Starting phenix.real_space_refine on Thu Jul 2 19:58:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f2a_28810/07_2026/8f2a_28810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2a_28810/07_2026/8f2a_28810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f2a_28810/07_2026/8f2a_28810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2a_28810/07_2026/8f2a_28810.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8f2a_28810/07_2026/8f2a_28810.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f2a_28810/07_2026/8f2a_28810.cif" model { file = "/net/cci-nas-00/data/ceres_data/8f2a_28810/07_2026/8f2a_28810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2a_28810/07_2026/8f2a_28810.cif" } resolution = 2.2 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= 0.100 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 75 5.16 5 C 6392 2.51 5 N 1734 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10044 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 810 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 59 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 279 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2996 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1899 Classifications: {'peptide': 231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.70, per 1000 atoms: 0.17 Number of scatterers: 10044 At special positions: 0 Unit cell: (93.4375, 168.188, 92.625, 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 75 16.00 O 1843 8.00 N 1734 7.00 C 6392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 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=1, symmetry=0 Links applied NAG-ASN " NAG E 201 " - " ASN E 29 " " NAG E 202 " - " ASN E 71 " " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 295.9 milliseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 43.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'E' and resid 29 through 37 removed outlier: 3.707A pdb=" N MET E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 48 removed outlier: 3.555A pdb=" N GLY E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 63 removed outlier: 3.565A pdb=" N ILE E 63 " --> pdb=" O SER E 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 60 through 63' Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.848A pdb=" N THR E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 101 removed outlier: 3.605A pdb=" N GLN E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 120 through 141 Proline residue: E 126 - end of helix removed outlier: 3.613A pdb=" N VAL E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 16 Processing helix chain 'R' and resid 42 through 62 removed outlier: 3.589A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.332A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.612A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 204 removed outlier: 3.536A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.720A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG R 213 " --> pdb=" O GLY R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.812A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.620A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.644A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.632A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.831A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.232A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.833A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.793A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.975A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.553A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'R' and resid 89 through 94 removed outlier: 3.565A pdb=" N VAL R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.319A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.537A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.530A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.824A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.502A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.859A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.579A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.800A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.075A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1380 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: 1.32 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3261 1.34 - 1.46: 2532 1.46 - 1.58: 4382 