pdb=" CA MET S 192 " pdb=" C MET S 192 " ideal model delta sigma weight residual 110.80 118.75 -7.95 2.13e+00 2.20e-01 1.39e+01 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 108.30 5.60 1.80e+00 3.09e-01 9.68e+00 angle pdb=" N ASP R 113 " pdb=" CA ASP R 113 " pdb=" C ASP R 113 " ideal model delta sigma weight residual 111.14 107.95 3.19 1.08e+00 8.57e-01 8.73e+00 angle pdb=" C ASP R 300 " pdb=" N ASN R 301 " pdb=" CA ASN R 301 " ideal model delta sigma weight residual 123.91 128.80 -4.89 1.66e+00 3.63e-01 8.67e+00 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.63e+00 ... (remaining 13089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5159 16.81 - 33.61: 375 33.61 - 50.42: 60 50.42 - 67.22: 13 67.22 - 84.03: 10 Dihedral angle restraints: 5617 sinusoidal: 1996 harmonic: 3621 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -11.51 -74.49 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.26 34.74 1 1.00e+01 1.00e-02 1.71e+01 dihedral pdb=" CA ILE B 232 " pdb=" C ILE B 232 " pdb=" N CYS B 233 " pdb=" CA CYS B 233 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 5614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1309 0.059 - 0.118: 196 0.118 - 0.177: 10 0.177 - 0.237: 0 0.237 - 0.296: 2 Chirality restraints: 1517 Sorted by residual: chirality pdb=" CA ARG S 191 " pdb=" N ARG S 191 " pdb=" C ARG S 191 " pdb=" CB ARG S 191 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA MET S 192 " pdb=" N MET S 192 " pdb=" C MET S 192 " pdb=" CB MET S 192 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 1514 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 112 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C ILE R 112 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE R 112 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP R 113 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO S 236 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " -0.020 2.00e-02 2.50e+03 1.40e-02 3.90e+00 pdb=" CG TYR S 235 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " -0.003 2.00e-02 2.50e+03 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2391 2.80 - 3.32: 8453 3.32 - 3.85: 15382 3.85 - 4.37: 18533 4.37 - 4.90: 32547 Nonbonded interactions: 77306 Sorted by model distance: nonbonded pdb=" ND2 ASN B 119 " pdb=" O GLY B 144 " model vdw 2.270 3.120 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.293 3.120 nonbonded pdb=" OD1 ASN A 239 " pdb=" NZ LYS B 57 " model vdw 2.297 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.304 3.120 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.313 3.120 ... (remaining 77301 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=0.50 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: 1.620 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.003 0.097 9627 Z= 0.164 Angle : 0.518 7.946 13106 Z= 0.283 Chirality : 0.042 0.296 1517 Planarity : 0.003 0.054 1653 Dihedral : 12.480 84.029 3263 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.09 % 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 are not related in a simple way. whole: 0.09 (0.24), residues: 1225 helix: 0.65 (0.27), residues: 413 sheet: 0.46 (0.29), residues: 311 loop : -0.58 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 15 TYR 0.033 0.001 TYR S 235 PHE 0.012 0.001 PHE B 278 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9621) covalent geometry : angle 0.51713 (13094) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.85561 ( 12) hydrogen bonds : bond 0.20865 ( 462) hydrogen bonds : angle 7.00608 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.350 Fit side-chains REVERT: A 28 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7982 (mttm) REVERT: A 29 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8506 (tm-30) REVERT: A 380 ARG cc_start: 0.8444 (ttt-90) cc_final: 0.8207 (ttt90) REVERT: B 31 SER cc_start: 0.8971 (m) cc_final: 0.8709 (m) REVERT: B 46 ARG cc_start: 0.8111 (ptm-80) cc_final: 0.7810 (ptm160) REVERT: S 3 GLN cc_start: 0.8350 (pt0) cc_final: 0.8013 (pt0) REVERT: N 34 MET cc_start: 0.9368 (mmm) cc_final: 0.9127 (mmm) REVERT: R 156 MET cc_start: 0.7878 (mtm) cc_final: 0.7659 (mtp) REVERT: R 227 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8291 (mmtt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.5724 time to