Starting phenix.real_space_refine on Tue Nov 18 21:37:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n16_24114/11_2025/7n16_24114.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n16_24114/11_2025/7n16_24114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n16_24114/11_2025/7n16_24114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n16_24114/11_2025/7n16_24114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n16_24114/11_2025/7n16_24114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n16_24114/11_2025/7n16_24114.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.092 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 P 12 5.49 5 S 96 5.16 5 Na 1 4.78 5 C 11300 2.51 5 N 2860 2.21 5 O 3088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17357 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "A" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'CPL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 4, 'CPL:plan-4': 4, 'CPL:plan-1': 1, 'CPL:plan-2': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {' NA': 1, 'CPL': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 4, 'CPL:plan-4': 4, 'CPL:plan-1': 1, 'CPL:plan-2': 1} Unresolved non-hydrogen planarities: 38 Restraints were copied for chains: B, C Time building chain proxies: 4.70, per 1000 atoms: 0.27 Number of scatterers: 17357 At special positions: 0 Unit cell: (133.63, 133.63, 136.95, 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) S 96 16.00 P 12 15.00 Na 1 11.00 O 3088 8.00 N 2860 7.00 C 11300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 548.3 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 59.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'D' and resid 119 through 145 Processing helix chain 'D' and resid 197 through 224 Processing helix chain 'D' and resid 236 through 247 Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.139A pdb=" N ILE D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 6.114A pdb=" N LEU D 260 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP D 261 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.648A pdb=" N LEU D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 280 " --> pdb=" O PRO D 277 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 283 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 4.067A pdb=" N VAL D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 335 removed outlier: 3.632A pdb=" N GLY D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 375 Processing helix chain 'D' and resid 385 through 418 removed outlier: 3.522A pdb=" N MET D 417 " --> pdb=" O MET D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 439 removed outlier: 3.844A pdb=" N THR D 422 " --> pdb=" O SER D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 458 removed outlier: 3.852A pdb=" N GLU D 445 " --> pdb=" O SER D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 Processing helix chain 'D' and resid 472 through 489 removed outlier: 4.026A pdb=" N VAL D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 507 removed outlier: 3.642A pdb=" N LEU D 502 " --> pdb=" O GLU D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 601 Processing helix chain 'D' and resid 602 through 620 removed outlier: 3.902A pdb=" N ASP D 620 " --> pdb=" O ILE D 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 119 through 145 Processing helix chain 'A' and resid 197 through 224 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 248 through 256 removed outlier: 4.140A pdb=" N ILE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 6.114A pdb=" N LEU A 260 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP A 261 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.648A pdb=" N LEU A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 280 " --> pdb=" O PRO A 277 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 4.067A pdb=" N VAL A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 335 removed outlier: 3.633A pdb=" N GLY A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 385 through 418 removed outlier: 3.522A pdb=" N MET A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.844A pdb=" N THR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 458 removed outlier: 3.852A pdb=" N GLU A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 Processing helix chain 'A' and resid 472 through 489 removed outlier: 4.026A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 507 removed outlier: 3.642A pdb=" N LEU A 502 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 602 through 620 removed outlier: 3.903A pdb=" N ASP A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 111 Processing helix chain 'B' and resid 119 through 145 Processing helix chain 'B' and resid 197 through 224 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 248 through 256 removed outlier: 4.139A pdb=" N ILE B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 6.113A pdb=" N LEU B 260 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP B 261 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 removed outlier: 3.648A pdb=" N LEU B 279 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 280 " --> pdb=" O PRO B 277 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 4.067A pdb=" N VAL B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 335 removed outlier: 3.632A pdb=" N GLY B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 385 through 418 removed outlier: 3.522A pdb=" N MET B 417 " --> pdb=" O MET B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 439 removed outlier: 3.844A pdb=" N THR B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 458 removed outlier: 3.852A pdb=" N GLU B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 Processing helix chain 'B' and resid 472 through 489 removed outlier: 4.026A pdb=" N VAL B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 507 removed outlier: 3.642A pdb=" N LEU B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 602 through 620 removed outlier: 3.901A pdb=" N ASP B 620 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 