1.58 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 10281 Sorted by residual: bond pdb=" N VAL R 171 " pdb=" CA VAL R 171 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.28e-02 6.10e+03 7.46e+00 bond pdb=" N ILE B 338 " pdb=" CA ILE B 338 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.18e+00 bond pdb=" N LYS A 24 " pdb=" CA LYS A 24 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.66e+00 bond pdb=" N LEU A 30 " pdb=" CA LEU A 30 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.63e+00 ... (remaining 10276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 13562 1.56 - 3.12: 340 3.12 - 4.68: 51 4.68 - 6.24: 8 6.24 - 7.80: 2 Bond angle restraints: 13963 Sorted by residual: angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 111.81 107.88 3.93 8.60e-01 1.35e+00 2.08e+01 angle pdb=" N HIS B 311 " pdb=" CA HIS B 311 " pdb=" C HIS B 311 " ideal model delta sigma weight residual 110.10 116.66 -6.56 1.49e+00 4.50e-01 1.94e+01 angle pdb=" N ARG R 174 " pdb=" CA ARG R 174 " pdb=" C ARG R 174 " ideal model delta sigma weight residual 112.54 107.20 5.34 1.22e+00 6.72e-01 1.91e+01 angle pdb=" CA GLY R 177 " pdb=" C GLY R 177 " pdb=" O GLY R 177 " ideal model delta sigma weight residual 121.41 118.14 3.27 8.80e-01 1.29e+00 1.38e+01 angle pdb=" N LEU R 176 " pdb=" CA LEU R 176 " pdb=" C LEU R 176 " ideal model delta sigma weight residual 112.54 108.15 4.39 1.22e+00 6.72e-01 1.29e+01 ... (remaining 13958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5496 17.59 - 35.18: 434 35.18 - 52.77: 86 52.77 - 70.36: 22 70.36 - 87.96: 10 Dihedral angle restraints: 6048 sinusoidal: 2330 harmonic: 3718 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 93.00 161.90 -68.90 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -27.97 -58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 130.91 -37.91 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1348 0.061 - 0.122: 185 0.122 - 0.183: 20 0.183 - 0.243: 4 0.243 - 0.304: 3 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA HIS B 311 " pdb=" N HIS B 311 " pdb=" C HIS B 311 " pdb=" CB HIS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LEU B 308 " pdb=" N LEU B 308 " pdb=" C LEU B 308 " pdb=" CB LEU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LEU B 336 " pdb=" N LEU B 336 " pdb=" C LEU B 336 " pdb=" CB LEU B 336 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1557 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 312 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.21e+00 pdb=" C ASP B 312 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP B 312 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN B 313 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 269 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO R 270 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 270 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 270 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO B 236 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.023 5.00e-02 4.00e+02 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 484 2.73 - 3.27: 10204 3.27 - 3.82: 16920 3.82 - 4.36: 21980 4.36 - 4.90: 35913 Nonbonded interactions: 85501 Sorted by model distance: nonbonded pdb=" OE1 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.188 3.040 nonbonded pdb=" OD1 ASN R 130 " pdb=" OG1 THR R 132 " model vdw 2.252 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.253 3.120 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.289 3.040 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.292 3.120 ... (remaining 85496 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.630 Find NCS groups from input model: 0.050 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:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 10296 Z= 0.236 Angle : 0.609 7.805 13995 Z= 0.385 Chirality : 0.046 0.304 1560 Planarity : 0.003 0.043 1783 Dihedral : 13.840 87.956 3618 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.76 % Allowed : 6.84 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.70 (0.20), residues: 1258 helix: -2.68 (0.16), residues: 497 sheet: -0.61 (0.31), residues: 237 loop : -1.20 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.009 0.001 TYR R 391 PHE 0.012 0.001 PHE B 151 TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.21 (10281) covalent geometry : angle 0.60232 / 0.38 (13963) SS BOND : bond 0.00384 / 0.27 ( 10) SS BOND : angle 1.75862 / 1.05 ( 20) hydrogen bonds : bond 0.25497 / 17.21 ( 488) hydrogen bonds : angle 8.83156 / 6.44 ( 1380) Misc. bond : bond 0.10567 / 5.56 ( 1) link_NAG-ASN : bond 0.00160 / 0.08 ( 4) link_NAG-ASN : angle 2.16008 / 1.