Starting phenix.real_space_refine on Sat Aug 23 05:37:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f2a_28810/08_2025/8f2a_28810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2a_28810/08_2025/8f2a_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 { model { file = "/net/cci-nas-00/data/ceres_data/8f2a_28810/08_2025/8f2a_28810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2a_28810/08_2025/8f2a_28810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f2a_28810/08_2025/8f2a_28810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2a_28810/08_2025/8f2a_28810.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.18, per 1000 atoms: 0.22 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: 0.74 Conformation dependent library (CDL) restraints added in 245.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.31 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: 1.29 Time building geometry restraints manager: 0.92 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: 5572 17.59 - 35.18: 438 35.18 - 52.77: 89 52.77 - 70.36: 23 70.36 - 87.96: 10 Dihedral angle restraints: 6132 sinusoidal: 2414 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 6129 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.900 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 13.826 87.956 3702 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 aren 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 covalent geometry : bond 0.00361 (10281) covalent geometry : angle 0.60232 (13963) SS BOND : bond 0.00384 ( 10) SS BOND : angle 1.75862 ( 20) hydrogen bonds : bond 0.25497 ( 488) hydrogen bonds : angle 8.83156 ( 1380) Misc. bond : bond 0.10567 ( 1) link_NAG-ASN : bond 0.00160 ( 4) link_NAG-ASN : angle 2.16008 ( 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 : 0.322 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: 0.6280 time to fit residues: 118.5962 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 : 0.412 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.198591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135062 restraints weight = 10769.431| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.02 r_work: 0.3493 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10296 Z= 0.121 Angle : 0.544 7.467 13995 Z= 0.293 Chirality : 0.042 0.170 1560 Planarity : 0.004 0.050 1783 Dihedral : 5.231 53.346 1475 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.52 % Allowed : 11.40 % Favored : 87.08 % 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 aren not related in a simple way. whole: -0.55 (0.22), residues: 1258 helix: 0.06 (0.22), residues: 514 sheet: -0.03 (0.31), residues: 231 loop : -0.82 (0.25), residues: 513 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 A 212 TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00245 (10281) covalent geometry : angle 0.53983 (13963) SS BOND : bond 0.00317 ( 10) SS BOND : angle 1.65022 ( 20) hydrogen bonds : bond 0.05135 ( 488) hydrogen bonds : angle 5.06210 ( 1380) Misc. bond : bond 0.00038 ( 1) link_NAG-ASN : bond 0.00245 ( 4) link_NAG-ASN : angle 1.43904 ( 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 174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: E 140 ARG cc_start: 0.6885 (mmm-85) cc_final: 0.5566 (mmm160) REVERT: P 10 GLN cc_start: 0.7468 (mp10) cc_final: 0.7235 (mp10) REVERT: R 94 PHE cc_start: 0.6963 (m-80) cc_final: 0.6549 (m-10) REVERT: R 107 LYS cc_start: 0.6452 (mmmt) cc_final: 0.5994 (mmmm) REVERT: R 215 ASP cc_start: 0.5191 (t0) cc_final: 0.4772 (m-30) REVERT: R 260 ARG cc_start: 0.6684 (ptp-170) cc_final: 0.6306 (ptp-110) REVERT: R 314 PHE cc_start: 0.7731 (m-10) cc_final: 0.7143 (t80) REVERT: R 340 LYS cc_start: 0.7615 (mmmt) cc_final: 0.7124 (mttp) REVERT: R 367 MET cc_start: 0.5236 (tpp) cc_final: 0.4849 (ptp) REVERT: R 370 LYS cc_start: 0.7235 (ttpp) cc_final: 0.6882 (ptmm) REVERT: R 374 TYR cc_start: 0.7590 (m-80) cc_final: 0.7367 (m-80) REVERT: R 399 GLN cc_start: 0.6737 (mt0) cc_final: 0.6285 (mt0) REVERT: R 405 GLN cc_start: 0.7386 (mt0) cc_final: 0.6530 (tp40) REVERT: A 55 THR cc_start: 0.8047 (m) cc_final: 0.7181 (m) REVERT: A 59 