Starting phenix.real_space_refine on Thu Jun 4 07:39:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hcy_0199/06_2026/6hcy_0199.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hcy_0199/06_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_0199/06_2026/6hcy_0199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hcy_0199/06_2026/6hcy_0199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hcy_0199/06_2026/6hcy_0199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hcy_0199/06_2026/6hcy_0199.map" } 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-dev-6079/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: A, B Time building chain proxies: 3.61, per 1000 atoms: 0.33 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: 1.08 Conformation dependent library (CDL) restraints added in 622.8 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: 0.36 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: 1.74 Time building geometry restraints manager: 1.38 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: 6546 34.81 - 69.63: 228 69.63 - 104.44: 36 104.44 - 139.25: 0 139.25 - 174.06: 3 Dihedral angle restraints: 6813 sinusoidal: 2988 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 6810 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: 1.980 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.940 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: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 17.403 174.064 4359 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 : 0.456 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: 0.1507 time to fit residues: 45.2741 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 : 0.431 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3371 r_free = 0.3371 target = 0.118780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.081456 restraints weight = 14102.841| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.05 r_work: 0.2686 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.252 11331 Z= 0.134 Angle : 0.684 8.279 15507 Z= 0.324 Chirality : 0.043 0.132 1743 Planarity : 0.006 0.047 1839 Dihedral : 17.703 168.725 1950 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.17 % Allowed : 7.12 % Favored : 89.71 % 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: -3.10 (0.21), residues: 1302 helix: -1.55 (0.16), residues: 819 sheet: -1.91 (0.42), residues: 141 loop : -2.90 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 377 TYR 0.017 0.001 TYR A 415 PHE 0.009 0.001 PHE C 300 TRP 0.028 0.002 TRP C 286 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (11325) covalent geometry : angle 0.67922 / 0.32 (15498) hydrogen bonds : bond 0.04346 / 2.88 ( 501) hydrogen bonds : angle 4.42568 / 2.96 ( 1467) Misc. bond : bond 0.24729 / 12.39 ( 3) link_NAG-ASN : bond 0.00578 / 0.29 ( 3) link_NAG-ASN : angle 3.43503 / 2.22 ( 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 166 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.430 Fit side-chains REVERT: C 119 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8240 (mt-10) REVERT: C 147 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8133 (pp) REVERT: C 151 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8174 (ttm-80) REVERT: C 161 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8721 (mtpp) REVERT: C 191 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8211 (ttmm) REVERT: C 231 LYS cc_start: 0.8418 (mttt) cc_final: 0.7867 (tmtt) REVERT: C 281 ASP cc_start: 0.8968 (t0) cc_final: 0.8499 (t0) REVERT: C 416 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8035 (pp) REVERT: C 450 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7535 (mtp180) REVERT: A 20 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7946 (tp30) REVERT: A 147 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8239 (pp) REVERT: A 161 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8423 (ttpp) REVERT: A 199 MET cc_start: 0.9297 (mmm) cc_final: 0.9064 (mmm) REVERT: A 231 LYS cc_start: 0.8446 (mttt) cc_final: 0.8044 (tmtt) REVERT: A 281 ASP cc_start: 0.9113 (t0) cc_final: 0.8761 (t0) REVERT: A 435 PHE cc_start: 0.8627 (t80) cc_final: 0.8413 (t80) REVERT: A 453 TRP cc_start: 0.7483 (t-100) cc_final: 0.7214 (t-100) REVERT: B 119 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8229 (mt-10) REVERT: B 147 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7900 (pp) REVERT: B 151 ARG cc_start: 0.8372 (tpp80) cc_final: 0.7662 (ttm-80) REVERT: B 184 MET cc_start: 0.9036 (mmp) cc_final: 0.8325 (ptp) REVERT: B 217 TYR cc_start: 0.8892 (t80) cc_final: 0.8513 (t80) REVERT: B 231 LYS cc_start: 0.8432 (mttt) cc_final: 0.7903 (tmtt) REVERT: B 281 ASP cc_start: 0.8921 (t0) cc_final: 0.8475 (t0) REVERT: B 448 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7432 (ttp-110) outliers start: 36 outliers final: 17 residues processed: 159 average time/residue: 0.1340 time to fit residues: 29.0543 Evaluate side-chains 132 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 2.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN A 85 HIS B 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.078477 restraints weight = 14122.793| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.06 r_work: 0.2636 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 11331 Z= 0.162 Angle : 0.646 9.396 15507 Z= 0.298 Chirality : 0.044 0.129 1743 Planarity : 0.005 0.042 1839 Dihedral : 15.274 169.368 1950 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.17 % Allowed : 8.44 % 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: -1.54 (0.23), residues: 1302 helix: -0.15 (0.18), residues: 846 sheet: -1.77 (0.44), residues: 117 loop : -2.74 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 278 TYR 0.015 0.001 TYR C 415 PHE 0.010 0.001 PHE C 302 TRP 0.024 0.002 TRP C 286 HIS 0.004 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.16 (11325) covalent geometry : angle 0.64216 / 0.30 (15498) hydrogen bonds : bond 0.03691 / 2.47 ( 501) hydrogen bonds : angle 3.84214 / 2.58 ( 1467) Misc. bond : bond 0.20256 / 10.14 ( 3) link_NAG-ASN : bond 0.00588 / 0.29 ( 3) link_NAG-ASN : angle 3.14581 / 2.07 ( 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: 36 poor density : 115 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8210 (mt-10) REVERT: C 147 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8079 (pp) REVERT: C 151 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8128 (ttm-80) REVERT: C 231 LYS cc_start: 0.8392 (mttt) cc_final: 0.7770 (tmtt) REVERT: C 281 ASP cc_start: 0.8957 (t0) cc_final: 0.8532 (t0) REVERT: C 416 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7865 (pp) REVERT: C 450 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7482 (mtp180) REVERT: A 20 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7976 (tp30) REVERT: A 39 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8354 (mm) REVERT: A 147 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8016 (pp) REVERT: A 161 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8466 (mtpp) REVERT: A 199 MET cc_start: 0.9293 (mmm) cc_final: 0.9052 (mmm) REVERT: A 231 LYS cc_start: 0.8395 (mttt) cc_final: 0.7997 (tmtt) REVERT: A 281 ASP cc_start: 0.9153 (t0) cc_final: 0.8755 (t0) REVERT: B 119 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8186 (mt-10) REVERT: B 147 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7963 (pp) REVERT: B 151 ARG cc_start: 0.8330 (tpp80) cc_final: 0.8120 (ttm-80) REVERT: B 231 LYS cc_start: 0.8450 (mttt) cc_final: 0.7911 (tmtt) REVERT: B 270 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8105 (mp) REVERT: B 281 ASP cc_start: 0.8962 (t0) cc_final: 0.8541 (t0) REVERT: B 290 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7978 (mtm110) REVERT: B 448 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7437 (ttp-110) outliers start: 36 outliers final: 16 residues processed: 147 average time/residue: 0.1456 time to fit residues: 28.6568 Evaluate side-chains 117 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3343 r_free = 0.3343 target = 0.116920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.079582 restraints weight = 14285.292| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.08 r_work: 0.2652 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2805 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= 0.117 Angle : 0.586 7.177 15507 Z= 0.272 Chirality : 0.042 0.131 1743 