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7464 (mp10) cc_final: 0.7243 (mp10) REVERT: R 94 PHE cc_start: 0.6972 (m-80) cc_final: 0.6592 (m-10) REVERT: R 260 ARG cc_start: 0.6683 (ptp-170) cc_final: 0.6350 (ptp-110) REVERT: R 314 PHE cc_start: 0.7770 (m-80) cc_final: 0.7160 (t80) REVERT: R 340 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7114 (mttp) REVERT: R 399 GLN cc_start: 0.6784 (mt0) cc_final: 0.6565 (mt0) REVERT: R 405 GLN cc_start: 0.7592 (mt0) cc_final: 0.6841 (tp40) REVERT: A 55 THR cc_start: 0.8407 (m) cc_final: 0.8010 (m) REVERT: A 356 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6534 (ptt-90) REVERT: B 46 ARG cc_start: 0.7491 (mtp85) cc_final: 0.7233 (mtm-85) REVERT: B 186 ASP cc_start: 0.8594 (m-30) cc_final: 0.8377 (m-30) REVERT: B 325 MET cc_start: 0.8463 (mmt) cc_final: 0.8198 (tpt) outliers start: 8 outliers final: 3 residues processed: 177 average time/residue: 0.5050 time to fit residues: 95.5705 Evaluate side-chains 148 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 97 HIS P 3 ASN P 18 HIS P 31 ASN R 121 HIS R 179 GLN R 186 ASN R 223 HIS R 227 GLN R 277 HIS R 383 GLN R 395 ASN A 19 GLN A 294 GLN A 387 HIS B 6 GLN B 17 GLN B 88 ASN B 175 GLN B 268 ASN B 293 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.198541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135030 restraints weight = 10762.105| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.01 r_work: 0.3494 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10296 Z= 0.123 Angle : 0.544 7.507 13995 Z= 0.293 Chirality : 0.042 0.172 1560 Planarity : 0.004 0.050 1783 Dihedral : 4.815 52.550 1391 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.71 % Allowed : 11.11 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.53 (0.22), residues: 1258 helix: 0.09 (0.22), residues: 510 sheet: -0.03 (0.31), residues: 231 loop : -0.81 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 321 TYR 0.011 0.001 TYR B 124 PHE 0.013 0.001 PHE R 161 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (10281) covalent geometry : angle 0.54000 / 0.29 (13963) SS BOND : bond 0.00314 / 0.21 ( 10) SS BOND : angle 1.52066 / 1.02 ( 20) hydrogen bonds : bond 0.05166 / 3.53 ( 488) hydrogen bonds : angle 5.06345 / 3.74 ( 1380) Misc. bond : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : bond 0.00161 / 0.08 ( 4) link_NAG-ASN : angle 1.52428 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 140 ARG cc_start: 0.6870 (mmm-85) cc_final: 0.5555 (mmm160) REVERT: P 10 GLN cc_start: 0.7477 (mp10) cc_final: 0.7238 (mp10) REVERT: R 94 PHE cc_start: 0.6966 (m-80) cc_final: 0.6551 (m-10) REVERT: R 107 LYS cc_start: 0.6455 (mmmt) cc_final: 0.5995 (mmmm) REVERT: R 215 ASP cc_start: 0.5176 (t0) cc_final: 0.4757 (m-30) REVERT: R 260 ARG cc_start: 0.6669 (ptp-170) cc_final: 0.6296 (ptp-110) REVERT: R 314 PHE cc_start: 0.7746 (m-10) cc_final: 0.7166 (t80) REVERT: R 340 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7111 (mttp) REVERT: R 367 MET cc_start: 0.5231 (tpp) cc_final: 0.4833 (ptp) REVERT: R 370 LYS cc_start: 0.7192 (ttpp) cc_final: 0.6831 (ptmm) REVERT: R 374 TYR cc_start: 0.7586 (m-80) cc_final: 0.7359 (m-80) REVERT: R 399 GLN cc_start: 0.6734 (mt0) cc_final: 0.6276 (mt0) REVERT: R 405 GLN cc_start: 0.7373 (mt0) cc_final: 0.6510 (tp40) REVERT: A 55 THR cc_start: 0.8064 (m) cc_final: 0.7193 (m) REVERT: A 59 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.6462 (mp10) REVERT: A 356 ARG cc_start: 0.7324 (mtm110) cc_final: 0.6567 (ptt-90) REVERT: B 44 GLN cc_start: 0.7669 (mt0) cc_final: 0.7360 (mt0) REVERT: B 186 ASP cc_start: 0.8566 (m-30) cc_final: 0.8364 (m-30) outliers start: 18 outliers final: 4 residues processed: 164 average time/residue: 0.5237 time to fit residues: 91.3968 Evaluate side-chains 149 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain R residue 400 THR Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 9.9990 chunk 98 optimal weight: 0.1980 chunk 56 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN R 227 GLN R 383 GLN A 54 ASN A 292 ASN B 268 ASN N 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.196107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130935 restraints weight = 10692.831| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.74 