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.6464 (mp10) REVERT: A 356 ARG cc_start: 0.7327 (mtm110) cc_final: 0.6573 (ptt-90) REVERT: B 44 GLN cc_start: 0.7686 (mt0) cc_final: 0.7372 (mt0) REVERT: B 186 ASP cc_start: 0.8570 (m-30) cc_final: 0.8367 (m-30) outliers start: 16 outliers final: 3 residues processed: 164 average time/residue: 0.7571 time to fit residues: 131.6901 Evaluate side-chains 148 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 98 optimal weight: 0.0170 chunk 56 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 383 GLN A 54 ASN A 292 ASN B 268 ASN N 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.194639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128899 restraints weight = 10672.172| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.74 r_work: 0.3447 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10296 Z= 0.217 Angle : 0.618 6.520 13995 Z= 0.334 Chirality : 0.046 0.152 1560 Planarity : 0.005 0.055 1783 Dihedral : 5.479 51.730 1474 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.23 % Allowed : 12.06 % Favored : 84.71 % 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 aren not related in a simple way. whole: -0.01 (0.22), residues: 1258 helix: 0.74 (0.23), residues: 508 sheet: 0.03 (0.31), residues: 237 loop : -0.68 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 314 TYR 0.015 0.002 TYR N 95 PHE 0.015 0.002 PHE B 151 TRP 0.018 0.002 TRP A 234 HIS 0.007 0.002 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00482 (10281) covalent geometry : angle 0.61543 (13963) SS BOND : bond 0.00472 ( 10) SS BOND : angle 1.13626 ( 20) hydrogen bonds : bond 0.05793 ( 488) hydrogen bonds : angle 5.11874 ( 1380) Misc. bond : bond 0.00032 ( 1) link_NAG-ASN : bond 0.00518 ( 4) link_NAG-ASN : angle 1.50870 ( 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 181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7464 (mp10) cc_final: 0.7233 (mp10) REVERT: R 94 PHE cc_start: 0.6930 (m-80) cc_final: 0.6441 (m-10) REVERT: R 202 LEU cc_start: 0.7948 (mt) cc_final: 0.7680 (mm) REVERT: R 260 ARG cc_start: 0.6853 (ptp-170) cc_final: 0.6530 (ptp-110) REVERT: R 314 PHE cc_start: 0.7761 (m-10) cc_final: 0.7194 (t80) REVERT: R 340 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7154 (mttp) REVERT: R 367 MET cc_start: 0.5708 (tpp) cc_final: 0.5505 (ptp) REVERT: R 374 TYR cc_start: 0.7602 (m-80) cc_final: 0.7361 (m-80) REVERT: R 405 GLN cc_start: 0.7305 (mt0) cc_final: 0.6784 (mm-40) REVERT: A 38 ARG cc_start: 0.8491 (mmt90) cc_final: 0.8282 (mmt180) REVERT: A 55 THR cc_start: 0.8166 (m) cc_final: 0.7284 (m) REVERT: A 59 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6421 (mp10) REVERT: A 356 ARG cc_start: 0.7368 (mtm110) cc_final: 0.6544 (ptt-90) REVERT: B 44 GLN cc_start: 0.7618 (mt0) cc_final: 0.7252 (mt0) REVERT: B 298 ASP cc_start: 0.8603 (t0) cc_final: 0.8400 (t0) outliers start: 34 outliers final: 7 residues processed: 170 average time/residue: 0.6906 time to fit residues: 125.1735 Evaluate side-chains 151 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 400 THR 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 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: 7.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 7 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN P 31 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.194962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129147 restraints weight = 10648.489| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.74 r_work: 0.3456 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10296 Z= 0.206 Angle : 0.606 7.260 13995 Z= 0.326 Chirality : 0.046 0.162 1560 Planarity : 0.005 0.055 1783 Dihedral : 5.321 49.968 1469 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.37 % Allowed : 13.87 % Favored : 83.76 % 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 aren not related in a simple way. whole: 0.14 (0.22), residues: 1258 helix: 0.98 (0.23), residues: 507 sheet: -0.01 (0.31), residues: 239 loop : -0.66 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.016 0.002 TYR A 358 PHE 0.016 0.002 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00462 (10281) covalent geometry : angle 0.60161 (13963) SS BOND : bond 0.00508 ( 10) SS BOND : angle 1.51838 ( 20) hydrogen bonds : bond 0.05435 ( 488) hydrogen bonds : angle 4.98125 ( 1380) Misc. bond : bond 0.00014 ( 1) link_NAG-ASN : bond 0.00291 ( 4) link_NAG-ASN : angle 1.70050 ( 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 176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 140 ARG cc_start: 0.6831 (mmm-85) cc_final: 0.6151 (mmp-170) REVERT: P 10 GLN cc_start: 0.7480 (mp10) cc_final: 0.7277 (mp10) REVERT: R 59 MET cc_start: 0.5171 (OUTLIER) cc_final: 0.4350 (tpp) REVERT: R 202 LEU cc_start: 0.7961 (mt) cc_final: 0.7698 (mm) REVERT: R 260 ARG cc_start: 0.6963 (ptp-170) cc_final: 0.6634 (ptp-110) REVERT: R 314 PHE cc_start: 0.7748 (m-10) cc_final: 0.7175 (t80) REVERT: R 340 LYS cc_start: 0.7683 (mmmt) cc_final: 0.7296 (mttt) REVERT: R 367 MET cc_start: 0.5746 (tpp) cc_final: 0.5526 (ptp) REVERT: R 374 TYR cc_start: 0.7694 (m-80) cc_final: 0.7395 (m-80) REVERT: R 405 GLN cc_start: 0.7458 (mt0) cc_final: 0.7091 (mm-40) REVERT: A 38 ARG cc_start: 0.8511 (mmt90) cc_final: 0.8303 (mmt180) REVERT: A 55 THR cc_start: 0.8187 (m) cc_final: 0.7321 (m) REVERT: A 59 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6411 (mp10) REVERT: A 356 ARG cc_start: 0.7347 (mtm110) cc_final: 0.6521 (ptt-90) REVERT: B 44 GLN cc_start: 0.7613 (mt0) cc_final: 0.7254 (mt0) REVERT: B 46 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7362 (mtm-85) REVERT: B 186 ASP cc_start: 0.8781 (m-30) cc_final: 0.8577 (m-30) outliers start: 25 outliers final: 11 residues processed: 167 average time/residue: 0.6983 time to fit residues: 124.3686 Evaluate side-chains 167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 59 MET Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 330 THR 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 11 LEU 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: 0.7980 chunk 6 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN P 22 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.195631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130436 restraints weight = 10689.264| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.75 r_work: 0.3472 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10296 Z= 0.163 Angle : 0.563 7.338 13995 Z= 0.302 Chirality : 0.044 0.183 1560 Planarity : 0.004 0.055 1783 Dihedral : 5.156 49.293 1469 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.99 % Allowed : 15.00 % 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 aren not related in a simple way. whole: 0.37 (0.23), residues: 1258 helix: 1.28 (0.23), residues: 507 sheet: 0.03 (0.31), residues: 239 loop : -0.62 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.016 0.002 TYR R 146 PHE 0.015 0.002 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00361 (10281) covalent geometry : angle 0.55707 (13963) SS BOND : bond 0.00457 ( 10) SS BOND : angle 1.82758 ( 20) hydrogen bonds : bond 0.04947 ( 488) hydrogen bonds : angle 4.80274 ( 1380) Misc. bond : bond 0.00015 ( 1) link_NAG-ASN : bond 0.00205 ( 4) link_NAG-ASN : angle 1.71450 ( 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 174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 140 ARG cc_start: 0.6785 (mmm-85) cc_final: 0.6024 (mmp-170) REVERT: P 10 GLN cc_start: 0.7468 (mp10) cc_final: 0.7195 (mp10) REVERT: R 59 MET cc_start: 0.5159 (OUTLIER) cc_final: 0.4417 (tpp) REVERT: R 94 PHE cc_start: 0.6746 (m-80) cc_final: 0.6324 (m-10) REVERT: R 202 LEU cc_start: 0.7931 (mt) cc_final: 0.7681 (mm) REVERT: R 260 ARG cc_start: 0.7032 (ptp-170) cc_final: 0.6769 (ptp-110) REVERT: R 314 PHE cc_start: 0.7713 (m-10) cc_final: 0.7141 (t80) REVERT: R 340 LYS cc_start: 0.7493 (mmmt) cc_final: 0.7082 (mttp) REVERT: R 367 MET cc_start: 0.5670 (tpp) cc_final: 0.5453 (ptp) REVERT: R 374 TYR cc_start: 0.7692 (m-80) cc_final: 0.7367 (m-80) REVERT: R 405 GLN cc_start: 0.7353 (mt0) cc_final: 0.7034 (mm-40) REVERT: A 55 THR cc_start: 0.8140 (m) cc_final: 0.7228 (m) REVERT: A 59 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6398 (mp10) REVERT: A 356 ARG cc_start: 0.7351 (mtm110) cc_final: 0.6558 (ptt-90) REVERT: B 44 GLN cc_start: 0.7581 (mt0) cc_final: 0.7210 (mt0) REVERT: B 46 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7400 (mtm-85) REVERT: B 186 ASP cc_start: 0.8770 (m-30) cc_final: 0.8558 (m-30) outliers start: 21 outliers final: 13 residues processed: 168 average time/residue: 0.7165 time to fit residues: 128.1956 Evaluate side-chains 159 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 59 MET 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 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 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN P 31 ASN R 227 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.197251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133336 restraints weight = 10827.019| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.73 r_work: 0.3501 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10296 Z= 0.112 Angle : 0.504 7.458 13995 Z= 0.268 Chirality : 0.041 0.172 1560 Planarity : 0.004 0.056 1783 Dihedral : 4.786 50.118 1469 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.80 % Allowed : 15.19 % 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 aren not related in a simple way. whole: 0.78 (0.23), residues: 1258 helix: 1.76 (0.24), residues: 502 sheet: 0.11 (0.31), residues: 239 loop : -0.47 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.010 0.001 TYR N 60 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 covalent geometry : bond 0.00236 (10281) covalent geometry : angle 0.50027 (13963) SS BOND : bond 0.00309 ( 10) SS BOND : angle 1.04146 ( 20) hydrogen bonds : bond 0.04216 ( 488) hydrogen bonds : angle 4.52481 ( 1380) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.00198 ( 4) link_NAG-ASN : angle 1.75089 ( 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 166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 140 ARG cc_start: 0.6843 (mmm-85) cc_final: 0.6117 (mmp-170) REVERT: P 10 GLN cc_start: 0.7503 (mp10) cc_final: 0.7256 (mp10) REVERT: R 59 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4003 (mtp) REVERT: R 94 PHE cc_start: 0.6741 (m-80) cc_final: 0.6325 (m-10) REVERT: R 202 LEU cc_start: 0.7915 (mt) cc_final: 0.7674 (mm) REVERT: R 257 GLN cc_start: 0.7775 (mt0) cc_final: 0.7563 (pt0) REVERT: R 260 ARG cc_start: 0.7049 (ptp-170) cc_final: 0.6717 (ptp-170) REVERT: R 314 PHE cc_start: 0.7610 (m-10) cc_final: 0.7155 (t80) REVERT: R 340 LYS cc_start: 0.7457 (mmmt) cc_final: 0.7037 (mttp) REVERT: R 346 MET cc_start: 0.8299 (mmm) cc_final: 0.8051 (mmm) REVERT: R 405 GLN cc_start: 0.7347 (mt0) cc_final: 0.7075 (mm-40) REVERT: A 55 THR cc_start: 0.8120 (m) cc_final: 0.7194 (m) REVERT: A 59 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.6432 (mp10) REVERT: A 356 ARG cc_start: 0.7310 (mtm110) cc_final: 0.6564 (ptt-90) REVERT: B 46 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7285 (mtm-85) REVERT: B 134 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7094 (ppt170) REVERT: B 186 ASP cc_start: 0.8609 (m-30) cc_final: 0.8399 (m-30) outliers start: 19 outliers final: 9 residues processed: 159 average time/residue: 0.7178 time to fit residues: 121.2951 Evaluate side-chains 158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 59 MET Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 295 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 134 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN P 31 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 = 0.4317 r_free = 0.4317 target = 0.197298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132638 restraints weight = 10740.140| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.76 r_work: 0.3495 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10296 Z= 0.118 Angle : 0.512 8.306 13995 Z= 0.272 Chirality : 0.042 0.163 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.751 50.482 1469 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.90 % Allowed : 15.48 % Favored : 82.62 % 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 aren not related in a simple way. whole: 0.88 (0.23), residues: 1258 helix: 1.85 (0.24), residues: 506 sheet: 0.15 (0.31), residues: 242 loop : -0.43 