fit residues: 106.3066 Evaluate side-chains 128 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 119 ASN S 179 GLN ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.093147 restraints weight = 21172.261| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.43 r_work: 0.2782 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9627 Z= 0.164 Angle : 0.561 6.812 13106 Z= 0.304 Chirality : 0.043 0.223 1517 Planarity : 0.004 0.060 1653 Dihedral : 4.642 50.149 1350 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.09 % Allowed : 9.62 % Favored : 88.28 % 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 are not related in a simple way. whole: 0.40 (0.24), residues: 1225 helix: 1.14 (0.26), residues: 409 sheet: 0.49 (0.29), residues: 305 loop : -0.51 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 63 TYR 0.034 0.002 TYR S 235 PHE 0.012 0.001 PHE B 278 TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9621) covalent geometry : angle 0.56074 (13094) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.98436 ( 12) hydrogen bonds : bond 0.05226 ( 462) hydrogen bonds : angle 4.97036 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8481 (ttmt) cc_final: 0.7992 (mttm) REVERT: A 29 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8592 (tm-30) REVERT: B 46 ARG cc_start: 0.8508 (ptm-80) cc_final: 0.8225 (ptm160) REVERT: B 263 THR cc_start: 0.9093 (t) cc_final: 0.8707 (m) REVERT: S 3 GLN cc_start: 0.8849 (pt0) cc_final: 0.8410 (pt0) REVERT: R 63 ARG cc_start: 0.7967 (ttp-110) cc_final: 0.7661 (ttp-110) outliers start: 20 outliers final: 11 residues processed: 149 average time/residue: 0.5915 time to fit residues: 93.7141 Evaluate side-chains 142 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 105 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 294 GLN B 16 ASN R 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.094061 restraints weight = 15770.090| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.11 r_work: 0.2820 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9627 Z= 0.128 Angle : 0.512 6.319 13106 Z= 0.277 Chirality : 0.042 0.205 1517 Planarity : 0.004 0.057 1653 Dihedral : 4.491 45.813 1350 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.82 % Allowed : 11.72 % Favored : 85.46 % 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 are not related in a simple way. whole: 0.60 (0.24), residues: 1225 helix: 1.46 (0.26), residues: 409 sheet: 0.66 (0.29), residues: 303 loop : -0.59 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.031 0.001 TYR S 235 PHE 0.013 0.001 PHE R 61 TRP 0.012 0.001 TRP A 234 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9621) covalent geometry : angle 0.51102 (13094) SS BOND : bond 0.00166 ( 6) SS BOND : angle 0.97090 ( 12) hydrogen bonds : bond 0.04309 ( 462) hydrogen bonds : angle 4.57060 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8653 (mttm) REVERT: A 28 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8018 (mttm) REVERT: A 29 GLN cc_start: 0.8789 (tp-100) cc_final: 0.8453 (tm-30) REVERT: B 19 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.8059 (ttm170) REVERT: B 46 ARG cc_start: 0.8475 (ptm-80) cc_final: 0.8171 (ptm160) REVERT: B 258 ASP cc_start: 0.8671 (t0) cc_final: 0.8288 (t0) REVERT: B 263 THR cc_start: 0.9093 (t) cc_final: 0.8705 (m) REVERT: S 3 GLN cc_start: 0.8808 (pt0) cc_final: 0.8378 (pt0) REVERT: S 82 GLN cc_start: 0.8737 (tp40) cc_final: 0.8536 (mm-40) REVERT: S 192 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7487 (ptm) REVERT: R 63 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7380 (ttp-110) REVERT: R 331 ASP cc_start: 0.7776 (t0) cc_final: 0.7409 (t0) outliers start: 27 outliers final: 14 residues processed: 152 average time/residue: 0.5644 time to fit residues: 91.4179 Evaluate side-chains 143 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 148 ASN Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 16 ASN R 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097317 restraints weight = 20880.779| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.27 r_work: 0.2868 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9627 Z= 0.135 Angle : 0.516 6.447 13106 Z= 0.279 Chirality : 0.042 0.210 1517 Planarity : 0.004 0.058 1653 Dihedral : 4.451 41.837 1350 