r_work: 0.3471 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10296 Z= 0.156 Angle : 0.556 6.700 13995 Z= 0.299 Chirality : 0.043 0.146 1560 Planarity : 0.004 0.054 1783 Dihedral : 4.908 45.016 1390 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.75 % Allowed : 11.78 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.19 (0.23), residues: 1258 helix: 1.01 (0.23), residues: 505 sheet: 0.06 (0.31), residues: 237 loop : -0.64 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.016 0.002 TYR R 146 PHE 0.013 0.002 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (10281) covalent geometry : angle 0.55276 / 0.30 (13963) SS BOND : bond 0.00324 / 0.22 ( 10) SS BOND : angle 1.11072 / 0.73 ( 20) hydrogen bonds : bond 0.05207 / 3.53 ( 488) hydrogen bonds : angle 4.92272 / 3.64 ( 1380) Misc. bond : bond 0.00013 / 0.01 ( 1) link_NAG-ASN : bond 0.00375 / 0.18 ( 4) link_NAG-ASN : angle 1.52554 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7528 (mp10) cc_final: 0.7317 (mp10) REVERT: R 94 PHE cc_start: 0.6879 (m-80) cc_final: 0.6554 (m-10) REVERT: R 144 ASN cc_start: 0.7793 (m-40) cc_final: 0.7518 (m-40) REVERT: R 202 LEU cc_start: 0.7974 (mt) cc_final: 0.7717 (mm) REVERT: R 260 ARG cc_start: 0.6839 (ptp-170) cc_final: 0.6525 (ptp-110) REVERT: R 314 PHE cc_start: 0.7694 (m-10) cc_final: 0.7149 (t80) REVERT: R 340 LYS cc_start: 0.7603 (mmmt) cc_final: 0.7176 (mttp) REVERT: R 367 MET cc_start: 0.5421 (tpp) cc_final: 0.5049 (ptp) REVERT: R 370 LYS cc_start: 0.7236 (ttpp) cc_final: 0.6844 (ptmm) REVERT: R 374 TYR cc_start: 0.7570 (m-80) cc_final: 0.7336 (m-80) REVERT: R 399 GLN cc_start: 0.7042 (mt0) cc_final: 0.6496 (mt0) REVERT: R 405 GLN cc_start: 0.7368 (mt0) cc_final: 0.6822 (mm-40) REVERT: A 38 ARG cc_start: 0.8417 (mmt90) cc_final: 0.8215 (mmt180) REVERT: A 55 THR cc_start: 0.8104 (m) cc_final: 0.7221 (m) REVERT: A 59 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6420 (mp10) REVERT: A 356 ARG cc_start: 0.7351 (mtm110) cc_final: 0.6548 (ptt-90) REVERT: B 44 GLN cc_start: 0.7662 (mt0) cc_final: 0.7303 (mt0) REVERT: B 46 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7304 (mtm-85) REVERT: B 59 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8183 (t80) REVERT: B 186 ASP cc_start: 0.8754 (m-30) cc_final: 0.8547 (m-30) outliers start: 29 outliers final: 7 residues processed: 167 average time/residue: 0.5072 time to fit residues: 90.3353 Evaluate side-chains 154 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain R residue 400 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 9 optimal weight: 0.0060 chunk 35 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN A 292 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.195736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130582 restraints weight = 10763.406| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.75 r_work: 0.3468 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10296 Z= 0.164 Angle : 0.560 6.764 13995 Z= 0.301 Chirality : 0.044 0.184 1560 Planarity : 0.004 0.054 1783 Dihedral : 4.936 43.213 1390 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.99 % Allowed : 13.58 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.39 (0.23), residues: 1258 helix: 1.26 (0.23), residues: 507 sheet: 0.09 (0.31), residues: 237 loop : -0.59 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 321 TYR 0.011 0.002 TYR N 95 PHE 0.014 0.002 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10281) covalent geometry : angle 0.55568 / 0.30 (13963) SS BOND : bond 0.00453 / 0.34 ( 10) SS BOND : angle 1.39449 / 0.86 ( 20) hydrogen bonds : bond 0.04993 / 3.38 ( 488) hydrogen bonds : angle 4.83367 / 3.57 ( 1380) Misc. bond : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : bond 0.00309 / 0.15 ( 4) link_NAG-ASN : angle 1.71673 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: E 140 ARG cc_start: 0.6915 (mmm-85) cc_final: 0.6144 (mmp-170) REVERT: P 10 GLN cc_start: 0.7504 (mp10) cc_final: 0.7299 (mp10) REVERT: R 59 MET cc_start: 0.4557 (mmt) cc_final: 0.3754 (mtp) REVERT: R 94 PHE cc_start: 0.6945 (m-80) cc_final: 0.6522 (m-10) REVERT: R 202 LEU cc_start: 0.7945 (mt) cc_final: 0.7692 (mm) REVERT: R 260 ARG cc_start: 0.6946 (ptp-170) cc_final: 0.6619 (ptp-110) REVERT: R 314 PHE cc_start: 0.7687 (m-10) cc_final: 0.7138 (t80) REVERT: R 340 LYS cc_start: 0.7571 (mmmt) cc_final: 0.7155 (mttt) REVERT: R 405 GLN cc_start: 0.7397 (mt0) cc_final: 0.6931 (mm-40) REVERT: A 