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 321 TYR 0.008 0.001 TYR N 95 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00250 (10281) covalent geometry : angle 0.50907 (13963) SS BOND : bond 0.00276 ( 10) SS BOND : angle 0.86334 ( 20) hydrogen bonds : bond 0.04255 ( 488) hydrogen bonds : angle 4.50002 ( 1380) Misc. bond : bond 0.00011 ( 1) link_NAG-ASN : bond 0.00204 ( 4) link_NAG-ASN : angle 1.75460 ( 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 167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7469 (mp10) cc_final: 0.7198 (mp10) REVERT: R 59 MET cc_start: 0.5233 (OUTLIER) cc_final: 0.4031 (mtp) REVERT: R 94 PHE cc_start: 0.6746 (m-80) cc_final: 0.6281 (m-10) REVERT: R 107 LYS cc_start: 0.6583 (mmtt) cc_final: 0.6018 (mmmm) REVERT: R 202 LEU cc_start: 0.7918 (mt) cc_final: 0.7673 (mm) REVERT: R 260 ARG cc_start: 0.7045 (ptp-170) cc_final: 0.6727 (ptp-170) REVERT: R 314 PHE cc_start: 0.7610 (m-10) cc_final: 0.7158 (t80) REVERT: R 340 LYS cc_start: 0.7448 (mmmt) cc_final: 0.7040 (mttp) REVERT: R 346 MET cc_start: 0.8265 (mmm) cc_final: 0.8049 (mmm) REVERT: R 374 TYR cc_start: 0.7679 (m-80) cc_final: 0.7308 (m-80) REVERT: R 405 GLN cc_start: 0.7307 (mt0) cc_final: 0.7065 (mm-40) REVERT: A 55 THR cc_start: 0.8129 (m) cc_final: 0.7199 (m) REVERT: A 59 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6300 (mp10) REVERT: A 356 ARG cc_start: 0.7311 (mtm110) cc_final: 0.6563 (ptt-90) REVERT: B 46 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7292 (mtm-85) REVERT: B 134 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7079 (ppt170) REVERT: B 186 ASP cc_start: 0.8615 (m-30) cc_final: 0.8387 (m-30) REVERT: B 214 ARG cc_start: 0.7354 (mpt-90) cc_final: 0.7037 (mpt-90) outliers start: 20 outliers final: 11 residues processed: 160 average time/residue: 0.6487 time to fit residues: 110.9595 Evaluate side-chains 155 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 59 MET 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 134 ARG 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: 20.0000 chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN P 31 ASN R 383 GLN A 294 GLN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.197719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133399 restraints weight = 10676.761| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.75 r_work: 0.3504 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10296 Z= 0.116 Angle : 0.528 9.744 13995 Z= 0.278 Chirality : 0.042 0.163 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.764 50.608 1469 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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 aren not related in a simple way. whole: 1.03 (0.24), residues: 1258 helix: 2.01 (0.24), residues: 502 sheet: 0.17 (0.32), residues: 240 loop : -0.35 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 321 TYR 0.011 0.001 TYR R 146 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00249 (10281) covalent geometry : angle 0.51710 (13963) SS BOND : bond 0.00265 ( 10) SS BOND : angle 2.50914 ( 20) hydrogen bonds : bond 0.04171 ( 488) hydrogen bonds : angle 4.45780 ( 1380) Misc. bond : bond 0.00008 ( 1) link_NAG-ASN : bond 0.00199 ( 4) link_NAG-ASN : angle 1.73794 ( 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 163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 75 MET cc_start: 0.3461 (mpt) cc_final: 0.3177 (mtm) REVERT: P 10 GLN cc_start: 0.7431 (mp10) cc_final: 0.7176 (mp10) REVERT: R 59 MET cc_start: 0.5218 (OUTLIER) cc_final: 0.4023 (mtp) REVERT: R 94 PHE cc_start: 0.6661 (m-80) cc_final: 0.6271 (m-10) REVERT: R 96 PRO cc_start: 0.7219 (Cg_endo) cc_final: 0.7001 (Cg_exo) REVERT: R 107 LYS cc_start: 0.6529 (mmtt) cc_final: 0.5948 (mmmm) REVERT: R 202 LEU cc_start: 0.7893 (mt) cc_final: 0.7646 (mm) REVERT: R 260 ARG cc_start: 0.7094 (ptp-170) cc_final: 0.6840 (ptp-170) REVERT: R 314 PHE cc_start: 0.7606 (m-10) cc_final: 0.7155 (t80) REVERT: R 340 LYS cc_start: 0.7426 (mmmt) cc_final: 0.7040 (mttp) REVERT: R 374 TYR cc_start: 0.7657 (m-80) cc_final: 0.7250 (m-80) REVERT: R 405 GLN cc_start: 0.7203 (mt0) cc_final: 0.6977 (mm-40) REVERT: A 55 