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.93 % Allowed : 13.39 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1225 helix: 1.61 (0.26), residues: 403 sheet: 0.72 (0.29), residues: 293 loop : -0.62 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.032 0.001 TYR S 235 PHE 0.016 0.001 PHE R 61 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9621) covalent geometry : angle 0.51537 (13094) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.93855 ( 12) hydrogen bonds : bond 0.04180 ( 462) hydrogen bonds : angle 4.43437 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7614 (mttm) REVERT: A 29 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8083 (tm-30) REVERT: B 19 ARG cc_start: 0.8133 (ttp-170) cc_final: 0.7918 (ttm170) REVERT: B 46 ARG cc_start: 0.8335 (ptm-80) cc_final: 0.8005 (ptm160) REVERT: B 258 ASP cc_start: 0.8522 (t0) cc_final: 0.8054 (t0) REVERT: B 263 THR cc_start: 0.9048 (t) cc_final: 0.8642 (m) REVERT: S 3 GLN cc_start: 0.8667 (pt0) cc_final: 0.8146 (pt0) REVERT: S 82 GLN cc_start: 0.8771 (tp40) cc_final: 0.8539 (mm-40) REVERT: R 63 ARG cc_start: 0.7601 (ttp-110) cc_final: 0.7164 (ttp-110) REVERT: R 65 GLN cc_start: 0.8865 (mt0) cc_final: 0.8393 (mt0) REVERT: R 331 ASP cc_start: 0.7772 (t0) cc_final: 0.7276 (t0) outliers start: 28 outliers final: 16 residues processed: 152 average time/residue: 0.5569 time to fit residues: 90.6166 Evaluate side-chains 151 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 16 ASN R 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.094464 restraints weight = 21797.258| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.35 r_work: 0.2831 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9627 Z= 0.195 Angle : 0.573 8.558 13106 Z= 0.308 Chirality : 0.044 0.260 1517 Planarity : 0.004 0.056 1653 Dihedral : 4.715 40.322 1350 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.77 % Allowed : 13.70 % Favored : 82.53 % 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 are not related in a simple way. whole: 0.56 (0.23), residues: 1225 helix: 1.54 (0.26), residues: 404 sheet: 0.47 (0.29), residues: 302 loop : -0.57 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.037 0.002 TYR S 235 PHE 0.016 0.002 PHE R 61 TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 9621) covalent geometry : angle 0.57227 (13094) SS BOND : bond 0.00231 ( 6) SS BOND : angle 1.13447 ( 12) hydrogen bonds : bond 0.04691 ( 462) hydrogen bonds : angle 4.55884 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.332 Fit side-chains REVERT: A 28 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7563 (mttm) REVERT: A 29 GLN cc_start: 0.8497 (tp-100) cc_final: 0.8074 (tm-30) REVERT: A 209 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6699 (mm-30) REVERT: B 46 ARG cc_start: 0.8321 (ptm-80) cc_final: 0.7792 (ptt90) REVERT: B 258 ASP cc_start: 0.8615 (t0) cc_final: 0.8177 (t0) REVERT: S 3 GLN cc_start: 0.8693 (pt0) cc_final: 0.8407 (pt0) REVERT: S 82 GLN cc_start: 0.8782 (tp40) cc_final: 0.8582 (mm-40) REVERT: S 147 VAL cc_start: 0.8435 (m) cc_final: 0.8153 (p) REVERT: S 192 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7596 (ptm) REVERT: S 235 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.5991 (t80) REVERT: R 63 ARG cc_start: 0.7787 (ttp-110) cc_final: 0.7330 (ttp-110) REVERT: R 331 ASP cc_start: 0.7634 (t0) cc_final: 0.7075 (t0) outliers start: 36 outliers final: 20 residues processed: 160 average time/residue: 0.5257 time to fit residues: 90.2213 Evaluate side-chains 155 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 294 GLN B 16 ASN R 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.094548 restraints weight = 15909.599| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.89 r_work: 0.2868 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9627 Z= 0.153 Angle : 0.542 6.701 13106 Z= 0.291 Chirality : 0.043 0.229 1517 Planarity : 0.004 0.055 1653 Dihedral : 4.597 37.440 1350 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.87 % Allowed : 14.54 % Favored : 81.59 % 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 are not related in a simple way. whole: 0.61 (0.23), residues: 1225 helix: 1.62 (0.26), residues: 404 sheet: 0.51 (0.29), residues: 301 loop : -0.58 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 283 TYR 0.034 0.001 