Planarity : 0.004 0.041 1839 Dihedral : 14.229 169.012 1950 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.87 % Allowed : 8.00 % 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: -0.90 (0.24), residues: 1302 helix: 0.45 (0.18), residues: 840 sheet: -1.69 (0.44), residues: 117 loop : -2.71 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.018 0.001 TYR B 415 PHE 0.008 0.001 PHE C 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 0.00306 / 0.12 (11325) covalent geometry : angle 0.58115 / 0.27 (15498) hydrogen bonds : bond 0.03114 / 2.07 ( 501) hydrogen bonds : angle 3.63314 / 2.44 ( 1467) Misc. bond : bond 0.14980 / 7.50 ( 3) link_NAG-ASN : bond 0.00625 / 0.31 ( 3) link_NAG-ASN : angle 3.04115 / 1.99 ( 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 141 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8266 (mt-10) REVERT: C 147 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8119 (pp) REVERT: C 151 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8097 (ttm-80) REVERT: C 231 LYS cc_start: 0.8435 (mttt) cc_final: 0.7803 (tmtt) REVERT: C 281 ASP cc_start: 0.8848 (t0) cc_final: 0.8421 (t0) REVERT: C 450 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7439 (mtp180) REVERT: A 20 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7997 (tp30) REVERT: A 39 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 147 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7952 (pp) REVERT: A 151 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8015 (ttm-80) REVERT: A 161 LYS cc_start: 0.8714 (mtpp) cc_final: 0.8434 (mtpp) REVERT: A 178 MET cc_start: 0.8214 (mmm) cc_final: 0.7972 (mmm) REVERT: A 199 MET cc_start: 0.9298 (mmm) cc_final: 0.9092 (mmm) REVERT: A 231 LYS cc_start: 0.8412 (mttt) cc_final: 0.7994 (tmtt) REVERT: A 281 ASP cc_start: 0.9074 (t0) cc_final: 0.8604 (t0) REVERT: A 415 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7613 (m-10) REVERT: B 115 GLU cc_start: 0.7952 (pm20) cc_final: 0.7559 (pm20) REVERT: B 119 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8277 (mt-10) REVERT: B 147 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8065 (pp) REVERT: B 151 ARG cc_start: 0.8374 (tpp80) cc_final: 0.8170 (ttm-80) REVERT: B 231 LYS cc_start: 0.8435 (mttt) cc_final: 0.7903 (tmtt) REVERT: B 270 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8118 (mp) REVERT: B 278 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8235 (mtp-110) REVERT: B 281 ASP cc_start: 0.8919 (t0) cc_final: 0.8535 (t0) REVERT: B 290 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8037 (mtm110) REVERT: B 310 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8463 (m) outliers start: 44 outliers final: 21 residues processed: 136 average time/residue: 0.1306 time to fit residues: 24.3537 Evaluate side-chains 125 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 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 359 PHE 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 209 VAL Chi-restraints excluded: chain B residue 219 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 102 optimal weight: 0.4980 chunk 89 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3346 r_free = 0.3346 target = 0.117060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.080034 restraints weight = 14259.242| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.05 r_work: 0.2638 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 11331 Z= 0.124 Angle : 0.576 6.801 15507 Z= 0.267 Chirality : 0.042 0.135 1743 Planarity : 0.004 0.038 1839 Dihedral : 13.796 166.813 1950 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.61 % Allowed : 7.74 % Favored : 88.65 % 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: -0.45 (0.24), residues: 1302 helix: 0.83 (0.19), residues: 840 sheet: -1.60 (0.43), residues: 117 loop : -2.58 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 278 TYR 0.015 0.001 TYR C 348 PHE 0.007 0.001 PHE B 300 TRP 0.015 0.001 TRP B 286 HIS 0.003 0.000 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.12 (11325) covalent geometry : angle 0.57211 / 0.27 (15498) hydrogen bonds : bond 0.03038 / 2.02 ( 501) hydrogen bonds : angle 3.54194 / 2.38 ( 1467) Misc. bond : bond 0.15593 / 7.80 ( 3) link_NAG-ASN : bond 0.00551 / 0.28 ( 3) link_NAG-ASN : angle 2.92057 / 1.94 ( 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 137 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8267 (mt-10) REVERT: C 147 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8122 (pp) REVERT: C 151 ARG cc_start: 0.8371 (tpp80) cc_final: 0.8087 (ttm-80) REVERT: C 231 LYS cc_start: 0.8434 (mttt) cc_final: 0.7799 (tmtt) REVERT: C 281 ASP cc_start: 0.8801 (t0) cc_final: 0.8377 (t0) REVERT: C 450 ARG cc_start: 0.7886 (mtm110) cc_final: 0.7394 (mtp180) REVERT: A 20 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7995 (tp30) REVERT: A 39 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8355 (mm) REVERT: A 147 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7889 (pp) REVERT: A 151 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8001 (ttm-80) REVERT: A 161 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8431 (mtpp) REVERT: A 199 MET cc_start: 0.9330 (mmm) cc_final: 0.9108 (mmm) REVERT: A 231 LYS cc_start: 0.8355 (mttt) cc_final: 0.7942 (tmtt) REVERT: A 281 ASP cc_start: 0.9010 (t0) cc_final: 0.8562 (t0) REVERT: A 415 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: B 115 GLU cc_start: 0.7964 (pm20) cc_final: 0.7546 (pm20) REVERT: B 119 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8278 (mt-10) REVERT: B 147 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8018 (pp) REVERT: B 231 LYS cc_start: 0.8422 (mttt) cc_final: 0.7888 (tmtt) REVERT: B 278 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8291 (mtp-110) REVERT: B 281 ASP cc_start: 0.8827 (t0) cc_final: 0.8450 (t0) REVERT: B 290 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7999 (mtm110) REVERT: B 310 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8471 (m) outliers start: 41 outliers final: 23 residues processed: 132 average time/residue: 0.1292 time to fit residues: 23.2369 Evaluate side-chains 123 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 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 147 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 271 TYR 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: 0.6980 chunk 69 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 78 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.080845 restraints weight = 14190.056| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.28 r_work: 0.2604 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 11331 Z= 0.100 Angle : 0.550 6.149 15507 Z= 0.255 Chirality : 0.041 0.131 1743 Planarity : 0.004 0.037 1839 Dihedral : 13.476 166.451 1950 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.99 % Allowed : 8.71 % Favored : 88.30 % 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: -0.15 (0.24), residues: 1302 helix: 1.10 (0.19), residues: 843 sheet: -1.52 (0.42), residues: 117 loop : -2.62 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 151 TYR 0.015 0.001 TYR A 348 PHE 0.007 0.001 PHE A 300 TRP 0.014 0.001 TRP A 286 HIS 0.002 0.000 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.10 (11325) covalent geometry : angle 0.54608 / 0.25 (15498) hydrogen bonds : bond 0.02751 / 1.83 ( 501) hydrogen bonds : angle 3.42564 / 2.30 ( 1467) Misc. bond : bond 0.11550 / 5.77 ( 3) link_NAG-ASN : bond 0.00584 / 0.29 ( 3) link_NAG-ASN : angle 2.78292 / 1.84 ( 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 134 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8392 (mt-10) REVERT: C 147 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8379 (pp) REVERT: C 151 ARG cc_start: 0.8523 (tpp80) cc_final: 0.8250 (ttm-80) REVERT: C 231 LYS cc_start: 0.8497 (mttt) cc_final: 0.7947 (tmtt) REVERT: C 281 ASP cc_start: 0.8752 (t0) cc_final: 0.8351 (t0) REVERT: C 450 ARG cc_start: 0.7937 (mtm110) cc_final: 0.7436 (mtp180) REVERT: A 20 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8101 (tp30) REVERT: A 39 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8578 (mm) REVERT: A 147 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8149 (pp) REVERT: A 151 ARG cc_start: 0.8571 (tpp80) cc_final: 0.8239 (ttm-80) REVERT: A 161 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8562 (mtpp) REVERT: A 231 LYS