119 through 145 Processing helix chain 'C' and resid 197 through 224 Processing helix chain 'C' and resid 236 through 247 Processing helix chain 'C' and resid 248 through 256 removed outlier: 4.140A pdb=" N ILE C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 6.114A pdb=" N LEU C 260 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP C 261 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 285 removed outlier: 3.648A pdb=" N LEU C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 280 " --> pdb=" O PRO C 277 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE C 285 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 removed outlier: 4.068A pdb=" N VAL C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 335 removed outlier: 3.632A pdb=" N GLY C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 385 through 418 removed outlier: 3.522A pdb=" N MET C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 439 removed outlier: 3.844A pdb=" N THR C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 458 removed outlier: 3.852A pdb=" N GLU C 445 " --> pdb=" O SER C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 Processing helix chain 'C' and resid 472 through 489 removed outlier: 4.026A pdb=" N VAL C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 507 removed outlier: 3.642A pdb=" N LEU C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 601 Processing helix chain 'C' and resid 602 through 620 removed outlier: 3.903A pdb=" N ASP C 620 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 167 through 171 Processing sheet with id=AA2, first strand: chain 'D' and resid 510 through 514 removed outlier: 3.525A pdb=" N THR D 585 " --> pdb=" O PHE D 514 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 519 through 521 removed outlier: 6.874A pdb=" N VAL D 579 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 540 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL D 550 " --> pdb=" O VAL D 540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 510 through 514 removed outlier: 3.525A pdb=" N THR A 585 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.874A pdb=" N VAL A 579 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 540 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL A 550 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 167 through 171 Processing sheet with id=AA8, first strand: chain 'B' and resid 510 through 514 removed outlier: 3.525A pdb=" N THR B 585 " --> pdb=" O PHE B 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 519 through 521 removed outlier: 6.873A pdb=" N VAL B 579 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 540 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 550 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 167 through 171 Processing sheet with id=AB2, first strand: chain 'C' and resid 510 through 514 removed outlier: 3.524A pdb=" N THR C 585 " --> pdb=" O PHE C 514 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 519 through 521 removed outlier: 6.874A pdb=" N VAL C 579 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 540 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL C 550 " --> pdb=" O VAL C 540 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2811 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: 2.27 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2672 1.30 - 1.43: 4990 1.43 - 1.56: 9906 1.56 - 1.68: 32 1.68 - 1.81: 156 Bond restraints: 17756 Sorted by residual: bond pdb=" C11 CPL B1804 " pdb=" O3 CPL B1804 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C11 CPL D 803 " pdb=" O3 CPL D 803 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C11 CPL C1804 " pdb=" O3 CPL C1804 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C11 CPL A1804 " pdb=" O3 CPL A1804 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C11 CPL C1801 " pdb=" O3 CPL C1801 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 17751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 23621 3.59 - 7.19: 359 7.19 - 10.78: 40 10.78 - 14.38: 4 14.38 - 17.97: 12 Bond angle restraints: 24036 Sorted by residual: angle pdb=" O3P CPL B1801 " pdb=" P CPL B1801 " pdb=" O4P CPL B1801 " ideal model delta sigma weight residual 93.29 111.26 -17.97 3.00e+00 1.11e-01 3.59e+01 angle pdb=" O3P CPL C1801 " pdb=" P CPL C1801 " pdb=" O4P CPL C1801 " ideal model delta sigma weight residual 93.29 111.24 -17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" O3P CPL A1801 " pdb=" P CPL A1801 " pdb=" O4P CPL A1801 " ideal model delta sigma weight residual 93.29 111.23 -17.94 3.00e+00 1.11e-01 3.57e+01 angle pdb=" O3P CPL D 804 " pdb=" P CPL D 804 " pdb=" O4P CPL D 804 " ideal model delta sigma weight residual 93.29 111.21 -17.92 3.00e+00 1.11e-01 3.57e+01 angle pdb=" O3P CPL C1804 " pdb=" P CPL C1804 " pdb=" O4P CPL C1804 " ideal model delta sigma weight residual 93.29 110.02 -16.73 3.00e+00 1.11e-01 3.11e+01 ... (remaining 24031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 10236 35.11 - 70.23: 272 70.23 - 105.34: 20 105.34 - 140.46: 16 140.46 - 175.57: 12 Dihedral angle restraints: 10556 sinusoidal: 4488 harmonic: 6068 Sorted by residual: dihedral pdb=" CA ASP A 191 " pdb=" C ASP A 191 " pdb=" N LEU A 192 " pdb=" CA LEU A 192 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ASP D 191 " pdb=" C ASP D 191 " pdb=" N LEU D 192 " pdb=" CA LEU D 192 " ideal model delta harmonic sigma weight residual -180.00 -154.32 -25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ASP C 191 " pdb=" C ASP C 191 " pdb=" N LEU C 192 " pdb=" CA LEU C 192 " ideal model delta harmonic sigma weight residual -180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 10553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1685 0.049 - 0.098: 715 0.098 - 0.147: 154 0.147 - 0.196: 33 0.196 - 0.245: 37 Chirality restraints: 2624 Sorted by residual: chirality pdb=" CB VAL A 170 " pdb=" CA VAL A 170 " pdb=" CG1 VAL A 170 " pdb=" CG2 VAL A 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL C 170 " pdb=" CA VAL C 170 " pdb=" CG1 VAL C 170 " pdb=" CG2 VAL C 