TYR S 235 PHE 0.018 0.001 PHE R 61 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9621) covalent geometry : angle 0.54160 (13094) SS BOND : bond 0.00192 ( 6) SS BOND : angle 0.96464 ( 12) hydrogen bonds : bond 0.04320 ( 462) hydrogen bonds : angle 4.43611 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7646 (mttm) REVERT: A 29 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8152 (tm-30) REVERT: A 209 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6523 (mm-30) REVERT: B 36 ASN cc_start: 0.8383 (p0) cc_final: 0.7937 (m-40) REVERT: B 46 ARG cc_start: 0.8326 (ptm-80) cc_final: 0.7811 (ptt90) REVERT: B 258 ASP cc_start: 0.8575 (t0) cc_final: 0.8224 (t0) REVERT: S 3 GLN cc_start: 0.8683 (pt0) cc_final: 0.8176 (pt0) REVERT: S 82 GLN cc_start: 0.8938 (tp40) cc_final: 0.8713 (mm-40) REVERT: S 142 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: S 147 VAL cc_start: 0.8516 (m) cc_final: 0.8242 (p) REVERT: S 192 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7558 (ptm) REVERT: S 235 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.5756 (t80) REVERT: R 63 ARG cc_start: 0.7737 (ttp-110) cc_final: 0.7249 (ttp-110) REVERT: R 331 ASP cc_start: 0.7636 (t0) cc_final: 0.7015 (t0) outliers start: 37 outliers final: 23 residues processed: 152 average time/residue: 0.5270 time to fit residues: 85.9520 Evaluate side-chains 155 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 84 optimal weight: 0.0270 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 16 ASN R 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.094116 restraints weight = 16658.200| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.24 r_work: 0.2855 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9627 Z= 0.139 Angle : 0.530 6.762 13106 Z= 0.285 Chirality : 0.042 0.217 1517 Planarity : 0.004 0.055 1653 Dihedral : 4.500 34.729 1350 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.77 % Allowed : 15.17 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.23), residues: 1225 helix: 1.67 (0.26), residues: 404 sheet: 0.58 (0.29), residues: 296 loop : -0.62 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.033 0.001 TYR S 235 PHE 0.018 0.001 PHE R 61 TRP 0.012 0.001 TRP R 173 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9621) covalent geometry : angle 0.52971 (13094) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.91823 ( 12) hydrogen bonds : bond 0.04193 ( 462) hydrogen bonds : angle 4.37794 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7468 (mttm) REVERT: A 29 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8000 (tm-30) REVERT: A 209 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6538 (mm-30) REVERT: B 36 ASN cc_start: 0.8415 (p0) cc_final: 0.7933 (m-40) REVERT: B 46 ARG cc_start: 0.8293 (ptm-80) cc_final: 0.7756 (ptt90) REVERT: B 258 ASP cc_start: 0.8546 (t0) cc_final: 0.8145 (t0) REVERT: S 3 GLN cc_start: 0.8652 (pt0) cc_final: 0.8103 (pt0) REVERT: S 82 GLN cc_start: 0.8950 (tp40) cc_final: 0.8723 (mm-40) REVERT: S 147 VAL cc_start: 0.8432 (m) cc_final: 0.8155 (p) REVERT: S 192 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7467 (ptm) REVERT: S 235 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.5811 (t80) REVERT: R 63 ARG cc_start: 0.7523 (ttp-110) cc_final: 0.7127 (ttp-110) REVERT: R 331 ASP cc_start: 0.7537 (t0) cc_final: 0.7065 (t0) outliers start: 36 outliers final: 20 residues processed: 155 average time/residue: 0.5360 time to fit residues: 89.0490 Evaluate side-chains 153 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 0.0270 chunk 49 optimal weight: 0.8980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 16 ASN R 93 HIS R 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.099767 restraints weight = 20920.991| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.34 r_work: 0.2914 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9627 Z= 0.103 Angle : 0.500 11.149 13106 Z= 0.269 Chirality : 0.041 0.175 1517 Planarity : 0.003 0.055 1653 Dihedral : 4.261 30.919 1350 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.14 % Allowed : 15.48 % Favored : 81.38 % 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 are not related in a simple way. whole: 0.77 (0.23), residues: 1225 helix: 1.82 (0.26), residues: 404 sheet: 0.64 (0.29), residues: 295 