55 THR cc_start: 0.8118 (m) cc_final: 0.7206 (m) REVERT: A 59 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.6405 (mp10) REVERT: A 356 ARG cc_start: 0.7351 (mtm110) cc_final: 0.6557 (ptt-90) REVERT: B 46 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7286 (mtm-85) outliers start: 21 outliers final: 7 residues processed: 160 average time/residue: 0.5534 time to fit residues: 94.5680 Evaluate side-chains 152 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 400 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN R 286 ASN R 383 GLN A 292 ASN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.196628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131534 restraints weight = 10682.771| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.76 r_work: 0.3484 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10296 Z= 0.138 Angle : 0.531 7.306 13995 Z= 0.283 Chirality : 0.042 0.163 1560 Planarity : 0.004 0.054 1783 Dihedral : 4.646 23.536 1387 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.09 % Allowed : 14.62 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1258 helix: 1.50 (0.23), residues: 507 sheet: 0.22 (0.31), residues: 235 loop : -0.56 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 321 TYR 0.015 0.001 TYR R 146 PHE 0.013 0.001 PHE B 151 TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (10281) covalent geometry : angle 0.52774 / 0.28 (13963) SS BOND : bond 0.00456 / 0.34 ( 10) SS BOND : angle 0.91249 / 0.60 ( 20) hydrogen bonds : bond 0.04634 / 3.14 ( 488) hydrogen bonds : angle 4.68250 / 3.46 ( 1380) Misc. bond : bond 0.00012 / 0.01 ( 1) link_NAG-ASN : bond 0.00261 / 0.13 ( 4) link_NAG-ASN : angle 1.80018 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 140 ARG cc_start: 0.6896 (mmm-85) cc_final: 0.6128 (mmp-170) REVERT: P 10 GLN cc_start: 0.7460 (mp10) cc_final: 0.7251 (mp10) REVERT: R 59 MET cc_start: 0.4622 (mmt) cc_final: 0.3888 (mtp) REVERT: R 94 PHE cc_start: 0.6911 (m-80) cc_final: 0.6515 (m-10) REVERT: R 202 LEU cc_start: 0.7936 (mt) cc_final: 0.7688 (mm) REVERT: R 260 ARG cc_start: 0.6943 (ptp-170) cc_final: 0.6626 (ptp-110) REVERT: R 314 PHE cc_start: 0.7626 (m-10) cc_final: 0.7145 (t80) REVERT: R 340 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7096 (mttp) REVERT: R 346 MET cc_start: 0.8306 (mmm) cc_final: 0.8069 (mmm) REVERT: R 405 GLN cc_start: 0.7399 (mt0) cc_final: 0.6948 (mm-40) REVERT: A 55 THR cc_start: 0.8108 (m) cc_final: 0.7153 (m) REVERT: A 59 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6292 (mp10) REVERT: A 356 ARG cc_start: 0.7342 (mtm110) cc_final: 0.6579 (ptt-90) REVERT: B 46 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7286 (mtm-85) REVERT: B 59 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8178 (t80) REVERT: B 186 ASP cc_start: 0.8753 (m-30) cc_final: 0.8528 (m-30) REVERT: B 197 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7575 (mmm160) REVERT: B 214 ARG cc_start: 0.7436 (mpt-90) cc_final: 0.7138 (mpt-90) outliers start: 22 outliers final: 13 residues processed: 164 average time/residue: 0.5580 time to fit residues: 97.6937 Evaluate side-chains 160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 400 THR Chi-restraints excluded: chain R residue 403 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 40 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN R 383 GLN A 292 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.196398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131174 restraints weight = 10689.680| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.75 r_work: 0.3479 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10296 Z= 0.148 Angle : 0.550 7.809 13995 Z= 0.293 Chirality : 0.043 0.155 1560 Planarity : 0.004 0.054 1783 Dihedral : 4.730 27.088 1387 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.18 % Allowed : 14.81 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.67 (0.23), residues: 1258 helix: 1.61 (0.23), residues: 508 sheet: 0.12 (0.31), residues: 240 loop : -0.51 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 321 TYR 0.011 0.001 TYR N 94 PHE 0.013 0.001 PHE B 151 TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10281) covalent geometry : angle 0.54287 / 0.29 (13963) SS BOND : bond 0.00401 / 0.30 ( 10) SS BOND : angle 1.96457 / 1.17 ( 20) hydrogen bonds : bond 0.04712 / 3.19 ( 488) hydrogen bonds : angle 4.68823 / 3.46 ( 1380) Misc. bond : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : bond 0.00206 / 0.10 ( 4) link_NAG-ASN : angle 1.86625 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7469 (mp10) cc_final: 0.7194 (mp10) REVERT: R 59 MET cc_start: 0.4603 (mmt) cc_final: 0.3907 (mtp) REVERT: R 94 PHE cc_start: 0.6849 (m-80) cc_final: 0.6418 (m-10) REVERT: R 202 LEU cc_start: 0.7947 (mt) cc_final: 0.7705 (mm) REVERT: R 257 GLN cc_start: 0.7929 (mt0) cc_final: 0.7631 (pt0) REVERT: R 260 ARG cc_start: 0.6972 (ptp-170) cc_final: 0.6684 (ptp-170) REVERT: R 314 PHE cc_start: 0.7636 (m-10) cc_final: 0.7155 (t80) REVERT: R 340 LYS cc_start: 0.7491 (mmmt) cc_final: 0.7079 (mttp) REVERT: R 405 GLN cc_start: 0.7390 (mt0) cc_final: 0.7002 (mm-40) REVERT: A 55 THR cc_start: 0.8149 (m) cc_final: 0.7196 (m) REVERT: A 59 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6301 (mp10) REVERT: A 292 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8941 (t0) REVERT: A 356 ARG cc_start: 0.7352 (mtm110) cc_final: 0.6580 (ptt-90) REVERT: B 46 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7340 (mtm-85) REVERT: B 186 ASP cc_start: 0.8812 (m-30) cc_final: 0.8575 (m-30) outliers start: 23 outliers final: 13 residues processed: 162 average time/residue: 0.5251 time to fit residues: 90.8058 Evaluate side-chains 156 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 400 THR Chi-restraints excluded: chain R residue 403 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN P 22 ASN R 383 GLN A 292 ASN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.196841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132354 restraints weight = 10729.901| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.74 r_work: 0.3489 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10296 Z= 0.124 Angle : 0.527 8.305 13995 Z= 0.280 Chirality : 0.042 0.201 1560 Planarity : 0.004 0.054 1783 Dihedral : 4.582 23.912 1387 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.61 % Allowed : 15.86 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.84 (0.23), residues: 1258 helix: 1.76 (0.23), residues: 509 sheet: 0.27 (0.31), residues: 237 loop : -0.49 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 321 TYR 0.013 0.001 TYR R 146 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10281) covalent geometry : angle 0.52189 / 0.28 (13963) SS BOND : bond 0.00330 / 0.25 ( 10) SS BOND : angle 1.46113 / 0.88 ( 20) hydrogen bonds : bond 0.04413 / 2.99 ( 488) hydrogen bonds : angle 4.58344 / 3.38 ( 1380) Misc. bond : bond 0.00012 / 0.01 ( 1) link_NAG-ASN : bond 0.00188 / 0.10 ( 4) link_NAG-ASN : angle 1.76256 / 1.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7434 (mp10) cc_final: 0.7168 (mp10) REVERT: R 59 MET cc_start: 0.4620 (mmt) cc_final: 0.3976 (mtp) REVERT: R 94 PHE cc_start: 0.6862 (m-80) cc_final: 0.6466 (m-10) REVERT: R 202 LEU cc_start: 0.7931 (mt) cc_final: 0.7688 (mm) REVERT: R 257 GLN cc_start: 0.7875 (mt0) cc_final: 0.7563 (pt0) REVERT: R 260 ARG cc_start: 0.6983 (ptp-170) cc_final: 0.6667 (ptp-170) REVERT: R 314 PHE cc_start: 0.7638 (m-10) cc_final: 0.7158 (t80) REVERT: R 340 LYS cc_start: 0.7477 (mmmt) cc_final: 0.7078 (mttp) REVERT: R 346 MET cc_start: 0.8289 (mmm) cc_final: 0.8068 (mmm) REVERT: R 405 GLN cc_start: 0.7357 (mt0) cc_final: 0.7003 (mm-40) REVERT: A 55 THR cc_start: 0.8140 (m) cc_final: 0.7189 (m) REVERT: A 59 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6401 (mp10) REVERT: A 356 ARG cc_start: 0.7358 (mtm110) cc_final: 0.6584 (ptt-90) REVERT: B 46 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7277 (mtm-85) REVERT: B 186 ASP cc_start: 0.8736 (m-30) cc_final: 0.8491 (m-30) REVERT: B 197 ARG cc_start: 0.7770 (mmm160) cc_final: 0.7537 (mmm160) REVERT: B 214 ARG cc_start: 0.7569 (mpt-90) cc_final: 0.7235 (mpt-90) outliers start: 17 outliers final: 11 residues processed: 157 average time/residue: 0.5507 time to fit residues: 92.3414 Evaluate side-chains 154 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 403 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 2 optimal weight: 40.0000 chunk 60 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN R 383 GLN A 292 ASN A 294 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.197412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132888 restraints weight = 10666.624| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.75 r_work: 0.3498 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10296 Z= 0.119 Angle : 0.514 7.551 13995 Z= 0.273 Chirality : 0.042 0.188 