Starting phenix.real_space_refine on Fri Sep 11 20:50:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hcy_0199/09_2026/6hcy_0199.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hcy_0199/09_2026/6hcy_0199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hcy_0199/09_2026/6hcy_0199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hcy_0199/09_2026/6hcy_0199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hcy_0199/09_2026/6hcy_0199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hcy_0199/09_2026/6hcy_0199.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6hcy_0199/09_2026/6hcy_0199.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hcy_0199/09_2026/6hcy_0199.cif" } resolution = 3.1 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= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 18 5.49 5 S 51 5.16 5 C 7209 2.51 5 N 1800 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11007 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: A, B Time building chain proxies: 3.83, per 1000 atoms: 0.35 Number of scatterers: 11007 At special positions: 0 Unit cell: (92.6478, 95.0859, 116.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 51 16.00 P 18 15.00 O 1926 8.00 N 1800 7.00 C 7209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Links applied NAG-ASN " NAG A 504 " - " ASN A 323 " " NAG B 504 " - " ASN B 323 " " NAG C 504 " - " ASN C 323 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 521.5 milliseconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 63.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.532A pdb=" N GLN C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.646A pdb=" N LEU C 89 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 93 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 125 Processing helix chain 'C' and resid 138 through 145 removed outlier: 3.511A pdb=" N LEU C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 removed outlier: 3.509A pdb=" N ARG C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.538A pdb=" N LYS C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 200 through 223 removed outlier: 3.708A pdb=" N PHE C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 221 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 235 through 239 removed outlier: 3.946A pdb=" N MET C 238 " --> pdb=" O THR C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 257 Proline residue: C 248 - end of helix Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.516A pdb=" N ALA C 266 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.581A pdb=" N LEU C 288 " --> pdb=" O ASP C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 309 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 314 through 331 Processing helix chain 'C' and resid 338 through 366 removed outlier: 3.577A pdb=" N ALA C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 384 Processing helix chain 'C' and resid 384 through 404 removed outlier: 3.554A pdb=" N LEU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 398 " --> pdb=" O CYS C 394 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 439 removed outlier: 3.756A pdb=" N MET C 439 " --> pdb=" O PHE C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.593A pdb=" N ASN C 444 " --> pdb=" O PRO C 440 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.532A pdb=" N GLN A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.647A pdb=" N LEU A 89 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 90 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 138 through 145 removed outlier: 3.512A pdb=" N LEU A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 173 removed outlier: 3.509A pdb=" N ARG A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 192 removed outlier: 3.538A pdb=" N LYS A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 200 through 223 removed outlier: 3.707A pdb=" N PHE A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.947A pdb=" N MET A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.516A pdb=" N ALA A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.580A pdb=" N LEU A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 309 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'A' and resid 314 through 331 Processing helix chain 'A' and resid 338 through 366 removed outlier: 3.578A pdb=" N ALA A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 384 through 404 removed outlier: 3.555A pdb=" N LEU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 398 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 439 removed outlier: 3.757A pdb=" N MET A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.593A pdb=" N ASN A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.532A pdb=" N GLN B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.646A pdb=" N LEU B 89 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 90 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B 93 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 138 through 145 removed outlier: 3.511A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 removed outlier: 3.509A pdb=" N ARG B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.538A pdb=" N LYS B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 200 through 223 removed outlier: 3.709A pdb=" N PHE B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.946A pdb=" N MET B 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 257 Proline residue: B 248 - end of helix Processing helix chain 'B' and resid 260 through 273 removed outlier: 3.516A pdb=" N ALA