cc_start: 0.8428 (mttt) cc_final: 0.8025 (tmtt) REVERT: A 281 ASP cc_start: 0.8920 (t0) cc_final: 0.8592 (t0) REVERT: A 415 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: B 103 ASP cc_start: 0.9011 (t70) cc_final: 0.8407 (t0) REVERT: B 115 GLU cc_start: 0.8022 (pm20) cc_final: 0.7653 (pm20) REVERT: B 119 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8335 (mt-10) REVERT: B 147 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8478 (pp) REVERT: B 231 LYS cc_start: 0.8486 (mttt) cc_final: 0.7953 (tmtt) REVERT: B 281 ASP cc_start: 0.8760 (t0) cc_final: 0.8297 (t0) REVERT: B 290 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8367 (mpp80) outliers start: 34 outliers final: 24 residues processed: 130 average time/residue: 0.1311 time to fit residues: 23.3743 Evaluate side-chains 123 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 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 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 271 TYR 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: 0.9980 chunk 51 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 0.0570 chunk 103 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.075642 restraints weight = 14168.324| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.05 r_work: 0.2578 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.252 11331 Z= 0.231 Angle : 0.649 7.886 15507 Z= 0.301 Chirality : 0.045 0.138 1743 Planarity : 0.004 0.038 1839 Dihedral : 13.817 167.099 1950 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.43 % Allowed : 8.88 % 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: -0.16 (0.24), residues: 1302 helix: 1.01 (0.19), residues: 846 sheet: -1.54 (0.41), residues: 117 loop : -2.39 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.017 0.001 TYR B 348 PHE 0.011 0.001 PHE C 302 TRP 0.018 0.002 TRP A 286 HIS 0.007 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.23 (11325) covalent geometry : angle 0.64522 / 0.30 (15498) hydrogen bonds : bond 0.03697 / 2.48 ( 501) hydrogen bonds : angle 3.60932 / 2.43 ( 1467) Misc. bond : bond 0.23054 / 11.51 ( 3) link_NAG-ASN : bond 0.00297 / 0.15 ( 3) link_NAG-ASN : angle 2.80485 / 1.94 ( 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 125 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8288 (mt-10) REVERT: C 147 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8210 (pp) REVERT: C 231 LYS cc_start: 0.8453 (mttt) cc_final: 0.7805 (tmtt) REVERT: C 281 ASP cc_start: 0.8930 (t0) cc_final: 0.8471 (t0) REVERT: C 450 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7378 (mtp180) REVERT: A 20 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7981 (tp30) REVERT: A 39 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 147 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7948 (pp) REVERT: A 161 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8458 (mtpp) REVERT: A 231 LYS cc_start: 0.8374 (mttt) cc_final: 0.7928 (tmtt) REVERT: A 281 ASP cc_start: 0.9039 (t0) cc_final: 0.8609 (t0) REVERT: A 415 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7908 (m-10) REVERT: B 119 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8302 (mt-10) REVERT: B 147 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8155 (pp) REVERT: B 231 LYS cc_start: 0.8417 (mttt) cc_final: 0.7857 (tmtt) REVERT: B 271 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7332 (t80) REVERT: B 278 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8220 (mtp-110) REVERT: B 281 ASP cc_start: 0.8951 (t0) cc_final: 0.8504 (t0) REVERT: B 310 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8475 (m) outliers start: 39 outliers final: 24 residues processed: 119 average time/residue: 0.1190 time to fit residues: 19.5189 Evaluate side-chains 113 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 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 147 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 271 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 54 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.076358 restraints weight = 14212.810| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.26 r_work: 0.2598 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 