loop : -0.57 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.029 0.001 TYR S 235 PHE 0.018 0.001 PHE R 61 TRP 0.013 0.001 TRP R 173 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9621) covalent geometry : angle 0.50021 (13094) SS BOND : bond 0.00176 ( 6) SS BOND : angle 0.70213 ( 12) hydrogen bonds : bond 0.03702 ( 462) hydrogen bonds : angle 4.22722 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.373 Fit side-chains REVERT: A 28 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7493 (mttm) REVERT: A 29 GLN cc_start: 0.8530 (tp-100) cc_final: 0.7795 (tp-100) REVERT: A 209 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6430 (mm-30) REVERT: B 19 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7927 (ttm170) REVERT: B 36 ASN cc_start: 0.8375 (p0) cc_final: 0.7868 (m-40) REVERT: B 46 ARG cc_start: 0.8290 (ptm-80) cc_final: 0.7646 (ptt90) REVERT: B 258 ASP cc_start: 0.8503 (t0) cc_final: 0.8166 (t0) REVERT: B 263 THR cc_start: 0.9139 (t) cc_final: 0.8635 (m) REVERT: B 337 LYS cc_start: 0.9286 (mttm) cc_final: 0.8901 (mttt) REVERT: S 3 GLN cc_start: 0.8633 (pt0) cc_final: 0.8114 (pt0) REVERT: S 82 GLN cc_start: 0.8944 (tp40) cc_final: 0.8725 (mm-40) REVERT: S 147 VAL cc_start: 0.8402 (m) cc_final: 0.8151 (p) REVERT: S 157 ILE cc_start: 0.8682 (mm) cc_final: 0.8459 (mt) REVERT: S 192 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7262 (ptm) REVERT: S 235 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.5710 (t80) REVERT: R 63 ARG cc_start: 0.7421 (ttp-110) cc_final: 0.7052 (ttp-110) REVERT: R 331 ASP cc_start: 0.7621 (t0) cc_final: 0.7283 (t0) outliers start: 30 outliers final: 19 residues processed: 157 average time/residue: 0.5167 time to fit residues: 87.1087 Evaluate side-chains 156 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 102 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 0.0470 chunk 9 optimal weight: 0.3980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 16 ASN N 35 ASN R 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100177 restraints weight = 21169.510| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.39 r_work: 0.2921 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9627 Z= 0.106 Angle : 0.514 14.427 13106 Z= 0.272 Chirality : 0.041 0.171 1517 Planarity : 0.003 0.056 1653 Dihedral : 4.162 27.456 1350 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.51 % Allowed : 17.15 % Favored : 80.33 % 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 are not related in a simple way. whole: 0.85 (0.24), residues: 1225 helix: 1.93 (0.26), residues: 404 sheet: 0.64 (0.29), residues: 296 loop : -0.54 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.029 0.001 TYR S 235 PHE 0.017 0.001 PHE R 61 TRP 0.014 0.001 TRP R 173 HIS 0.004 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9621) covalent geometry : angle 0.51370 (13094) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.70411 ( 12) hydrogen bonds : bond 0.03656 ( 462) hydrogen bonds : angle 4.19369 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.263 Fit side-chains REVERT: A 28 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7516 (mttm) REVERT: A 29 GLN cc_start: 0.8469 (tp-100) cc_final: 0.7770 (tp-100) REVERT: A 31 GLN cc_start: 0.7843 (tp40) cc_final: 0.7327 (tp-100) REVERT: A 209 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6365 (mm-30) REVERT: A 220 HIS cc_start: 0.7975 (m170) cc_final: 0.7630 (m-70) REVERT: B 19 ARG cc_start: 0.8146 (ttp-170) cc_final: 0.7932 (ttm170) REVERT: B 36 ASN cc_start: 0.8386 (p0) cc_final: 0.7921 (m-40) REVERT: B 46 ARG cc_start: 0.8302 (ptm-80) cc_final: 0.7726 (ptt90) REVERT: B 258 ASP cc_start: 0.8422 (t0) cc_final: 0.8039 (t0) REVERT: B 263 THR cc_start: 0.9116 (t) cc_final: 0.8707 (m) REVERT: S 3 GLN cc_start: 0.8642 (pt0) cc_final: 0.8129 (pt0) REVERT: S 82 GLN cc_start: 0.8925 (tp40) cc_final: 0.8649 (mm-40) REVERT: S 192 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7319 (ptt) REVERT: S 235 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.5734 (t80) REVERT: R 63 ARG cc_start: 0.7276 (ttp-110) cc_final: 0.6918 (ttp-110) REVERT: R 136 THR cc_start: 0.8161 (m) cc_final: 0.7546 (p) REVERT: R 225 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8131 (mm-30) REVERT: R 331 ASP cc_start: 0.7658 (t0) cc_final: 