B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 288 removed outlier: 3.581A pdb=" N LEU B 288 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 309 Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'B' and resid 314 through 331 Processing helix chain 'B' and resid 338 through 366 removed outlier: 3.578A pdb=" N ALA B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 384 Processing helix chain 'B' and resid 384 through 404 removed outlier: 3.554A pdb=" N LEU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 398 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 removed outlier: 3.756A pdb=" N MET B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.593A pdb=" N ASN B 444 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 64 through 65 removed outlier: 8.085A pdb=" N LEU C 65 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE C 47 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 22 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY C 48 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 24 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR C 21 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ILE C 78 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS C 23 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU C 101 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL C 153 " --> pdb=" O MET C 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 8.085A pdb=" N LEU A 65 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 47 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 22 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY A 48 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 24 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR A 21 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ILE A 78 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS A 23 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 101 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL A 153 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 65 removed outlier: 8.085A pdb=" N LEU B 65 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 47 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 22 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY B 48 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 24 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 21 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ILE B 78 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS B 23 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 101 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL B 153 " --> pdb=" O MET B 178 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1467 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: 1.65 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3496 1.36 - 1.55: 7702 1.55 - 1.73: 40 1.73 - 1.91: 78 1.91 - 2.10: 9 Bond restraints: 11325 Sorted by residual: bond pdb=" C1D NAP B 501 " pdb=" C2D NAP B 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1D NAP A 501 " pdb=" C2D NAP A 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1D NAP C 501 " pdb=" C2D NAP C 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1D NAP B 501 " pdb=" O4D NAP B 501 " ideal model delta sigma weight residual 1.375 1.611 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1D NAP C 501 " pdb=" O4D NAP C 501 " ideal model delta sigma weight residual 1.375 1.610 -0.235 2.00e-02 2.50e+03 1.39e+02 ... (remaining 11320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.91: 15468 10.91 - 21.83: 27 21.83 - 32.74: 0 32.74 - 43.65: 0 43.65 - 54.57: 3 Bond angle restraints: 15498 Sorted by residual: angle pdb=" O13 44E A 505 " pdb=" P 44E A 505 " pdb=" O14 44E A 505 " ideal model delta sigma weight residual 54.79 109.36 -54.57 3.00e+00 1.11e-01 3.31e+02 angle pdb=" O13 44E C 505 " pdb=" P 44E C 505 " pdb=" O14 44E C 505 " ideal model delta sigma weight residual 54.79 109.34 -54.55 3.00e+00 1.11e-01 3.31e+02 angle pdb=" O13 44E B 505 " pdb=" P 44E B 505 " pdb=" O14 44E B 505 " ideal model delta sigma weight residual 54.79 109.29 -54.50 3.00e+00 1.11e-01 3.30e+02 angle pdb=" O12 44E C 505 " pdb=" P 44E C 505 " pdb=" O14 44E C 505 " ideal model delta sigma weight residual 127.76 109.88 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" O12 44E B 505 " pdb=" P 44E B 505 " pdb=" O14 44E B 505 " ideal model delta sigma weight residual 127.76 109.90 17.86 3.00e+00 1.11e-01 3.54e+01 ... (remaining 15493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 6357 34.81 - 69.63: 99 69.63 - 104.44: 24 104.44 - 139.25: 0 139.25 - 174.06: 3 Dihedral angle restraints: 6483 sinusoidal: 2658 harmonic: 3825 Sorted by residual: dihedral pdb=" C2C HEM A 502 " pdb=" C3C HEM A 502 " pdb=" CAC HEM A 502 " pdb=" CBC HEM A 502 " ideal model delta sinusoidal sigma weight residual -0.00 -80.33 80.33 2 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" C2C HEM C 502 " pdb=" C3C HEM C 502 " pdb=" CAC HEM C 502 " pdb=" CBC HEM C 502 " ideal model delta sinusoidal sigma weight residual 0.00 -80.30 80.30 2 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" C2C HEM B 502 " pdb=" C3C HEM B 502 " pdb=" CAC HEM B 502 " pdb=" CBC HEM B 502 " ideal model delta sinusoidal sigma weight residual 0.00 -80.25 80.25 2 1.00e+01 1.00e-02 4.66e+01 ... (remaining 6480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1384 0.071 - 0.142: 300 0.142 - 0.214: 47 0.214 - 0.285: 6 0.285 - 0.356: 6 Chirality restraints: 1743 Sorted by residual: chirality pdb=" C2B NAP B 501 " pdb=" C1B NAP B 501 " pdb=" C3B NAP B 501 " pdb=" O2B NAP B 