THR cc_start: 0.8177 (m) cc_final: 0.7244 (m) REVERT: A 59 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6312 (mp10) REVERT: A 356 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6564 (ptt-90) REVERT: B 37 ILE cc_start: 0.7584 (tt) cc_final: 0.7257 (pt) REVERT: B 46 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7273 (mtm-85) REVERT: B 134 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7043 (ppt170) REVERT: B 186 ASP cc_start: 0.8600 (m-30) cc_final: 0.8381 (m-30) outliers start: 17 outliers final: 10 residues processed: 159 average time/residue: 0.6785 time to fit residues: 114.5181 Evaluate side-chains 155 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 59 MET Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 295 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 A residue 314 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS P 3 ASN P 14 ASN P 31 ASN R 383 GLN A 292 ASN B 268 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.195636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133245 restraints weight = 10596.802| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.23 r_work: 0.3409 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2529 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= 0.167 Angle : 0.583 9.595 13995 Z= 0.309 Chirality : 0.044 0.209 1560 Planarity : 0.004 0.054 1783 Dihedral : 5.039 50.185 1469 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.71 % Allowed : 15.86 % Favored : 82.43 % 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 aren not related in a simple way. whole: 0.83 (0.23), residues: 1258 helix: 1.75 (0.23), residues: 508 sheet: 0.18 (0.31), residues: 240 loop : -0.43 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 321 TYR 0.013 0.002 TYR A 358 PHE 0.014 0.002 PHE B 151 TRP 0.018 0.002 TRP A 234 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00371 (10281) covalent geometry : angle 0.57367 (13963) SS BOND : bond 0.00436 ( 10) SS BOND : angle 2.42831 ( 20) hydrogen bonds : bond 0.04816 ( 488) hydrogen bonds : angle 4.69015 ( 1380) Misc. bond : bond 0.00017 ( 1) link_NAG-ASN : bond 0.00231 ( 4) link_NAG-ASN : angle 1.77206 ( 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 165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7357 (mp10) cc_final: 0.7046 (mp10) REVERT: R 59 MET cc_start: 0.5286 (OUTLIER) cc_final: 0.4045 (mtp) REVERT: R 94 PHE cc_start: 0.6671 (m-80) cc_final: 0.6305 (m-10) REVERT: R 107 LYS cc_start: 0.6519 (mmtt) cc_final: 0.5928 (mmmm) REVERT: R 202 LEU cc_start: 0.7881 (mt) cc_final: 0.7620 (mm) REVERT: R 260 ARG cc_start: 0.7117 (ptp-170) cc_final: 0.6830 (ptp-170) REVERT: R 314 PHE cc_start: 0.7641 (m-10) cc_final: 0.7052 (t80) REVERT: R 340 LYS cc_start: 0.7403 (mmmt) cc_final: 0.6944 (mttp) REVERT: R 374 TYR cc_start: 0.7684 (m-80) cc_final: 0.7320 (m-80) REVERT: R 405 GLN cc_start: 0.7239 (mt0) cc_final: 0.6940 (mm-40) REVERT: A 55 THR cc_start: 0.8070 (m) cc_final: 0.7140 (m) REVERT: A 59 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6177 (mp10) REVERT: A 292 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8934 (t0) REVERT: A 356 ARG cc_start: 0.7343 (mtm110) cc_final: 0.6533 (ptt-90) REVERT: B 37 ILE cc_start: 0.7524 (tt) cc_final: 0.7146 (pt) REVERT: B 46 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7292 (mtm-85) REVERT: B 134 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7071 (ppt170) REVERT: B 186 ASP cc_start: 0.8758 (m-30) cc_final: 0.8534 (m-30) outliers start: 18 outliers final: 8 residues processed: 159 average time/residue: 0.6051 time to fit residues: 102.6934 Evaluate side-chains 158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 59 MET Chi-restraints excluded: chain R residue 295 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 A residue 292 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 270 ILE 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: 7.9990 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 383 GLN A 292 ASN A 294 GLN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.197274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.132169 restraints weight = 