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.494 24.186 1387 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.52 % Allowed : 15.95 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.96 (0.23), residues: 1258 helix: 1.89 (0.24), residues: 508 sheet: 0.35 (0.31), residues: 237 loop : -0.45 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 321 TYR 0.010 0.001 TYR A 339 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (10281) covalent geometry : angle 0.51021 / 0.27 (13963) SS BOND : bond 0.00318 / 0.24 ( 10) SS BOND : angle 1.21072 / 0.75 ( 20) hydrogen bonds : bond 0.04242 / 2.89 ( 488) hydrogen bonds : angle 4.50934 / 3.33 ( 1380) Misc. bond : bond 0.00008 / 0.00 ( 1) link_NAG-ASN : bond 0.00180 / 0.09 ( 4) link_NAG-ASN : angle 1.76699 / 1.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: E 75 MET cc_start: 0.3332 (mpt) cc_final: 0.3067 (mtm) REVERT: P 10 GLN cc_start: 0.7448 (mp10) cc_final: 0.7165 (mp10) REVERT: R 59 MET cc_start: 0.4624 (mmt) cc_final: 0.3946 (mtp) REVERT: R 94 PHE cc_start: 0.6840 (m-80) cc_final: 0.6431 (m-10) REVERT: R 96 PRO cc_start: 0.7246 (Cg_endo) cc_final: 0.7014 (Cg_exo) REVERT: R 202 LEU cc_start: 0.7930 (mt) cc_final: 0.7682 (mm) REVERT: R 260 ARG cc_start: 0.7006 (ptp-170) cc_final: 0.6687 (ptp-170) REVERT: R 314 PHE cc_start: 0.7616 (m-10) cc_final: 0.7154 (t80) REVERT: R 340 LYS cc_start: 0.7419 (mmmt) cc_final: 0.7020 (mttp) REVERT: R 346 MET cc_start: 0.8262 (mmm) cc_final: 0.8037 (mmm) REVERT: R 405 GLN cc_start: 0.7340 (mt0) cc_final: 0.6999 (mm-40) REVERT: A 55 THR cc_start: 0.8129 (m) cc_final: 0.7142 (m) REVERT: A 59 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6340 (mp10) REVERT: A 292 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8844 (t0) REVERT: A 356 ARG cc_start: 0.7338 (mtm110) cc_final: 0.6581 (ptt-90) REVERT: B 46 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7277 (mtm-85) REVERT: B 186 ASP cc_start: 0.8696 (m-30) cc_final: 0.8469 (m-30) REVERT: B 214 ARG cc_start: 0.7534 (mpt-90) cc_final: 0.7289 (mpt-90) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 0.5503 time to fit residues: 90.1110 Evaluate side-chains 149 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 403 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 0.0270 chunk 97 optimal weight: 0.0030 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 overall best weight: 1.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN P 14 ASN P 31 ASN R 383 GLN A 292 ASN B 268 ASN B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.197058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132001 restraints weight = 10694.776| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.76 r_work: 0.3490 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10296 Z= 0.137 Angle : 0.535 7.417 13995 Z= 0.285 Chirality : 0.043 0.182 1560 Planarity : 0.004 0.054 1783 Dihedral : 4.579 24.227 1387 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.71 % Allowed : 15.76 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.94 (0.23), residues: 1258 helix: 1.84 (0.23), residues: 509 sheet: 0.23 (0.31), residues: 241 loop : -0.39 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 321 TYR 0.012 0.001 TYR R 146 PHE 0.013 0.001 PHE B 151 TRP 0.016 0.001 TRP A 234 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (10281) covalent geometry : angle 0.53159 / 0.28 (13963) SS BOND : bond 0.00328 / 0.25 ( 10) SS BOND : angle 1.11412 / 0.71 ( 20) hydrogen bonds : bond 0.04457 / 3.02 ( 488) hydrogen bonds : angle 4.57338 / 3.37 ( 1380) Misc. bond : bond 0.00013 / 0.01 ( 1) link_NAG-ASN : bond 0.00218 / 0.11 ( 4) link_NAG-ASN : angle 1.72752 / 1.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7451 (mp10) cc_final: 0.7196 (mp10) REVERT: R 59 MET cc_start: 0.4564 (mmt) cc_final: 0.3897 (mtp) REVERT: R 96 PRO cc_start: 0.7268 (Cg_endo) cc_final: 0.7013 (Cg_exo) REVERT: R 202 LEU cc_start: 0.7938 (mt) cc_final: 0.7697 (mm) REVERT: R 260 ARG cc_start: 0.7059 (ptp-170) cc_final: 0.6798 (ptp-170) REVERT: R 314 PHE cc_start: 0.7636 (m-10) cc_final: 0.7167 (t80) REVERT: R 340 LYS cc_start: 0.7449 (mmmt) cc_final: 0.7026 (mttp) REVERT: R 405 GLN cc_start: 0.7334 (mt0) cc_final: 0.7052 (mm-40) REVERT: A 55 THR cc_start: 0.8128 (m) cc_final: 0.7172 (m) REVERT: A 59 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6343 (mp10) REVERT: A 356 ARG cc_start: 0.7345 (mtm110) cc_final: 0.6590 (ptt-90) REVERT: B 46 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7313 (mtm-85) REVERT: B 186 ASP cc_start: 0.8752 (m-30) cc_final: 0.8498 (m-30) outliers start: 18 outliers final: 12 residues processed: 153 average time/residue: 0.5413 time to fit residues: 88.5900 Evaluate side-chains 152 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 403 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 9.9990 chunk 76 optimal weight: 0.0070 chunk 25 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 97 HIS P 3 ASN R 383 GLN A 292 ASN A 294 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.197879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133523 restraints weight = 10714.993| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.75 r_work: 0.3504 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10296 Z= 0.115 Angle : 0.534 9.803 13995 Z= 0.280 Chirality : 0.042 0.178 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.510 32.729 1387 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.42 % Allowed : 16.43 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: 1.04 (0.23), residues: 1258 helix: 2.00 (0.24), residues: 506 sheet: 0.28 (0.31), residues: 238 loop : -0.39 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 321 TYR 0.010 0.001 TYR A 339 PHE 0.016 0.001 PHE A 212 TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10281) covalent geometry : angle 0.52569 / 0.28 (13963) SS BOND : bond 0.00187 / 0.13 ( 10) SS BOND : angle 2.30471 / 1.36 ( 20) hydrogen bonds : bond 0.04159 / 2.84 ( 488) hydrogen bonds : angle 4.44829 / 3.28 ( 1380) Misc. bond : bond 0.00009 / 0.00 ( 1) link_NAG-ASN : bond 0.00197 / 0.10 ( 4) link_NAG-ASN : angle 1.66334 / 1.04 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7432 (mp10) cc_final: 0.7173 (mp10) REVERT: R 59 MET cc_start: 0.4679 (mmt) cc_final: 0.3992 (mtp) REVERT: R 94 PHE cc_start: 0.6651 (m-80) cc_final: 0.6228 (m-10) REVERT: R 96 PRO cc_start: 0.7165 (Cg_endo) cc_final: 0.6889 (Cg_exo) REVERT: R 107 LYS cc_start: 0.6479 (mmtt) cc_final: 0.5974 (mmmm) REVERT: R 202 LEU cc_start: 0.7917 (mt) cc_final: 0.7673 (mm) REVERT: R 260 ARG cc_start: 0.7059 (ptp-170) cc_final: 0.6802 (ptp-170) REVERT: R 314 PHE cc_start: 0.7618 (m-10) cc_final: 0.7159 (t80) REVERT: R 339 LEU cc_start: 0.6811 (tm) cc_final: 0.5858 (mm) REVERT: R 340 LYS cc_start: 0.7409 (mmmt) cc_final: 0.7021 (mttp) REVERT: R 405 GLN cc_start: 0.7305 (mt0) cc_final: 0.7004 (mm-40) REVERT: A 55 THR cc_start: 0.8150 (m) cc_final: 0.7140 (m) REVERT: A 59 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6222 (mp10) REVERT: A 292 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8760 (t0) REVERT: A 356 ARG cc_start: 0.7318 (mtm110) cc_final: 0.6561 (ptt-90) REVERT: B 46 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7282 (mtm-85) REVERT: B 186 ASP cc_start: 0.8677 (m-30) cc_final: 0.8448 (m-30) outliers start: 15 outliers final: 10 residues processed: 150 average time/residue: 0.5668 time to fit residues: 91.0618 Evaluate side-chains 148 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 403 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 97 HIS P 3 ASN R 383 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.197686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133478 restraints weight = 10793.912| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.73 r_work: 0.3504 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 10296 Z= 0.205 Angle : 0.860 59.196 13995 Z= 0.497 Chirality : 0.052 1.193 1560 Planarity : 0.004 0.092 1783 Dihedral : 4.524 32.624 1387 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.23 % Allowed : 16.24 % Favored : 82.53 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: 1.04 (0.23), residues: 1258 helix: 2.00 (0.24), residues: 506 sheet: 0.28 (0.31), residues: 238 loop : -0.39 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 321 TYR 0.009 0.001 TYR A 339 PHE 0.015 0.001 PHE A 212 TRP 0.014 0.002 TRP R 236 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.21 (10281) covalent geometry : angle 0.85525 / 0.50 (13963) SS BOND : bond 0.00302 / 0.23 ( 10) SS BOND : angle 2.15672 / 1.27 ( 20) hydrogen bonds : bond 0.04213 / 2.87 ( 488) hydrogen bonds : angle 4.44775 / 3.28 ( 1380) Misc. bond : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : bond 0.00180 / 0.09 ( 4) link_NAG-ASN : angle 1.70801 / 1.03 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5172.40 seconds wall clock time: 88 minutes 26.04 seconds (5306.04 seconds total)