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C2B NAP C 501 " pdb=" C1B NAP C 501 " pdb=" C3B NAP C 501 " pdb=" O2B NAP C 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C2B NAP A 501 " pdb=" C1B NAP A 501 " pdb=" C3B NAP A 501 " pdb=" O2B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1740 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 286 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP B 286 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 286 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 286 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 286 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 286 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 286 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 286 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 286 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 286 " 0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP A 286 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 286 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 286 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 286 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 286 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 286 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 286 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 286 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 286 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 286 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP C 286 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 286 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP C 286 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 286 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 286 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 286 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 286 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 286 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 286 " -0.004 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 49 2.59 - 3.17: 8665 3.17 - 3.75: 16698 3.75 - 4.32: 24407 4.32 - 4.90: 39657 Nonbonded interactions: 89476 Sorted by model distance: nonbonded pdb=" NE2 HIS A 304 " pdb="FE HEM A 502 " model vdw 2.017 3.080 nonbonded pdb=" NE2 HIS C 304 " pdb="FE HEM C 502 " model vdw 2.018 3.080 nonbonded pdb=" NE2 HIS B 304 " pdb="FE HEM B 502 " model vdw 2.018 3.080 nonbonded pdb=" O3' FAD B 503 " pdb=" O5' FAD B 503 " model vdw 2.260 3.040 nonbonded pdb=" O3' FAD C 503 " pdb=" O5' FAD C 503 " model vdw 2.260 3.040 ... (remaining 89471 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.080 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 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 : 0.016 0.237 11331 Z= 0.696 Angle : 1.560 54.566 15507 Z= 0.664 Chirality : 0.065 0.356 1743 Planarity : 0.008 0.058 1839 Dihedral : 14.662 174.064 4029 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.79 % Allowed : 5.28 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.30 (0.15), residues: 1302 helix: -4.31 (0.07), residues: 846 sheet: -1.97 (0.42), residues: 141 loop : -3.85 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 290 TYR 0.021 0.002 TYR A 348 PHE 0.017 0.003 PHE A 302 TRP 0.062 0.005 TRP B 286 HIS 0.010 0.002 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.01567 / 0.70 (11325) covalent geometry : angle 1.55442 / 0.66 (15498) hydrogen bonds : bond 0.30213 / 20.21 ( 501) hydrogen bonds : angle 10.41344 / 7.18 ( 1467) Misc. bond : bond 0.15828 / 7.93 ( 3) link_NAG-ASN : bond 0.00548 / 0.27 ( 3) link_NAG-ASN : angle 5.65252 / 3.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 222 time to evaluate : 0.369 Fit side-chains REVERT: C 119 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8327 (mt-10) REVERT: C 147 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8522 (pp) REVERT: C 151 ARG cc_start: 0.8466 (tpp80) cc_final: 0.8179 (ttm-80) REVERT: C 161 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8795 (ttpp) REVERT: C 184 MET cc_start: 0.8550 (mmp) cc_final: 0.8333 (ptp) REVERT: C 191 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8232 (ttmm) REVERT: C 231 LYS cc_start: 0.8502 (mttt) cc_final: 0.7989 (tmtt) REVERT: C 281 ASP cc_start: 0.8594 (t0) cc_final: 0.8184 (t0) REVERT: C 450 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7831 (mtp180) REVERT: A 20 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7833 (tp30) REVERT: A 87 ASP cc_start: 0.8600 (m-30) cc_final: 0.8389 (m-30) REVERT: A 119 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8322 (mt-10) REVERT: A 147 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8595 (pp) REVERT: A 159 ASP cc_start: 0.8080 (t0) cc_final: 0.7800 (t0) REVERT: A 161 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8732 (ttpp) REVERT: A 184 MET cc_start: 0.8581 (mmp) cc_final: 0.8105 (ptp) REVERT: A 231 LYS cc_start: 0.8458 (mttt) cc_final: 0.8082 (tmtt) REVERT: A 281 ASP cc_start: 0.8822 (t0) cc_final: 0.8392 (t0) REVERT: B 38 MET cc_start: 0.8885 (mtt) cc_final: 0.8674 (mtt) REVERT: B 115 GLU cc_start: 0.8002 (pm20) cc_final: 0.7733 (pm20) REVERT: B 119 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8273 (mt-10) REVERT: B 147 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8298 (pp) REVERT: B 151 ARG cc_start: 0.8447 (tpp80) cc_final: 0.8091 (tpp-160) REVERT: B 184 MET cc_start: 0.8539 (mmp) cc_final: 0.8335 (ptp) REVERT: B 188 GLU cc_start: 0.7912 (tt0) cc_final: 0.7694 (tm-30) REVERT: B 191 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8371 (ttmm) REVERT: B 217 TYR cc_start: 0.9068 (t80) cc_final: 0.8799 (t80) REVERT: B 231 LYS cc_start: 0.8493 (mttt) cc_final: 0.8018 (tmtt) REVERT: B 281 ASP cc_start: 0.8525 (t0) cc_final: 0.8140 (t0) outliers start: 9 outliers final: 0 residues processed: 231 average time/residue: 0.1289 time to fit residues: 39.1918 Evaluate side-chains 117 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN C 143 GLN C 234 ASN A 234 ASN B 111 ASN B 234 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.081504 restraints weight = 14088.254| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.06 r_work: 0.2687 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 11331 Z= 0.133 Angle : 0.662 7.616 15507 Z= 0.317 Chirality : 0.042 0.132 1743 Planarity : 0.006 0.046 1839 Dihedral : 14.557 167.868 1620 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.17 % Allowed : 7.30 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.21), residues: 1302 helix: -1.60 (0.15), residues: 819 sheet: -1.91 (0.42), residues: 141 loop : -2.87 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 377 TYR 0.017 0.001 TYR A 415 PHE 0.009 0.001 PHE C 300 TRP 0.029 0.002 TRP C 286 HIS 0.003 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (11325) covalent geometry : angle 0.65804 / 0.32 (15498) hydrogen bonds : bond 0.04366 / 2.90 ( 501) hydrogen bonds : angle 4.45516 / 2.98 ( 1467) Misc. bond : bond 0.22425 / 11.24 ( 3) link_NAG-ASN : bond 0.00567 / 0.28 ( 3) link_NAG-ASN : angle 3.13535 / 2.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.372 Fit side-chains REVERT: C 119 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8238 (mt-10) REVERT: C 147 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8111 (pp) REVERT: C 151 ARG cc_start: 0.8408 (tpp80) cc_final: 0.8000 (ttm-80) REVERT: C 161 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8713 (mtpp) REVERT: C 191 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8202 (ttmm) REVERT: C 231 LYS cc_start: 0.8414 (mttt) cc_final: 0.7863 (tmtt) REVERT: C 281 ASP cc_start: 0.8967 (t0) cc_final: 0.8497 (t0) REVERT: C 416 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8011 (pp) REVERT: C 448 ARG cc_start: 0.8036 (ttp-110) cc_final: 0.7668 (ttp-110) REVERT: C 450 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7520 (mtp180) REVERT: A 20 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7942 (tp30) REVERT: A 147 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8213 (pp) REVERT: A 161 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8418 (ttpp) REVERT: A 199 MET cc_start: 0.9295 (mmm) cc_final: 0.9065 (mmm) REVERT: A 231 LYS cc_start: 0.8413 (mttt) cc_final: 0.8017 (tmtt) REVERT: A 281 ASP cc_start: 0.9096 (t0) cc_final: 0.8758 (t0) REVERT: A 435 PHE cc_start: 0.8628 (t80) cc_final: 0.8414 (t80) REVERT: A 453 TRP cc_start: 0.7469 (t-100) cc_final: 0.7202 (t-100) REVERT: B 119 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8229 (mt-10) REVERT: B 147 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7881 (pp) REVERT: B 151 ARG cc_start: 0.8366 (tpp80) cc_final: 0.7660 (ttm-80) REVERT: B 184 MET cc_start: 0.9033 (mmp) cc_final: 0.8326 (ptp) REVERT: B 188 GLU cc_start: 0.8378 (tt0) cc_final: 0.7839 (tm-30) REVERT: B 217 TYR cc_start: 0.8894 (t80) cc_final: 0.8507 (t80) REVERT: B 231 LYS cc_start: 0.8428 (mttt) cc_final: 0.7900 (tmtt) REVERT: B 281 ASP cc_start: 0.8919 (t0) cc_final: 0.8480 (t0) REVERT: B 448 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7449 (ttp-110) outliers start: 36 outliers final: 17 residues processed: 161 average time/residue: 0.1165 time to fit residues: 25.6970 Evaluate side-chains 134 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN C 383 GLN B 111 ASN B 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.078129 restraints weight = 14126.906| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.06 r_work: 0.2632 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.228 11331 Z= 0.169 Angle : 0.643 9.004 15507 Z= 0.300 Chirality : 0.043 0.129 1743 Planarity : 0.005 0.042 1839 Dihedral : 13.812 167.484 1620 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.25 % Allowed : 8.27 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.23), residues: 1302 helix: -0.10 (0.18), residues: 828 sheet: -1.80 (0.44), residues: 117 loop : -2.70 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.015 0.001 TYR C 348 PHE 0.011 0.001 PHE A 302 TRP 0.024 0.002 TRP C 286 HIS 0.005 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.17 (11325) covalent geometry : angle 0.63960 / 0.30 (15498) hydrogen bonds : bond 0.03763 / 2.52 ( 501) hydrogen bonds : angle 3.88181 / 2.60 ( 1467) Misc. bond : bond 0.21726 / 10.88 ( 3) link_NAG-ASN : bond 0.00550 / 0.27 ( 3) link_NAG-ASN : angle 2.69466 / 1.