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB VAL B 170 " pdb=" CA VAL B 170 " pdb=" CG1 VAL B 170 " pdb=" CG2 VAL B 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2621 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 380 " -0.046 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO C 381 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 381 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 381 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 380 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO A 381 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 380 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO B 381 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 381 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 381 " 0.038 5.00e-02 4.00e+02 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3229 2.77 - 3.30: 14769 3.30 - 3.83: 29423 3.83 - 4.37: 33272 4.37 - 4.90: 57909 Nonbonded interactions: 138602 Sorted by model distance: nonbonded pdb=" O ASP A 191 " pdb=" OD1 ASP A 191 " model vdw 2.235 3.040 nonbonded pdb=" O ASP C 191 " pdb=" OD1 ASP C 191 " model vdw 2.235 3.040 nonbonded pdb=" O ASP D 191 " pdb=" OD1 ASP D 191 " model vdw 2.235 3.040 nonbonded pdb=" O ASP B 191 " pdb=" OD1 ASP B 191 " model vdw 2.235 3.040 nonbonded pdb=" O SER B 562 " pdb=" OG SER B 562 " model vdw 2.339 3.040 ... (remaining 138597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 104 through 1801 or (resid 1803 and (name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17)) or (resid 1804 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name O11 or name O1P or name O2 or name O \ 2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 104 through 1801 or (resid 1803 and (name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17)) or (resid 1804 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name O11 or name O1P or name O2 or name O \ 2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 104 through 1801 or (resid 1803 and (name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17)) or (resid 1804 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name O11 or name O1P or name O2 or name O \ 2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 104 through 620 or (resid 801 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C4 or name C5 or name O11 or name O1P or name O2 \ or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or (resi \ d 803 and (name C12 or name C13 or name C14 or name C15 or name C16 or name C17) \ ) or (resid 804 and (name C1 or name C11 or name C12 or name C13 or name C14 or \ name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 o \ r name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P \ or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.460 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.008 0.079 17760 Z= 0.374 Angle : 1.179 17.974 24044 Z= 0.600 Chirality : 0.061 0.245 2624 Planarity : 0.008 0.068 2948 Dihedral : 18.872 175.569 6648 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.86 % Allowed : 9.87 % Favored : 89.27 % 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: -4.54 (0.13), residues: 2040 helix: -3.33 (0.09), residues: 1140 sheet: -0.52 (0.45), residues: 120 loop : -2.64 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 447 TYR 0.026 0.003 TYR D 363 PHE 0.028 0.003 PHE B 145 TRP 0.026 0.003 TRP A 266 HIS 0.004 0.001 HIS C 321 Details of bonding type rmsd covalent geometry : bond 0.00831 (17756) covalent geometry : angle 1.17877 (24036) SS BOND : bond 0.00374 ( 4) SS BOND : angle 0.51241 ( 8) hydrogen bonds : bond 0.13344 ( 961) hydrogen bonds : angle 7.06766 ( 2811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 322 time to evaluate : 0.630 Fit side-chains REVERT: D 159 PHE cc_start: 0.8226 (t80) cc_final: 0.7886 (t80) REVERT: D 272 ASN cc_start: 0.8215 (m-40) cc_final: 0.7987 (t0) REVERT: D 424 PHE cc_start: 0.7779 (t80) cc_final: 0.7478 (t80) REVERT: D 525 ASP cc_start: 0.7881 (t0) cc_final: 0.7484 (t0) REVERT: D 535 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7474 (ptp-110) REVERT: D 558 PHE cc_start: 0.6782 (t80) cc_final: 0.6541 (t80) REVERT: A 159 PHE cc_start: 0.8196 (t80) cc_final: 0.7864 (t80) REVERT: A 272 ASN cc_start: 0.8224 (m-40) cc_final: 0.8008 (t0) REVERT: A 458 ASN cc_start: 0.8112 (t0) cc_final: 0.7899 (t0) REVERT: A 525 ASP cc_start: 0.7807 (t0) cc_final: 0.7339 (t0) REVERT: A 535 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7485 (ptp-110) REVERT: A 558 PHE cc_start: 0.6771 (t80) cc_final: 0.6552 (t80) REVERT: B 159 PHE cc_start: 0.8240 (t80) cc_final: 0.7889 (t80) REVERT: B 525 ASP cc_start: 0.7853 (t0) cc_final: 0.7475 (t0) REVERT: B 535 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7481 (ptp-110) REVERT: B 558 PHE cc_start: 0.6843 (t80) cc_final: 0.6567 (t80) REVERT: C 159 PHE cc_start: 0.8188 (t80) cc_final: 0.7870 (t80) REVERT: C 272 ASN cc_start: 0.8251 (m-40) cc_final: 0.8040 (t0) REVERT: C 413 MET cc_start: 0.7802 (tmm) cc_final: 0.7575 (ttp) REVERT: C 421 TRP cc_start: 0.6328 (t-100) cc_final: 0.5977 (t-100) REVERT: C 525 ASP cc_start: 0.7829 (t0) cc_final: 0.7524 (t0) REVERT: C 535 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7464 (ptp-110) outliers start: 16 outliers final: 0 residues processed: 338 average time/residue: 0.1559 time to fit residues: 75.3140 Evaluate side-chains 236 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 188 GLN D 199 HIS D 416 ASN D 458 ASN D 484 HIS D 510 GLN D 539 GLN A 114 GLN A 188 GLN A 199 HIS A 416 ASN A 484 HIS A 539 GLN B 114 GLN B 188 GLN B 199 HIS B 349 GLN B 416 ASN B 458 ASN B 484 HIS B 510 GLN B 539 GLN C 114 GLN C 188 GLN C 199 HIS C 416 ASN C 458 ASN C 484 HIS C 510 GLN C 539 GLN C 578 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.170202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119442 restraints weight = 23313.616| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.12 r_work: 0.3358 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17760 Z= 0.134 Angle : 0.559 7.151 24044 