0.7376 (t0) outliers start: 24 outliers final: 18 residues processed: 155 average time/residue: 0.5060 time to fit residues: 84.3947 Evaluate side-chains 153 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 0.0370 chunk 100 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 16 ASN S 194 ASN N 35 ASN R 142 GLN R 301 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.097333 restraints weight = 15551.465| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.06 r_work: 0.2921 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9627 Z= 0.122 Angle : 0.532 12.374 13106 Z= 0.283 Chirality : 0.042 0.186 1517 Planarity : 0.004 0.056 1653 Dihedral : 4.204 26.662 1350 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.62 % Allowed : 17.26 % Favored : 80.13 % 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 are not related in a simple way. whole: 0.83 (0.24), residues: 1225 helix: 1.89 (0.26), residues: 404 sheet: 0.67 (0.29), residues: 291 loop : -0.55 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.031 0.001 TYR S 235 PHE 0.018 0.001 PHE R 61 TRP 0.017 0.001 TRP R 173 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9621) covalent geometry : angle 0.53131 (13094) SS BOND : bond 0.00214 ( 6) SS BOND : angle 0.75324 ( 12) hydrogen bonds : bond 0.03831 ( 462) hydrogen bonds : angle 4.22931 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.257 Fit side-chains REVERT: A 28 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7546 (mttm) REVERT: A 29 GLN cc_start: 0.8423 (tp40) cc_final: 0.7819 (tp-100) REVERT: A 31 GLN cc_start: 0.7773 (tp40) cc_final: 0.7314 (tp40) REVERT: A 209 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6406 (mm-30) REVERT: A 220 HIS cc_start: 0.7954 (m170) cc_final: 0.7602 (m-70) REVERT: B 19 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7910 (ttm170) REVERT: B 36 ASN cc_start: 0.8375 (p0) cc_final: 0.7921 (m-40) REVERT: B 46 ARG cc_start: 0.8287 (ptm-80) cc_final: 0.7713 (ptt90) REVERT: B 258 ASP cc_start: 0.8415 (t0) cc_final: 0.8023 (t0) REVERT: B 263 THR cc_start: 0.9139 (t) cc_final: 0.8675 (m) REVERT: S 3 GLN cc_start: 0.8632 (pt0) cc_final: 0.8117 (pt0) REVERT: S 147 VAL cc_start: 0.8390 (m) cc_final: 0.8158 (p) REVERT: S 192 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7333 (ptt) REVERT: S 194 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7968 (m110) REVERT: S 235 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.5794 (t80) REVERT: R 63 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.6909 (ttp-110) REVERT: R 178 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7246 (p90) REVERT: R 225 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8042 (mm-30) REVERT: R 331 ASP cc_start: 0.7655 (t0) cc_final: 0.7402 (t0) outliers start: 25 outliers final: 17 residues processed: 150 average time/residue: 0.5294 time to fit residues: 85.2104 Evaluate side-chains 153 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 178 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 3.9990 chunk 84 optimal weight: 0.0470 chunk 117 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN S 82 GLN S 194 ASN N 35 ASN R 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.097365 restraints weight = 21756.455| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.52 r_work: 0.2808 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9627 Z= 0.129 Angle : 0.546 15.717 13106 Z= 0.288 Chirality : 0.042 0.194 1517 Planarity : 0.004 0.056 1653 Dihedral : 4.268 26.487 1350 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.93 % Allowed : 17.15 % Favored : 79.92 % 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 are not related in a simple way. whole: 0.82 (0.23), residues: 1225 helix: 1.88 (0.26), residues: 404 sheet: 0.65 (0.29), residues: 291 loop : -0.55 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.031 0.001 TYR S 235 PHE 0.017 0.001 PHE R 61 TRP 0.018 0.001 TRP R 173 HIS 0.004 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9621) covalent geometry : angle 0.54517 (13094) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.85914 ( 12) hydrogen bonds : bond 0.03926 ( 462) hydrogen bonds : angle 4.26246 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3609.61 seconds wall clock time: 62 minutes 1.20 seconds (3721.20 seconds total)