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8232 (mt-10) REVERT: C 147 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8046 (pp) REVERT: C 151 ARG cc_start: 0.8387 (tpp80) cc_final: 0.8130 (ttm-80) REVERT: C 231 LYS cc_start: 0.8389 (mttt) cc_final: 0.7775 (tmtt) REVERT: C 281 ASP cc_start: 0.8983 (t0) cc_final: 0.8546 (t0) REVERT: C 416 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7900 (pp) REVERT: C 450 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7533 (mtp180) REVERT: A 20 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7980 (tp30) REVERT: A 39 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 147 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8019 (pp) REVERT: A 161 LYS cc_start: 0.8750 (mtpp) cc_final: 0.8477 (mtpp) REVERT: A 199 MET cc_start: 0.9303 (mmm) cc_final: 0.9064 (mmm) REVERT: A 231 LYS cc_start: 0.8397 (mttt) cc_final: 0.7995 (tmtt) REVERT: A 281 ASP cc_start: 0.9156 (t0) cc_final: 0.8754 (t0) REVERT: B 119 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8247 (mt-10) REVERT: B 147 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7971 (pp) REVERT: B 151 ARG cc_start: 0.8332 (tpp80) cc_final: 0.8125 (ttm-80) REVERT: B 231 LYS cc_start: 0.8452 (mttt) cc_final: 0.7908 (tmtt) REVERT: B 270 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8075 (mp) REVERT: B 281 ASP cc_start: 0.8983 (t0) cc_final: 0.8557 (t0) REVERT: B 290 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8007 (mtm110) REVERT: B 448 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7434 (ttp-110) outliers start: 37 outliers final: 18 residues processed: 146 average time/residue: 0.1255 time to fit residues: 24.9663 Evaluate side-chains 121 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.0000 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN B 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.079573 restraints weight = 14290.518| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.08 r_work: 0.2626 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 11331 Z= 0.119 Angle : 0.578 7.036 15507 Z= 0.270 Chirality : 0.041 0.131 1743 Planarity : 0.004 0.041 1839 Dihedral : 13.428 168.127 1620 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.69 % Allowed : 8.18 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.24), residues: 1302 helix: 0.45 (0.18), residues: 840 sheet: -1.66 (0.44), residues: 117 loop : -2.67 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 278 TYR 0.019 0.001 TYR B 415 PHE 0.009 0.001 PHE B 300 TRP 0.016 0.001 TRP C 286 HIS 0.003 0.000 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.12 (11325) covalent geometry : angle 0.57478 / 0.27 (15498) hydrogen bonds : bond 0.03133 / 2.09 ( 501) hydrogen bonds : angle 3.63400 / 2.44 ( 1467) Misc. bond : bond 0.14987 / 7.50 ( 3) link_NAG-ASN : bond 0.00637 / 0.32 ( 3) link_NAG-ASN : angle 2.56394 / 1.72 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8257 (mt-10) REVERT: C 147 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8101 (pp) REVERT: C 151 ARG cc_start: 0.8358 (tpp80) cc_final: 0.8076 (ttm-80) REVERT: C 231 LYS cc_start: 0.8433 (mttt) cc_final: 0.7796 (tmtt) REVERT: C 281 ASP cc_start: 0.8878 (t0) cc_final: 0.8440 (t0) REVERT: C 450 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7437 (mtp180) REVERT: A 20 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7968 (tp30) REVERT: A 39 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 147 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8064 (pp) REVERT: A 161 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8417 (mtpp) REVERT: A 178 MET cc_start: 0.8193 (mmm) cc_final: 0.7948 (mmm) REVERT: A 199 MET cc_start: 0.9293 (mmm) cc_final: 0.9091 (mmm) REVERT: A 231 LYS cc_start: 0.8411 (mttt) cc_final: 0.7985 (tmtt) REVERT: A 281 ASP cc_start: 0.9081 (t0) cc_final: 0.8611 (t0) REVERT: A 415 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7625 (m-10) REVERT: B 119 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8236 (mt-10) REVERT: B 147 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8053 (pp) REVERT: B 231 LYS cc_start: 0.8432 (mttt) cc_final: 0.7897 (tmtt) REVERT: B 281 ASP cc_start: 0.8924 (t0) cc_final: 0.8424 (t0) REVERT: B 290 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8075 (mtm110) REVERT: B 310 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8458 (m) REVERT: B 405 ARG cc_start: 0.6424 (mmt90) cc_final: 0.6221 (mpt-90) outliers start: 42 outliers final: 16 residues processed: 138 average time/residue: 0.1121 time to fit residues: 21.2984 Evaluate side-chains 120 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.078620 restraints weight = 14335.920| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.05 r_work: 0.2620 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 11331 Z= 0.152 Angle : 0.595 6.854 15507 Z= 0.277 Chirality : 0.042 0.137 1743 Planarity : 0.004 0.039 1839 Dihedral : 13.100 165.791 1620 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.34 % Allowed : 8.27 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1302 helix: 0.87 (0.19), residues: 825 sheet: -1.62 (0.43), residues: 117 loop : -2.49 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.016 0.001 TYR A 348 PHE 0.008 0.001 PHE B 134 TRP 0.016 0.001 TRP B 286 HIS 0.005 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.15 (11325) covalent geometry : angle 0.59156 / 0.28 (15498) hydrogen bonds : bond 0.03260 / 2.17 ( 501) hydrogen bonds : angle 3.59113 / 2.41 ( 1467) Misc. bond : bond 0.18870 / 9.44 ( 3) link_NAG-ASN : bond 0.00488 / 0.24 ( 3) link_NAG-ASN : angle 2.56917 / 1.