Z= 0.291 Chirality : 0.040 0.144 2624 Planarity : 0.005 0.040 2948 Dihedral : 15.813 176.093 2564 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.23 % Allowed : 15.02 % Favored : 83.74 % 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: -1.90 (0.16), residues: 2040 helix: -0.64 (0.14), residues: 1152 sheet: -0.90 (0.44), residues: 108 loop : -2.17 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 280 TYR 0.013 0.001 TYR B 108 PHE 0.014 0.001 PHE B 138 TRP 0.013 0.001 TRP A 421 HIS 0.002 0.000 HIS C 321 Details of bonding type rmsd covalent geometry : bond 0.00291 (17756) covalent geometry : angle 0.55865 (24036) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.70216 ( 8) hydrogen bonds : bond 0.04402 ( 961) hydrogen bonds : angle 4.76058 ( 2811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.682 Fit side-chains REVERT: D 115 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7787 (p0) REVERT: D 146 ASN cc_start: 0.8527 (t0) cc_final: 0.7976 (t0) REVERT: D 182 GLU cc_start: 0.8877 (pm20) cc_final: 0.8295 (pm20) REVERT: D 272 ASN cc_start: 0.8641 (m-40) cc_final: 0.8142 (t0) REVERT: D 525 ASP cc_start: 0.7875 (t70) cc_final: 0.7313 (t0) REVERT: D 535 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7599 (ptp-110) REVERT: D 615 GLU cc_start: 0.8462 (tt0) cc_final: 0.8054 (mt-10) REVERT: A 115 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7794 (p0) REVERT: A 146 ASN cc_start: 0.8523 (t0) cc_final: 0.7975 (t0) REVERT: A 182 GLU cc_start: 0.8880 (pm20) cc_final: 0.8299 (pm20) REVERT: A 272 ASN cc_start: 0.8651 (m-40) cc_final: 0.8150 (t0) REVERT: A 525 ASP cc_start: 0.7862 (t70) cc_final: 0.7235 (t0) REVERT: A 535 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7635 (ptp-110) REVERT: A 599 LEU cc_start: 0.8040 (tp) cc_final: 0.7171 (tp) REVERT: B 115 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7800 (p0) REVERT: B 146 ASN cc_start: 0.8562 (t0) cc_final: 0.8026 (t0) REVERT: B 159 PHE cc_start: 0.8092 (t80) cc_final: 0.7837 (t80) REVERT: B 182 GLU cc_start: 0.8836 (pm20) cc_final: 0.8577 (pm20) REVERT: B 272 ASN cc_start: 0.8818 (t0) cc_final: 0.8581 (t0) REVERT: B 507 LEU cc_start: 0.8331 (mm) cc_final: 0.8096 (mm) REVERT: B 525 ASP cc_start: 0.7946 (t70) cc_final: 0.7443 (t0) REVERT: C 115 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7778 (p0) REVERT: C 146 ASN cc_start: 0.8540 (t0) cc_final: 0.7982 (t0) REVERT: C 182 GLU cc_start: 0.8864 (pm20) cc_final: 0.8280 (pm20) REVERT: C 272 ASN cc_start: 0.8651 (m-40) cc_final: 0.8199 (t0) REVERT: C 421 TRP cc_start: 0.6348 (t-100) cc_final: 0.6134 (t-100) REVERT: C 507 LEU cc_start: 0.8334 (mm) cc_final: 0.8111 (mm) REVERT: C 525 ASP cc_start: 0.7980 (t70) cc_final: 0.7511 (t0) outliers start: 23 outliers final: 15 residues processed: 269 average time/residue: 0.1443 time to fit residues: 57.0197 Evaluate side-chains 244 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 578 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 2 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 12 optimal weight: 0.0070 chunk 157 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN D 510 GLN B 458 ASN C 458 ASN C 510 GLN C 578 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.173500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.123226 restraints weight = 23498.898| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.13 r_work: 0.3393 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17760 Z= 0.107 Angle : 0.496 6.935 24044 Z= 0.260 Chirality : 0.038 0.134 2624 Planarity : 0.004 0.041 2948 Dihedral : 13.900 165.427 2564 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.34 % Allowed : 16.36 % Favored : 82.30 % 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: -0.75 (0.18), residues: 2040 helix: 0.39 (0.15), residues: 1184 sheet: -1.00 (0.42), residues: 116 loop : -1.82 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 535 TYR 0.009 0.001 TYR C 365 PHE 0.020 0.001 PHE D 159 TRP 0.014 0.001 TRP A 421 HIS 0.002 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00223 (17756) covalent geometry : angle 0.49635 (24036) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.75602 ( 8) hydrogen bonds : bond 0.03867 ( 961) hydrogen bonds : angle 4.25872 ( 2811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 0.667 Fit side-chains REVERT: D 115 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7751 (p0) REVERT: D 117 SER cc_start: 0.8469 (m) cc_final: 0.8083 (p) REVERT: D 146 ASN cc_start: 0.8437 (t0) cc_final: 0.7910 (t0) REVERT: D 182 GLU cc_start: 0.8834 (pm20) cc_final: 0.8416 (pm20) REVERT: D 272 ASN cc_start: 0.8658 (m-40) cc_final: 0.8137 (t0) REVERT: D 489 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7331 (tpt170) REVERT: D 525 ASP cc_start: 0.7940 (t70) cc_final: 0.7371 (t0) REVERT: D 535 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7627 (ptp-110) REVERT: D 558 PHE cc_start: 0.6661 (t80) cc_final: 0.6305 (t80) REVERT: D 608 LEU cc_start: 0.7823 (mt) cc_final: 0.7372 (pp) REVERT: A 115 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7742 (p0) REVERT: A 117 SER cc_start: 0.8473 (m) cc_final: 0.8071 (p) REVERT: A 146 ASN cc_start: 0.8437 (t0) cc_final: 0.7908 (t0) REVERT: A 182 GLU cc_start: 0.8850 (pm20) cc_final: 0.8433 (pm20) REVERT: A 272 ASN cc_start: 0.8643 (m-40) cc_final: 0.8147 (t0) REVERT: A 507 LEU cc_start: 0.8340 (mm) cc_final: 0.8095 (mm) REVERT: A 525 ASP cc_start: 0.7909 (t70) cc_final: 0.7328 (t0) REVERT: A 535 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7691 (ptp-110) REVERT: A 558 PHE cc_start: 0.6538 (t80) cc_final: 0.6212 (t80) REVERT: B 115 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7963 (p0) REVERT: B 117 SER cc_start: 0.8435 (m) cc_final: 0.8039 (p) REVERT: B 146 ASN cc_start: 0.8430 (t0) cc_final: 0.7878 (t0) REVERT: B 159 PHE cc_start: 0.8040 (t80) cc_final: 0.7799 (t80) REVERT: B 182 GLU cc_start: 0.8818 (pm20) cc_final: 0.8557 (pm20) REVERT: B 272 ASN cc_start: 0.8772 (t0) cc_final: 0.8489 (t0) REVERT: B 507 LEU cc_start: 0.8289 (mm) cc_final: 0.8056 (mm) REVERT: B 525 ASP cc_start: 0.7950 (t70) cc_final: 0.7396 (t0) REVERT: C 115 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7725 (p0) REVERT: C 117 SER cc_start: 0.8469 (m) cc_final: 0.8078 (p) REVERT: C 146 ASN cc_start: 0.8433 (t0) cc_final: 0.7894 (t0) REVERT: C 182 GLU cc_start: 0.8837 (pm20) cc_final: 0.8414 (pm20) REVERT: C 272 ASN cc_start: 0.8655 (m-40) cc_final: 0.8184 (t0) REVERT: C 458 ASN cc_start: 0.7900 (t0) cc_final: 0.7650 (t0) REVERT: C 507 LEU cc_start: 0.8307 (mm) cc_final: 0.8083 (mm) REVERT: C 525 ASP cc_start: 0.7945 (t70) cc_final: 0.7449 (t0) outliers start: 25 outliers final: 16 residues processed: 269 average time/residue: 0.1346 time to fit residues: 54.5542 Evaluate side-chains 242 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 349 GLN D 458 ASN A 349 GLN A 458 ASN B 458 ASN B 510 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.161648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108854 restraints weight = 23248.195| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.20 r_work: 0.3175 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 17760 Z= 0.345 Angle : 0.693 9.800 24044 Z= 0.356 Chirality : 0.046 0.179 2624 Planarity : 0.005 0.043 2948 Dihedral : 13.908 170.716 2564 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.63 % Allowed : 17.97 % Favored : 79.40 % 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: -0.78 (0.18), residues: 2040 helix: 0.44 (0.15), residues: 1156 sheet: -0.63 (0.42), residues: 116 loop : -1.97 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 606 TYR 0.023 0.002 TYR B 363 PHE 0.024 0.003 PHE A 145 TRP 0.012 0.002 TRP C 451 HIS 0.005 0.002 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00818 (17756) covalent geometry : angle 0.69253 (24036) SS BOND : bond 0.00201 ( 4) SS BOND : angle 1.02693 ( 8) hydrogen bonds : bond 0.05186 ( 961) hydrogen bonds : angle 4.69486 ( 2811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.653 Fit side-chains REVERT: D 115 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8145 (p0) REVERT: D 146 ASN cc_start: 0.8678 (t0) cc_final: 0.8109 (t0) REVERT: D 272 ASN cc_start: 0.8650 (m-40) cc_final: 0.8065 (t0) REVERT: D 525 ASP cc_start: 0.7961 (t70) cc_final: 0.7295 (t0) REVERT: D 558 PHE cc_start: 0.6727 (t80) cc_final: 0.6517 (t80) REVERT: A 115 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8148 (p0) REVERT: A 146 ASN cc_start: 0.8681 (t0) cc_final: 0.8112 (t0) REVERT: A 272 ASN cc_start: 0.8657 (m-40) cc_final: 0.8060 (t0) REVERT: A 507 LEU cc_start: 0.8231 (mm) cc_final: 0.8001 (mm) REVERT: A 525 ASP cc_start: 0.7939 (t70) cc_final: 0.7261 (t0) REVERT: A 558 PHE cc_start: 0.6684 (t80) cc_final: 0.6476 (t80) REVERT: B 115 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8132 (p0) REVERT: B 146 ASN cc_start: 0.8706 (t0) cc_final: 0.8115 (t0) REVERT: B 159 PHE cc_start: 0.7971 (t80) cc_final: 0.7756 (t80) REVERT: B 182 GLU cc_start: 0.8805 (pm20) cc_final: 0.8428 (pm20) REVERT: B 272 ASN cc_start: 0.8912 (t0) cc_final: 0.8611 (t0) REVERT: B 507 LEU cc_start: 0.8221 (mm) cc_final: 0.7993 (mm) REVERT: B 525 ASP cc_start: 0.7986 (t70) cc_final: 0.7339 (t0) REVERT: B 558 PHE cc_start: 0.6688 (t80) cc_final: 0.6360 (t80) REVERT: C 115 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8133 (p0) REVERT: C 146 ASN cc_start: 0.8686 (t0) cc_final: 0.8102 (t0) REVERT: C 272 ASN cc_start: 0.8684 (m-40) cc_final: 0.8084 (t0) REVERT: C 507 LEU cc_start: 0.8216 (mm) cc_final: 0.7987 (mm) REVERT: C 525 ASP cc_start: 0.7988 (t70) cc_final: 0.7305 (t0) REVERT: C 606 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7332 (ttm110) outliers start: 49 outliers final: 35 residues processed: 279 average time/residue: 0.1361 time to fit residues: 56.9649 Evaluate side-chains 274 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN A 458 ASN B 458 ASN C 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.167830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115881 restraints weight = 22607.460| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.19 r_work: 0.3281 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17760 Z= 0.123 Angle : 0.504 8.265 24044 Z= 0.263 Chirality : 0.039 0.138 2624 Planarity : 0.003 0.039 2948 Dihedral : 13.051 165.463 2564 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.36 % Allowed : 18.03 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 2040 helix: 0.84 (0.15), residues: 1180 sheet: -1.19 (0.40), residues: 116 loop : -1.49 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 606 TYR 0.012 0.001 TYR C 363 PHE 0.021 0.001 PHE D 159 TRP 0.018 0.001 TRP D 421 HIS 0.005 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00270 (17756) covalent geometry : angle 0.50413 (24036) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.76675 ( 8) hydrogen bonds : bond 0.04085 ( 961) hydrogen bonds : angle 4.22136 ( 2811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.672 Fit side-chains REVERT: D 115 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8025 (p0) REVERT: D 117 SER cc_start: 0.8521 (m) cc_final: 0.8097 (p) REVERT: D 146 ASN cc_start: 0.8447 (t0) cc_final: 0.7882 (t0) REVERT: D 272 ASN cc_start: 0.8596 (m-40) cc_final: 0.8060 (t0) REVERT: D 413 MET cc_start: 0.7538 (ttp) cc_final: 0.7327 (ttp) REVERT: D 458 ASN cc_start: 0.7942 (t0) cc_final: 0.7732 (t0) REVERT: D 525 ASP cc_start: 0.7936 (t70) cc_final: 0.7331 (t0) REVERT: D 558 PHE cc_start: 0.6401 (t80) cc_final: 0.6165 (t80) REVERT: A 115 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8007 (p0) REVERT: A 117 SER cc_start: 0.8509 (m) cc_final: 0.8078 (p) REVERT: A 146 ASN cc_start: 0.8440 (t0) cc_final: 0.7870 (t0) REVERT: A 272 ASN cc_start: 0.8602 (m-40) cc_final: 0.8062 (t0) REVERT: A 458 ASN cc_start: 0.7882 (t0) cc_final: 0.7653 (t0) REVERT: A 507 LEU cc_start: 0.8282 (mm) cc_final: 0.8052 (mm) REVERT: A 525 ASP cc_start: 0.7906 (t70) cc_final: 0.7285 (t0) REVERT: A 558 PHE cc_start: 0.6385 (t80) cc_final: 0.6158 (t80) REVERT: B 115 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8041 (p0) REVERT: B 117 SER cc_start: 0.8504 (m) cc_final: 0.8064 (p) REVERT: B 146 ASN cc_start: 0.8501 (t0) cc_final: 0.7865 (t0) REVERT: B 182 GLU cc_start: 0.8833 (pm20) cc_final: 0.8541 (pm20) REVERT: B 272 ASN cc_start: 0.8873 (t0) cc_final: 0.8556 (t0) REVERT: B 458 ASN cc_start: 0.7956 (t0) cc_final: 0.7749 (t0) REVERT: B 507 LEU cc_start: 0.8277 (mm) cc_final: 0.8050 (mm) REVERT: B 525 ASP cc_start: 0.7945 (t70) cc_final: 0.7344 (t0) REVERT: B 558 PHE cc_start: 0.6421 (t80) cc_final: 0.6035 (t80) REVERT: B 608 LEU cc_start: 0.7716 (mt) cc_final: 0.7337 (pp) REVERT: C 115 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8030 (p0) REVERT: C 117 SER cc_start: 0.8514 (m) cc_final: 0.8092 (p) REVERT: C 146 ASN cc_start: 0.8455 (t0) cc_final: 0.7873 (t0) REVERT: C 272 ASN cc_start: 0.8627 (m-40) cc_final: 0.8068 (t0) REVERT: C 413 MET cc_start: 0.7559 (ttp) cc_final: 0.7334 (ttp) REVERT: C 458 ASN cc_start: 0.7823 (t0) cc_final: 0.7597 (t0) REVERT: C 507 LEU cc_start: 0.8209 (mm) cc_final: 0.7986 (mm) REVERT: C 508 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8329 (ptpt) REVERT: C 525 ASP cc_start: 0.7975 (t70) cc_final: 0.7370 (t0) REVERT: C 606 ARG cc_start: 0.7959 (ttm110) cc_final: 0.7328 (ttm110) REVERT: C 608 LEU cc_start: 0.7720 (mt) cc_final: 0.7307 (pp) outliers start: 44 outliers final: 29 residues processed: 276 average time/residue: 0.1350 time to fit residues: 56.6026 Evaluate side-chains 259 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 148 optimal weight: 0.0040 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 510 GLN C 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.166229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113718 restraints weight = 22822.988| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.22 r_work: 0.3240 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17760 Z= 0.165 Angle : 0.524 8.071 24044 Z= 0.274 Chirality : 0.040 0.150 2624 Planarity : 0.003 0.036 2948 Dihedral : 12.629 162.793 2564 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.79 % Allowed : 17.38 % Favored : 79.83 % 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: -0.05 (0.19), residues: 2040 helix: 0.92 (0.15), residues: 1180 sheet: -1.14 (0.40), residues: 116 loop : -1.36 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 606 TYR 0.015 0.001 TYR B 363 PHE 0.021 0.002 PHE B 159 TRP 0.026 0.001 TRP C 421 HIS 0.002 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00380 (17756) covalent geometry : angle 0.52436 (24036) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.80211 ( 8) hydrogen bonds : bond 0.04278 ( 961) hydrogen bonds : angle 4.21911 ( 2811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8002 (p0) REVERT: D 146 ASN cc_start: 0.8455 (t0) cc_final: 0.7905 (t0) REVERT: D 182 GLU cc_start: 0.8845 (pm20) cc_final: 0.8205 (pm20) REVERT: D 272 ASN cc_start: 0.8610 (m-40) cc_final: 0.8058 (t0) REVERT: D 458 ASN cc_start: 0.7981 (t0) cc_final: 0.7700 (t0) REVERT: D 525 ASP cc_start: 0.7954 (t70) cc_final: 0.7359 (t0) REVERT: D 558 PHE cc_start: 0.6385 (t80) cc_final: 0.6155 (t80) REVERT: D 608 LEU cc_start: 0.7720 (mt) cc_final: 0.7303 (pp) REVERT: A 115 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8002 (p0) REVERT: A 146 ASN cc_start: 0.8458 (t0) cc_final: 0.7903 (t0) REVERT: A 182 GLU cc_start: 0.8840 (pm20) cc_final: 0.8197 (pm20) REVERT: A 272 ASN cc_start: 0.8617 (m-40) cc_final: 0.8059 (t0) REVERT: A 507 LEU cc_start: 0.8243 (mm) cc_final: 0.8018 (mm) REVERT: A 525 ASP cc_start: 0.7938 (t70) cc_final: 0.7324 (t0) REVERT: A 558 PHE cc_start: 0.6367 (t80) cc_final: 0.6112 (t80) REVERT: B 115 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8033 (p0) REVERT: B 146 ASN cc_start: 0.8504 (t0) cc_final: 0.7891 (t0) REVERT: B 182 GLU cc_start: 0.8827 (pm20) cc_final: 0.8535 (pm20) REVERT: B 270 TYR cc_start: 0.7669 (m-80) cc_final: 0.7423 (t80) REVERT: B 272 ASN cc_start: 0.8901 (t0) cc_final: 0.8601 (t0) REVERT: B 458 ASN cc_start: 0.7977 (t0) cc_final: 0.7696 (t0) REVERT: B 507 LEU cc_start: 0.8243 (mm) cc_final: 0.8022 (mm) REVERT: B 525 ASP cc_start: 0.7960 (t70) cc_final: 0.7354 (t0) REVERT: B 588 PHE cc_start: 0.8506 (m-10) cc_final: 0.8241 (m-10) REVERT: C 115 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8060 (p0) REVERT: C 146 ASN cc_start: 0.8466 (t0) cc_final: 0.7909 (t0) REVERT: C 272 ASN cc_start: 0.8616 (m-40) cc_final: 0.8061 (t0) REVERT: C 458 ASN cc_start: 0.7885 (t0) cc_final: 0.7591 (t0) REVERT: C 507 LEU cc_start: 0.8244 (mm) cc_final: 0.8019 (mm) REVERT: C 508 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8347 (ptpt) REVERT: C 525 ASP cc_start: 0.7982 (t70) cc_final: 0.7378 (t0) REVERT: C 588 PHE cc_start: 0.8454 (m-10) cc_final: 0.8189 (m-10) REVERT: C 608 LEU cc_start: 0.7770 (mt) cc_final: 0.7368 (pp) outliers start: 52 outliers final: 42 residues processed: 275 average time/residue: 0.1308 time to fit residues: 54.6297 Evaluate side-chains 277 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 64 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 510 GLN A 458 ASN A 510 GLN B 510 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111816 restraints weight = 22851.196| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.21 r_work: 0.3214 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17760 Z= 0.211 Angle : 0.565 8.493 24044 Z= 0.293 Chirality : 0.042 0.159 2624 Planarity : 0.004 0.036 2948 Dihedral : 12.573 163.584 2564 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.90 % Allowed : 17.92 % Favored : 79.18 % 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: -0.10 (0.19), residues: 2040 helix: 0.72 (0.15), residues: 1212 sheet: -0.97 (0.41), residues: 116 loop : -1.18 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 606 TYR 0.018 0.001 TYR B 363 PHE 0.021 0.002 PHE C 159 TRP 0.020 0.001 TRP C 421 HIS 0.003 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00493 (17756) covalent geometry : angle 0.56526 (24036) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.87661 ( 8) hydrogen bonds : bond 0.04542 ( 961) hydrogen bonds : angle 4.29773 ( 2811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8036 (p0) REVERT: D 146 ASN cc_start: 0.8529 (t0) cc_final: 0.7963 (t0) REVERT: D 272 ASN cc_start: 0.8616 (m-40) cc_final: 0.8064 (t0) REVERT: D 525 ASP cc_start: 0.7948 (t70) cc_final: 0.7300 (t70) REVERT: D 608 LEU cc_start: 0.7712 (mt) cc_final: 0.7289 (pp) REVERT: A 115 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8042 (p0) REVERT: A 146 ASN cc_start: 0.8541 (t0) cc_final: 0.7964 (t0) REVERT: A 272 ASN cc_start: 0.8617 (m-40) cc_final: 0.8061 (t0) REVERT: A 507 LEU cc_start: 0.8260 (mm) cc_final: 0.8027 (mm) REVERT: A 525 ASP cc_start: 0.7941 (t70) cc_final: 0.7323 (t0) REVERT: B 115 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8031 (p0) REVERT: B 146 ASN cc_start: 0.8552 (t0) cc_final: 0.7922 (t0) REVERT: B 182 GLU cc_start: 0.8814 (pm20) cc_final: 0.8413 (pm20) REVERT: B 270 TYR cc_start: 0.7700 (m-80) cc_final: 0.7467 (t80) REVERT: B 272 ASN cc_start: 0.8930 (t0) cc_final: 0.8623 (t0) REVERT: B 507 LEU cc_start: 0.8258 (mm) cc_final: 0.8036 (mm) REVERT: B 525 ASP cc_start: 0.7986 (t70) cc_final: 0.7329 (t70) REVERT: B 588 PHE cc_start: 0.8527 (m-10) cc_final: 0.8287 (m-10) REVERT: C 115 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8046 (p0) REVERT: C 146 ASN cc_start: 0.8540 (t0) cc_final: 0.7960 (t0) REVERT: C 182 GLU cc_start: 0.8855 (pm20) cc_final: 0.8370 (pm20) REVERT: C 272 ASN cc_start: 0.8615 (m-40) cc_final: 0.8060 (t0) REVERT: C 421 TRP cc_start: 0.6813 (t-100) cc_final: 0.6350 (t-100) REVERT: C 507 LEU cc_start: 0.8241 (mm) cc_final: 0.8013 (mm) REVERT: C 525 ASP cc_start: 0.7985 (t70) cc_final: 0.7322 (t70) REVERT: C 588 PHE cc_start: 0.8464 (m-10) cc_final: 0.8241 (m-10) outliers start: 54 outliers final: 44 residues processed: 277 average time/residue: 0.1394 time to fit residues: 59.1482 Evaluate side-chains 287 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN B 458 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111180 restraints weight = 23027.147| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.21 r_work: 0.3207 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17760 Z= 0.225 Angle : 0.581 8.366 24044 Z= 0.300 Chirality : 0.042 0.158 2624 Planarity : 0.004 0.039 2948 Dihedral : 12.604 166.750 2564 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.38 % Allowed : 17.81 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 2040 helix: 0.70 (0.15), residues: 1212 sheet: -0.95 (0.41), residues: 116 loop : -1.19 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 606 TYR 0.019 0.001 TYR C 363 PHE 0.022 0.002 PHE B 159 TRP 0.016 0.001 TRP C 421 HIS 0.003 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00528 (17756) covalent geometry : angle 0.58061 (24036) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.90519 ( 8) hydrogen bonds : bond 0.04618 ( 961) hydrogen bonds : angle 4.33854 ( 2811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 239 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8063 (p0) REVERT: D 146 ASN cc_start: 0.8550 (t0) cc_final: 0.7969 (t0) REVERT: D 272 ASN cc_start: 0.8624 (m-40) cc_final: 0.8051 (t0) REVERT: D 525 ASP cc_start: 0.7975 (t70) cc_final: 0.7318 (t70) REVERT: A 115 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8041 (p0) REVERT: A 146 ASN cc_start: 0.8545 (t0) cc_final: 0.7970 (t0) REVERT: A 272 ASN cc_start: 0.8630 (m-40) cc_final: 0.8054 (t0) REVERT: A 507 LEU cc_start: 0.8278 (mm) cc_final: 0.8044 (mm) REVERT: A 525 ASP cc_start: 0.7947 (t70) cc_final: 0.7312 (t0) REVERT: B 115 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8075 (p0) REVERT: B 146 ASN cc_start: 0.8589 (t0) cc_final: 0.7963 (t0) REVERT: B 182 GLU cc_start: 0.8817 (pm20) cc_final: 0.8369 (pm20) REVERT: B 270 TYR cc_start: 0.7681 (m-80) cc_final: 0.7478 (t80) REVERT: B 272 ASN cc_start: 0.8944 (t0) cc_final: 0.8653 (t0) REVERT: B 507 LEU cc_start: 0.8278 (mm) cc_final: 0.8048 (mm) REVERT: B 525 ASP cc_start: 0.7983 (t70) cc_final: 0.7330 (t70) REVERT: B 588 PHE cc_start: 0.8526 (m-10) cc_final: 0.8297 (m-10) REVERT: C 115 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8064 (p0) REVERT: C 146 ASN cc_start: 0.8541 (t0) cc_final: 0.7961 (t0) REVERT: C 182 GLU cc_start: 0.8878 (pm20) cc_final: 0.8389 (pm20) REVERT: C 272 ASN cc_start: 0.8622 (m-40) cc_final: 0.8079 (t0) REVERT: C 458 ASN cc_start: 0.7849 (t0) cc_final: 0.7596 (t0) REVERT: C 507 LEU cc_start: 0.8259 (mm) cc_final: 0.8036 (mm) REVERT: C 525 ASP cc_start: 0.8006 (t70) cc_final: 0.7517 (t70) outliers start: 63 outliers final: 52 residues processed: 286 average time/residue: 0.1382 time to fit residues: 60.6442 Evaluate side-chains 294 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 92 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.167926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115348 restraints weight = 22563.996| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.22 r_work: 0.3254 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17760 Z= 0.136 Angle : 0.512 8.196 24044 Z= 0.266 Chirality : 0.039 0.142 2624 Planarity : 0.003 0.038 2948 Dihedral : 12.198 163.842 2564 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.84 % Allowed : 18.45 % Favored : 78.70 % 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: 0.24 (0.19), residues: 2040 helix: 1.02 (0.15), residues: 1208 sheet: -0.76 (0.42), residues: 116 loop : -1.11 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 606 TYR 0.013 0.001 TYR B 363 PHE 0.020 0.002 PHE C 159 TRP 0.026 0.001 TRP D 421 HIS 0.002 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00305 (17756) covalent geometry : angle 0.51221 (24036) SS BOND : bond 0.00175 ( 4) SS BOND : angle 0.83392 ( 8) hydrogen bonds : bond 0.04106 ( 961) hydrogen bonds : angle 4.09243 ( 2811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8039 (p0) REVERT: D 146 ASN cc_start: 0.8359 (t0) cc_final: 0.7817 (t0) REVERT: D 272 ASN cc_start: 0.8604 (m-40) cc_final: 0.8071 (t0) REVERT: D 505 LEU cc_start: 0.8379 (tp) cc_final: 0.8013 (mp) REVERT: D 525 ASP cc_start: 0.7953 (t70) cc_final: 0.7345 (t70) REVERT: A 115 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7973 (p0) REVERT: A 146 ASN cc_start: 0.8386 (t0) cc_final: 0.7831 (t0) REVERT: A 272 ASN cc_start: 0.8611 (m-40) cc_final: 0.8070 (t0) REVERT: A 507 LEU cc_start: 0.8226 (mm) cc_final: 0.8003 (mm) REVERT: A 525 ASP cc_start: 0.7924 (t70) cc_final: 0.7294 (t70) REVERT: B 115 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7995 (p0) REVERT: B 146 ASN cc_start: 0.8429 (t0) cc_final: 0.7808 (t0) REVERT: B 182 GLU cc_start: 0.8830 (pm20) cc_final: 0.8410 (pm20) REVERT: B 270 TYR cc_start: 0.7621 (m-80) cc_final: 0.7359 (t80) REVERT: B 272 ASN cc_start: 0.8942 (t0) cc_final: 0.8655 (t0) REVERT: B 507 LEU cc_start: 0.8214 (mm) cc_final: 0.8004 (mm) REVERT: B 525 ASP cc_start: 0.7976 (t70) cc_final: 0.7374 (t70) REVERT: C 115 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8032 (p0) REVERT: C 146 ASN cc_start: 0.8384 (t0) cc_final: 0.7828 (t0) REVERT: C 182 GLU cc_start: 0.8864 (pm20) cc_final: 0.8377 (pm20) REVERT: C 272 ASN cc_start: 0.8624 (m-40) cc_final: 0.8087 (t0) REVERT: C 458 ASN cc_start: 0.7835 (t0) cc_final: 0.7598 (t0) REVERT: C 507 LEU cc_start: 0.8258 (mm) cc_final: 0.8039 (mm) REVERT: C 525 ASP cc_start: 0.7986 (t70) cc_final: 0.7383 (t70) outliers start: 53 outliers final: 45 residues processed: 281 average time/residue: 0.1407 time to fit residues: 60.3489 Evaluate side-chains 284 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 92 optimal weight: 0.0870 chunk 107 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN A 433 GLN B 433 GLN C 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.172720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121804 restraints weight = 22984.581| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.11 r_work: 0.3378 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17760 Z= 0.108 Angle : 0.493 7.113 24044 Z= 0.256 Chirality : 0.038 0.149 2624 Planarity : 0.003 0.038 2948 Dihedral : 11.503 155.785 2564 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.20 % Allowed : 19.53 % Favored : 78.27 % 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: 0.59 (0.19), residues: 2040 helix: 1.36 (0.15), residues: 1208 sheet: -0.57 (0.42), residues: 116 loop : -1.08 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 606 TYR 0.010 0.001 TYR D 365 PHE 0.021 0.001 PHE B 159 TRP 0.020 0.001 TRP D 421 HIS 0.002 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00230 (17756) covalent geometry : angle 0.49291 (24036) SS BOND : bond 0.00150 ( 4) SS BOND : angle 0.80288 ( 8) hydrogen bonds : bond 0.03786 ( 961) hydrogen bonds : angle 3.86759 ( 2811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8007 (p0) REVERT: D 117 SER cc_start: 0.8467 (m) cc_final: 0.8073 (p) REVERT: D 146 ASN cc_start: 0.8287 (t0) cc_final: 0.7747 (t0) REVERT: D 245 TRP cc_start: 0.8242 (m100) cc_final: 0.7859 (m-10) REVERT: D 272 ASN cc_start: 0.8599 (m-40) cc_final: 0.8115 (t0) REVERT: D 495 GLN cc_start: 0.7220 (tp40) cc_final: 0.7020 (tp40) REVERT: D 525 ASP cc_start: 0.7996 (t70) cc_final: 0.7492 (t70) REVERT: D 608 LEU cc_start: 0.7620 (mt) cc_final: 0.7171 (pp) REVERT: A 115 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7947 (p0) REVERT: A 117 SER cc_start: 0.8475 (m) cc_final: 0.8090 (p) REVERT: A 146 ASN cc_start: 0.8290 (t0) cc_final: 0.7745 (t0) REVERT: A 245 TRP cc_start: 0.8271 (m100) cc_final: 0.7883 (m-10) REVERT: A 272 ASN cc_start: 0.8600 (m-40) cc_final: 0.8115 (t0) REVERT: A 525 ASP cc_start: 0.7972 (t70) cc_final: 0.7407 (t70) REVERT: B 115 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7981 (p0) REVERT: B 117 SER cc_start: 0.8456 (m) cc_final: 0.8068 (p) REVERT: B 146 ASN cc_start: 0.8257 (t0) cc_final: 0.7705 (t0) REVERT: B 182 GLU cc_start: 0.8864 (pm20) cc_final: 0.8598 (pm20) REVERT: B 245 TRP cc_start: 0.8257 (m100) cc_final: 0.7844 (m-10) REVERT: B 272 ASN cc_start: 0.8906 (t0) cc_final: 0.8638 (t0) REVERT: B 525 ASP cc_start: 0.8064 (t70) cc_final: 0.7603 (t0) REVERT: C 115 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7967 (p0) REVERT: C 117 SER cc_start: 0.8460 (m) cc_final: 0.8073 (p) REVERT: C 146 ASN cc_start: 0.8305 (t0) cc_final: 0.7764 (t0) REVERT: C 182 GLU cc_start: 0.8757 (pm20) cc_final: 0.8281 (pm20) REVERT: C 245 TRP cc_start: 0.8268 (m100) cc_final: 0.7883 (m-10) REVERT: C 272 ASN cc_start: 0.8607 (m-40) cc_final: 0.8127 (t0) REVERT: C 525 ASP cc_start: 0.8042 (t70) cc_final: 0.7498 (t70) REVERT: C 558 PHE cc_start: 0.6429 (t80) cc_final: 0.6154 (t80) outliers start: 41 outliers final: 34 residues processed: 282 average time/residue: 0.1352 time to fit residues: 58.4926 Evaluate side-chains 266 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 0.9980 chunk 167 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 125 optimal weight: 0.0000 chunk 53 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.169472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.122312 restraints weight = 22870.391| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.06 r_work: 0.3355 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17760 Z= 0.135 Angle : 0.524 7.556 24044 Z= 0.269 Chirality : 0.040 0.145 2624 Planarity : 0.003 0.048 2948 Dihedral : 11.146 150.182 2564 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.09 % Allowed : 20.28 % Favored : 77.63 % 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: 0.64 (0.19), residues: 2040 helix: 1.39 (0.15), residues: 1208 sheet: -0.56 (0.42), residues: 116 loop : -1.05 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 606 TYR 0.013 0.001 TYR B 363 PHE 0.023 0.002 PHE A 159 TRP 0.017 0.001 TRP D 421 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00306 (17756) covalent geometry : angle 0.52417 (24036) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.81258 ( 8) hydrogen bonds : bond 0.04076 ( 961) hydrogen bonds : angle 3.93977 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4963.37 seconds wall clock time: 85 minutes 36.68 seconds (5136.68 seconds total)