11331 Z= 0.130 Angle : 0.580 6.585 15507 Z= 0.269 Chirality : 0.042 0.132 1743 Planarity : 0.004 0.038 1839 Dihedral : 13.561 167.387 1950 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.25 % Allowed : 9.15 % Favored : 87.60 % 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: -0.01 (0.24), residues: 1302 helix: 1.07 (0.19), residues: 861 sheet: -1.45 (0.42), residues: 117 loop : -2.33 (0.33), residues: 324 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 C 300 TRP 0.013 0.001 TRP C 286 HIS 0.003 0.000 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.13 (11325) covalent geometry : angle 0.57685 / 0.27 (15498) hydrogen bonds : bond 0.03084 / 2.05 ( 501) hydrogen bonds : angle 3.48589 / 2.35 ( 1467) Misc. bond : bond 0.16183 / 8.08 ( 3) link_NAG-ASN : bond 0.00465 / 0.23 ( 3) link_NAG-ASN : angle 2.72105 / 1.84 ( 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 120 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: C 20 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: C 119 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8412 (mt-10) REVERT: C 147 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8519 (pp) REVERT: C 231 LYS cc_start: 0.8524 (mttt) cc_final: 0.7915 (tmtt) REVERT: C 281 ASP cc_start: 0.8856 (t0) cc_final: 0.8456 (t0) REVERT: C 450 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7359 (mtp180) REVERT: A 20 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8113 (tp30) REVERT: A 39 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8573 (mm) REVERT: A 147 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8165 (pp) REVERT: A 161 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8562 (mtpp) REVERT: A 231 LYS cc_start: 0.8466 (mttt) cc_final: 0.8017 (tmtt) REVERT: A 281 ASP cc_start: 0.9003 (t0) cc_final: 0.8545 (t0) REVERT: A 290 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8491 (mtm180) REVERT: A 415 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7855 (m-10) REVERT: B 20 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: B 46 VAL cc_start: 0.8368 (t) cc_final: 0.8165 (p) REVERT: B 103 ASP cc_start: 0.8956 (t70) cc_final: 0.8745 (t0) REVERT: B 115 GLU cc_start: 0.8148 (pm20) cc_final: 0.7716 (pm20) REVERT: B 119 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8387 (mt-10) REVERT: B 147 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8486 (pp) REVERT: B 231 LYS cc_start: 0.8512 (mttt) cc_final: 0.7941 (tmtt) REVERT: B 278 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8340 (mtp-110) REVERT: B 281 ASP cc_start: 0.8921 (t0) cc_final: 0.8417 (t0) outliers start: 37 outliers final: 23 residues processed: 117 average time/residue: 0.1093 time to fit residues: 18.1101 Evaluate side-chains 114 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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 290 ARG 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 A residue 438 ILE 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 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 0.0170 chunk 100 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 110 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.080391 restraints weight = 14090.958| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.96 r_work: 0.2656 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 11331 Z= 0.103 Angle : 0.561 6.035 15507 Z= 0.262 Chirality : 0.041 0.132 1743 Planarity : 0.004 0.036 1839 Dihedral : 13.325 167.369 1950 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.99 % Allowed : 9.41 % Favored : 87.60 % 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: 0.17 (0.24), residues: 1302 helix: 1.23 (0.19), residues: 861 sheet: -1.35 (0.43), residues: 117 loop : -2.34 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 448 TYR 0.016 0.001 TYR A 348 PHE 0.008 0.001 PHE B 300 TRP 0.023 0.001 TRP A 453 HIS 0.002 0.000 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.10 (11325) covalent geometry : angle 0.55716 / 0.26 (15498) hydrogen bonds : bond 0.02754 / 1.83 ( 501) hydrogen bonds : angle 3.38820 / 2.28 ( 1467) Misc. bond : bond 0.12207 / 6.09 ( 3) link_NAG-ASN : bond 0.00541 / 0.27 ( 3) link_NAG-ASN : angle 2.61207 / 1.75 ( 