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8266 (mt-10) REVERT: C 147 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8159 (pp) REVERT: C 151 ARG cc_start: 0.8399 (tpp80) cc_final: 0.8111 (ttm-80) REVERT: C 231 LYS cc_start: 0.8421 (mttt) cc_final: 0.7784 (tmtt) REVERT: C 281 ASP cc_start: 0.8857 (t0) cc_final: 0.8421 (t0) REVERT: C 450 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7462 (mtp180) REVERT: A 20 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7963 (tp30) REVERT: A 39 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 147 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 161 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8479 (mtpp) REVERT: A 199 MET cc_start: 0.9355 (mmm) cc_final: 0.9129 (mmm) REVERT: A 231 LYS cc_start: 0.8350 (mttt) cc_final: 0.7948 (tmtt) REVERT: A 281 ASP cc_start: 0.9083 (t0) cc_final: 0.8643 (t0) REVERT: A 415 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7724 (m-10) REVERT: B 115 GLU cc_start: 0.7998 (pm20) cc_final: 0.7576 (pm20) REVERT: B 119 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8311 (mt-10) REVERT: B 147 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8275 (pp) REVERT: B 231 LYS cc_start: 0.8432 (mttt) cc_final: 0.7902 (tmtt) REVERT: B 278 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8263 (mtp-110) REVERT: B 281 ASP cc_start: 0.8934 (t0) cc_final: 0.8463 (t0) REVERT: B 290 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8138 (mtm180) REVERT: B 310 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8507 (m) outliers start: 38 outliers final: 23 residues processed: 128 average time/residue: 0.1300 time to fit residues: 23.0116 Evaluate side-chains 119 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 125 optimal weight: 0.0870 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.0570 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.081491 restraints weight = 14260.800| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.09 r_work: 0.2673 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 11331 Z= 0.098 Angle : 0.551 6.361 15507 Z= 0.255 Chirality : 0.040 0.130 1743 Planarity : 0.004 0.038 1839 Dihedral : 12.701 167.682 1620 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.64 % Allowed : 9.15 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1302 helix: 0.96 (0.19), residues: 858 sheet: -1.57 (0.42), residues: 117 loop : -2.46 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 278 TYR 0.016 0.001 TYR A 348 PHE 0.008 0.001 PHE A 300 TRP 0.011 0.001 TRP B 286 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 (11325) covalent geometry : angle 0.54765 / 0.25 (15498) hydrogen bonds : bond 0.02724 / 1.81 ( 501) hydrogen bonds : angle 3.42541 / 2.30 ( 1467) Misc. bond : bond 0.10420 / 5.20 ( 3) link_NAG-ASN : bond 0.00648 / 0.32 ( 3) link_NAG-ASN : angle 2.41642 / 1.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8265 (mt-10) REVERT: C 147 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8223 (pp) REVERT: C 151 ARG cc_start: 0.8352 (tpp80) cc_final: 0.8064 (ttm-80) REVERT: C 231 LYS cc_start: 0.8430 (mttt) cc_final: 0.7859 (tmtt) REVERT: C 281 ASP cc_start: 0.8757 (t0) cc_final: 0.8339 (t0) REVERT: C 290 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7911 (mtm110) REVERT: C 450 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7455 (mtp180) REVERT: A 20 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7987 (tp30) REVERT: A 39 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8414 (mm) REVERT: A 147 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7962 (pp) REVERT: A 151 ARG cc_start: 0.8415 (tpp80) cc_final: 0.8080 (ttm-80) REVERT: A 161 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8471 (mtpp) REVERT: A 231 LYS cc_start: 0.8303 (mttt) cc_final: 0.7881 (tmtt) REVERT: A 281 ASP cc_start: 0.8942 (t0) cc_final: 0.8472 (t0) REVERT: A 415 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7654 (m-10) REVERT: B 115 GLU cc_start: 0.7921 (pm20) cc_final: 0.7506 (pm20) REVERT: B 119 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8250 (mt-10) REVERT: B 147 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8278 (pp) REVERT: B 217 TYR cc_start: 0.8903 (t80) cc_final: 0.8579 (t80) REVERT: B 231 LYS cc_start: 0.8394 (mttt) cc_final: 0.7849 (tmtt) REVERT: B 278 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8274 (mtp-110) REVERT: B 281 ASP cc_start: 0.8773 (t0) cc_final: 0.8394 (t0) REVERT: B 290 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8106 (mpp80) outliers start: 30 outliers final: 20 residues processed: 128 average time/residue: 0.1279 time to fit residues: 22.8693 Evaluate side-chains 119 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 9 optimal weight: 0.0670 chunk 100 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.078232 restraints weight = 14190.721| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.97 r_work: 0.2625 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 11331 Z= 0.154 Angle : 0.583 6.159 15507 Z= 0.271 Chirality : 0.042 0.134 1743 Planarity : 0.004 0.037 1839 Dihedral : 12.661 165.895 1620 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.25 % Allowed : 9.06 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1302 helix: 1.12 (0.19), residues: 849 sheet: -1.47 (0.42), residues: 117 loop : -2.46 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 278 TYR 0.016 0.001 TYR C 348 PHE 0.007 0.001 PHE B 134 TRP 0.015 0.001 TRP C 286 HIS 0.005 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.15 (11325) covalent geometry : angle 0.57986 / 0.27 (15498) hydrogen bonds : bond 0.03127 / 2.08 ( 501) hydrogen bonds : angle 3.46695 / 2.33 ( 1467) Misc. bond : bond 0.18118 / 9.05 ( 3) link_NAG-ASN : bond 0.00420 / 0.21 ( 3) link_NAG-ASN : angle 2.51417 / 1.