10682.945| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.75 r_work: 0.3491 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10296 Z= 0.131 Angle : 0.549 8.062 13995 Z= 0.290 Chirality : 0.043 0.204 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.924 50.069 1469 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.23 % Allowed : 16.52 % Favored : 82.24 % 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 aren not related in a simple way. whole: 0.95 (0.23), residues: 1258 helix: 1.86 (0.23), residues: 505 sheet: 0.32 (0.31), residues: 242 loop : -0.42 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 G 44 Details of bonding type rmsd covalent geometry : bond 0.00285 (10281) covalent geometry : angle 0.54165 (13963) SS BOND : bond 0.00335 ( 10) SS BOND : angle 2.09685 ( 20) hydrogen bonds : bond 0.04465 ( 488) hydrogen bonds : angle 4.59037 ( 1380) Misc. bond : bond 0.00011 ( 1) link_NAG-ASN : bond 0.00211 ( 4) link_NAG-ASN : angle 1.69594 ( 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 155 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7436 (mp10) cc_final: 0.7181 (mp10) REVERT: R 59 MET cc_start: 0.5294 (OUTLIER) cc_final: 0.4055 (mtp) REVERT: R 94 PHE cc_start: 0.6664 (m-80) cc_final: 0.6319 (m-10) REVERT: R 107 LYS cc_start: 0.6592 (mmtt) cc_final: 0.5985 (mmmm) REVERT: R 202 LEU cc_start: 0.7930 (mt) cc_final: 0.7676 (mm) REVERT: R 260 ARG cc_start: 0.7173 (ptp-170) cc_final: 0.6899 (ptp-170) REVERT: R 314 PHE cc_start: 0.7625 (m-10) cc_final: 0.7171 (t80) REVERT: R 340 LYS cc_start: 0.7422 (mmmt) cc_final: 0.7027 (mttp) REVERT: R 374 TYR cc_start: 0.7686 (m-80) cc_final: 0.7322 (m-80) REVERT: R 405 GLN cc_start: 0.7212 (mt0) cc_final: 0.7002 (mm-40) REVERT: A 55 THR cc_start: 0.8164 (m) cc_final: 0.7217 (m) REVERT: A 59 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6306 (mp10) REVERT: A 356 ARG cc_start: 0.7321 (mtm110) cc_final: 0.6566 (ptt-90) REVERT: B 37 ILE cc_start: 0.7550 (tt) cc_final: 0.7239 (pt) REVERT: B 46 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7328 (mtm-85) REVERT: B 134 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7058 (ppt170) REVERT: B 186 ASP cc_start: 0.8695 (m-30) cc_final: 0.8477 (m-30) outliers start: 13 outliers final: 8 residues processed: 152 average time/residue: 0.6804 time to fit residues: 110.3917 Evaluate side-chains 154 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 59 MET Chi-restraints excluded: chain R residue 295 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 134 ARG Chi-restraints excluded: chain B residue 270 ILE 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 25 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 59 optimal weight: 0.0980 chunk 8 optimal weight: 0.0470 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 383 GLN A 294 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.198795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134760 restraints weight = 10825.075| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.75 r_work: 0.3524 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10296 Z= 0.106 Angle : 0.515 8.592 13995 Z= 0.271 Chirality : 0.041 0.200 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.697 50.615 1469 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.23 % Allowed : 16.52 % Favored : 82.24 % 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 aren not related in a simple way. whole: 1.18 (0.24), residues: 1258 helix: 2.13 (0.24), residues: 501 sheet: 0.31 (0.32), residues: 245 loop : -0.28 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 321 TYR 0.010 0.001 TYR A 339 PHE 0.011 0.001 PHE B 151 TRP 0.014 0.001 TRP R 236 HIS 0.002 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00222 (10281) covalent geometry : angle 0.50806 (13963) SS BOND : bond 0.00257 ( 10) SS BOND : angle 1.79009 ( 20) hydrogen bonds : bond 0.04003 ( 488) hydrogen bonds : angle 4.39143 ( 1380) Misc. bond : bond 0.00006 ( 1) link_NAG-ASN : bond 0.00243 ( 4) link_NAG-ASN : angle 1.76332 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6618.54 seconds wall clock time: 112 minutes 59.03 seconds (6779.03 seconds total)