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 119 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: C 20 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: C 119 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8334 (mt-10) REVERT: C 147 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8558 (pp) REVERT: C 231 LYS cc_start: 0.8555 (mttt) cc_final: 0.7987 (tmtt) REVERT: C 281 ASP cc_start: 0.8740 (t0) cc_final: 0.8308 (t0) REVERT: C 450 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7378 (mtp180) REVERT: A 20 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8115 (tp30) REVERT: A 39 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8526 (mm) REVERT: A 147 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8073 (pp) REVERT: A 151 ARG cc_start: 0.8557 (tpp80) cc_final: 0.8267 (ttm-80) REVERT: A 161 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8527 (mtpp) REVERT: A 231 LYS cc_start: 0.8456 (mttt) cc_final: 0.8018 (tmtt) REVERT: A 281 ASP cc_start: 0.8829 (t0) cc_final: 0.8408 (t0) REVERT: A 290 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8373 (mtm180) REVERT: A 415 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7848 (m-10) REVERT: B 20 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: B 103 ASP cc_start: 0.8977 (t70) cc_final: 0.8759 (t0) REVERT: B 115 GLU cc_start: 0.8140 (pm20) cc_final: 0.7703 (pm20) REVERT: B 147 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8497 (pp) REVERT: B 231 LYS cc_start: 0.8527 (mttt) cc_final: 0.7937 (tmtt) REVERT: B 278 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8295 (mtp-110) REVERT: B 281 ASP cc_start: 0.8710 (t0) cc_final: 0.8250 (t0) outliers start: 34 outliers final: 23 residues processed: 117 average time/residue: 0.1220 time to fit residues: 19.8877 Evaluate side-chains 114 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 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 A residue 449 ILE 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 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 449 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.439 > 50: distance: 47 - 64: 5.539 distance: 51 - 72: 4.840 distance: 56 - 76: 11.386 distance: 61 - 64: 3.119 distance: 62 - 87: 7.611 distance: 67 - 92: 5.521 distance: 68 - 69: 3.533 distance: 69 - 70: 3.922 distance: 69 - 71: 17.775 distance: 72 - 73: 4.412 distance: 73 - 74: 4.450 distance: 74 - 75: 5.812 distance: 74 - 76: 6.041 distance: 75 - 103: 14.086 distance: 77 - 78: 4.564 distance: 77 - 80: 3.819 distance: 78 - 79: 6.522 distance: 78 - 87: 5.690 distance: 79 - 111: 4.331 distance: 80 - 81: 5.852 distance: 81 - 82: 5.393 distance: 81 - 83: 3.272 distance: 82 - 84: 6.315 distance: 83 - 85: 6.676 distance: 85 - 86: 7.003 distance: 87 - 88: 5.536 distance: 88 - 91: 8.484 distance: 89 - 92: 3.848 distance: 90 - 121: 24.890 distance: 92 - 93: 6.027 distance: 93 - 94: 6.142 distance: 93 - 96: 6.031 distance: 94 - 95: 3.090 distance: 95 - 128: 7.002 distance: 96 - 97: 4.045 distance: 97 - 99: 5.612 distance: 100 - 102: 3.675 distance: 103 - 104: 5.178 distance: 104 - 105: 6.881 distance: 104 - 107: 6.656 distance: 105 - 106: 7.259 distance: 105 - 111: 6.541 distance: 106 - 136: 5.149 distance: 107 - 108: 5.801 distance: 108 - 109: 7.619 distance: 108 - 110: 13.028 distance: 112 - 113: 6.642 distance: 112 - 115: 7.282 distance: 113 - 114: 12.402 distance: 113 - 121: 20.075 distance: 114 - 148: 4.874 distance: 116 - 117: 4.776 distance: 116 - 118: 4.737 distance: 119 - 120: 4.214 distance: 121 - 122: 34.563 distance: 122 - 123: 12.306 distance: 122 - 125: 20.736 distance: 123 - 128: 6.829 distance: 124 - 155: 16.280 distance: 125 - 126: 24.329 distance: 125 - 127: 27.611 distance: 128 - 129: 4.963 distance: 129 - 130: 3.117 distance: 130 - 131: 8.511 distance: 132 - 133: 6.613 distance: 133 - 134: 3.527 distance: 133 - 135: 7.934 distance: 136 - 137: 4.857 distance: 137 - 138: 5.069 distance: 137 - 140: 5.929 distance: 138 - 139: 14.268 distance: 140 - 141: 3.162 distance: 141 - 142: 5.949 distance: 141 - 143: 15.002 distance: 142 - 144: 4.429 distance: 143 - 145: 4.330 distance: 144 - 146: 11.954 distance: 145 - 146: 8.374 distance: 146 - 147: 4.919