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8368 (mt-10) REVERT: C 147 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8469 (pp) REVERT: C 231 LYS cc_start: 0.8512 (mttt) cc_final: 0.7912 (tmtt) REVERT: C 281 ASP cc_start: 0.8776 (t0) cc_final: 0.8338 (t0) REVERT: C 290 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8078 (mtm110) REVERT: C 450 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7482 (mtp180) REVERT: A 20 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8059 (tp30) REVERT: A 39 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 147 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8095 (pp) REVERT: A 151 ARG cc_start: 0.8554 (tpp80) cc_final: 0.8230 (ttm-80) REVERT: A 161 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8530 (mtpp) REVERT: A 231 LYS cc_start: 0.8441 (mttt) cc_final: 0.8014 (tmtt) REVERT: A 281 ASP cc_start: 0.8958 (t0) cc_final: 0.8541 (t0) REVERT: A 415 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7788 (m-10) REVERT: B 115 GLU cc_start: 0.8071 (pm20) cc_final: 0.7639 (pm20) REVERT: B 119 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8351 (mt-10) REVERT: B 147 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8416 (pp) REVERT: B 231 LYS cc_start: 0.8514 (mttt) cc_final: 0.7996 (tmtt) REVERT: B 278 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8322 (mtp-110) REVERT: B 281 ASP cc_start: 0.8784 (t0) cc_final: 0.8332 (t0) REVERT: B 290 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8334 (mtm180) outliers start: 37 outliers final: 23 residues processed: 121 average time/residue: 0.1319 time to fit residues: 22.0072 Evaluate side-chains 116 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 415 TYR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 125 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 35 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 81 optimal weight: 0.0020 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.081565 restraints weight = 14133.077| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.05 r_work: 0.2671 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 11331 Z= 0.099 Angle : 0.549 6.072 15507 Z= 0.256 Chirality : 0.040 0.130 1743 Planarity : 0.004 0.037 1839 Dihedral : 12.496 167.590 1620 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.99 % Allowed : 9.50 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1302 helix: 1.18 (0.19), residues: 864 sheet: -1.34 (0.43), residues: 117 loop : -2.39 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 448 TYR 0.016 0.001 TYR A 348 PHE 0.008 0.001 PHE B 300 TRP 0.025 0.001 TRP A 453 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.10 (11325) covalent geometry : angle 0.54661 / 0.25 (15498) hydrogen bonds : bond 0.02713 / 1.80 ( 501) hydrogen bonds : angle 3.36653 / 2.26 ( 1467) Misc. bond : bond 0.11214 / 5.59 ( 3) link_NAG-ASN : bond 0.00598 / 0.30 ( 3) link_NAG-ASN : angle 2.37005 / 1.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 147 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8465 (pp) REVERT: C 231 LYS cc_start: 0.8430 (mttt) cc_final: 0.7852 (tmtt) REVERT: C 281 ASP cc_start: 0.8718 (t0) cc_final: 0.8300 (t0) REVERT: C 290 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7901 (mtm110) REVERT: C 450 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7413 (mtp180) REVERT: A 20 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8036 (tp30) REVERT: A 39 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8419 (mm) REVERT: A 147 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7935 (pp) REVERT: A 151 ARG cc_start: 0.8378 (tpp80) cc_final: 0.8078 (ttm-80) REVERT: A 161 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8453 (mtpp) REVERT: A 231 LYS cc_start: 0.8319 (mttt) cc_final: 0.7873 (tmtt) REVERT: A 281 ASP cc_start: 0.8856 (t0) cc_final: 0.8520 (t0) REVERT: A 415 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7711 (m-10) REVERT: B 115 GLU cc_start: 0.7933 (pm20) cc_final: 0.7507 (pm20) REVERT: B 119 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8238 (mt-10) REVERT: B 147 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8345 (pp) REVERT: B 231 LYS cc_start: 0.8410 (mttt) cc_final: 0.7836 (tmtt) REVERT: B 278 ARG cc_start: 0.8784 (mmm-85) cc_final: 0.8301 (mtp-110) REVERT: B 281 ASP cc_start: 0.8740 (t0) cc_final: 0.8351 (t0) REVERT: B 290 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8115 (mpp80) outliers start: 34 outliers final: 24 residues processed: 121 average time/residue: 0.1225 time to fit residues: 20.6744 Evaluate side-chains 115 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 415 TYR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 80 optimal weight: 0.0870 chunk 110 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.080682 restraints weight = 14116.849| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.98 r_work: 0.2663 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 11331 Z= 0.107 Angle : 0.549 6.152 15507 Z= 0.256 Chirality : 0.041 0.133 1743 Planarity : 0.004 0.036 1839 Dihedral : 12.380 167.109 1620 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.17 % Allowed : 9.85 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1302 helix: 1.31 (0.19), residues: 861 sheet: -1.20 (0.44), residues: 117 loop : -2.28 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 278 TYR 0.015 0.001 TYR A 348 PHE 0.006 0.001 PHE C 300 TRP 0.011 0.001 TRP B 286 HIS 0.003 0.000 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.11 (11325) covalent geometry : angle 0.54616 / 0.26 (15498) hydrogen bonds : bond 0.02747 / 1.83 ( 501) hydrogen bonds : angle 3.33701 / 2.25 ( 1467) Misc. bond : bond 0.13399 / 6.68 ( 3) link_NAG-ASN : bond 0.00489 / 0.24 ( 3) link_NAG-ASN : angle 2.37616 / 1.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 147 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8601 (pp) REVERT: C 231 LYS cc_start: 0.8488 (mttt) cc_final: 0.7916 (tmtt) REVERT: C 281 ASP cc_start: 0.8664 (t0) cc_final: 0.8358 (t0) REVERT: C 290 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8018 (mtm110) REVERT: C 450 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7464 (mtp180) REVERT: A 20 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8090 (tp30) REVERT: A 39 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 147 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8093 (pp) REVERT: A 151 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8238 (ttm-80) REVERT: A 161 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8527 (mtpp) REVERT: A 231 LYS cc_start: 0.8435 (mttt) cc_final: 0.7985 (tmtt) REVERT: A 281 ASP cc_start: 0.8787 (t0) cc_final: 0.8384 (t0) REVERT: A 290 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8297 (mtm180) REVERT: A 415 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: B 115 GLU cc_start: 0.8037 (pm20) cc_final: 0.7664 (pm20) REVERT: B 147 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8504 (pp) REVERT: B 161 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8380 (mtpp) REVERT: B 231 LYS cc_start: 0.8526 (mttt) cc_final: 0.7958 (tmtt) REVERT: B 278 ARG cc_start: 0.8729 (mmm-85) cc_final: 0.8328 (mtp-110) REVERT: B 281 ASP cc_start: 0.8683 (t0) cc_final: 0.8213 (t0) REVERT: B 290 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8284 (mpp80) outliers start: 36 outliers final: 24 residues processed: 120 average time/residue: 0.1392 time to fit residues: 22.7398 Evaluate side-chains 116 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 86 optimal weight: 7.9990 chunk 18 optimal weight: 0.2980 chunk 112 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 98 optimal weight: 4.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.081767 restraints weight = 14083.670| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.15 r_work: 0.2681 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 11331 Z= 0.096 Angle : 0.540 6.024 15507 Z= 0.251 Chirality : 0.040 0.131 1743 Planarity : 0.004 0.036 1839 Dihedral : 12.221 168.209 1620 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.90 % Allowed : 10.20 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1302 helix: 1.24 (0.19), residues: 885 sheet: -1.03 (0.45), residues: 117 loop : -2.43 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 278 TYR 0.015 0.001 TYR A 348 PHE 0.006 0.001 PHE B 300 TRP 0.009 0.001 TRP B 286 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 (11325) covalent geometry : angle 0.53717 / 0.25 (15498) hydrogen bonds : bond 0.02542 / 1.68 ( 501) hydrogen bonds : angle 3.26583 / 2.20 ( 1467) Misc. bond : bond 0.09668 / 4.82 ( 3) link_NAG-ASN : bond 0.00534 / 0.27 ( 3) link_NAG-ASN : angle 2.29358 / 1.55 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: C 147 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8523 (pp) REVERT: C 231 LYS cc_start: 0.8441 (mttt) cc_final: 0.7865 (tmtt) REVERT: C 281 ASP cc_start: 0.8648 (t0) cc_final: 0.8218 (t0) REVERT: C 290 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7827 (mtm110) REVERT: C 450 ARG cc_start: 0.7776 (mtm110) cc_final: 0.7346 (mtp180) REVERT: A 20 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8061 (tp30) REVERT: A 39 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8408 (mm) REVERT: A 147 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7955 (pp) REVERT: A 151 ARG cc_start: 0.8352 (tpp80) cc_final: 0.8070 (ttm-80) REVERT: A 161 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8423 (mtpp) REVERT: A 231 LYS cc_start: 0.8375 (mttt) cc_final: 0.7887 (tmtt) REVERT: A 281 ASP cc_start: 0.8779 (t0) cc_final: 0.8381 (t0) REVERT: A 415 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7704 (m-10) REVERT: B 20 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: B 115 GLU cc_start: 0.7999 (pm20) cc_final: 0.7565 (pm20) REVERT: B 147 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8347 (pp) REVERT: B 161 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8266 (mtpp) REVERT: B 231 LYS cc_start: 0.8440 (mttt) cc_final: 0.7834 (tmtt) REVERT: B 278 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8240 (mtp-110) REVERT: B 281 ASP cc_start: 0.8640 (t0) cc_final: 0.8163 (t0) REVERT: B 290 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8093 (mpp80) outliers start: 33 outliers final: 23 residues processed: 119 average time/residue: 0.1388 time to fit residues: 22.5050 Evaluate side-chains 115 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 83 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.081462 restraints weight = 14042.722| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.15 r_work: 0.2673 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 11331 Z= 0.101 Angle : 0.539 6.739 15507 Z= 0.251 Chirality : 0.040 0.132 1743 Planarity : 0.004 0.036 1839 Dihedral : 12.141 167.700 1620 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.99 % Allowed : 10.11 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.25), residues: 1302 helix: 1.29 (0.19), residues: 885 sheet: -0.86 (0.46), residues: 117 loop : -2.39 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 278 TYR 0.015 0.001 TYR B 348 PHE 0.006 0.001 PHE C 300 TRP 0.010 0.001 TRP B 286 HIS 0.002 0.000 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.10 (11325) covalent geometry : angle 0.53635 / 0.25 (15498) hydrogen bonds : bond 0.02602 / 1.72 ( 501) hydrogen bonds : angle 3.25418 / 2.19 ( 1467) Misc. bond : bond 0.12028 / 6.00 ( 3) link_NAG-ASN : bond 0.00469 / 0.23 ( 3) link_NAG-ASN : angle 2.30225 / 1.57 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2865.77 seconds wall clock time: 49 minutes 55.31 seconds (2995.31 seconds total)