Starting phenix.real_space_refine on Wed Mar 4 08:30:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tym_26185/03_2026/7tym_26185_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tym_26185/03_2026/7tym_26185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tym_26185/03_2026/7tym_26185_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tym_26185/03_2026/7tym_26185_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tym_26185/03_2026/7tym_26185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tym_26185/03_2026/7tym_26185.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 7670 2.51 5 N 2160 2.21 5 O 2212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12112 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6056 Classifications: {'peptide': 771} Link IDs: {'PTRANS': 40, 'TRANS': 730} Chain breaks: 7 Restraints were copied for chains: B Time building chain proxies: 4.95, per 1000 atoms: 0.41 Number of scatterers: 12112 At special positions: 0 Unit cell: (122.04, 154.44, 154.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2212 8.00 N 2160 7.00 C 7670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 232 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 321 " distance=2.04 Simple disulfide: pdb=" SG CYS A 631 " - pdb=" SG CYS A 838 " distance=2.03 Simple disulfide: pdb=" SG CYS A 764 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 232 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 838 " distance=2.03 Simple disulfide: pdb=" SG CYS B 764 " - pdb=" SG CYS B 773 " 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: 0.90 Conformation dependent library (CDL) restraints added in 606.2 milliseconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 11.2% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.510A pdb=" N GLN A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 19 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.831A pdb=" N ALA A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.580A pdb=" N CYS A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.636A pdb=" N CYS A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.916A pdb=" N GLY A 272 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 removed outlier: 4.268A pdb=" N GLN A 316 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 319 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.806A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.136A pdb=" N ILE A 427 " --> pdb=" O CYS A 423 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 Processing helix chain 'A' and resid 841 through 848 removed outlier: 3.899A pdb=" N PHE A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.510A pdb=" N GLN B 18 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 19 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.831A pdb=" N ALA B 138 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.581A pdb=" N CYS B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.637A pdb=" N CYS B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.915A pdb=" N GLY B 272 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 319 removed outlier: 4.267A pdb=" N GLN B 316 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP B 317 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 318 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 319 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.806A pdb=" N SER B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.136A pdb=" N ILE B 427 " --> pdb=" O CYS B 423 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 693 Processing helix chain 'B' and resid 841 through 848 removed outlier: 3.899A pdb=" N PHE B 847 " --> pdb=" O ARG B 843 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 8.186A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 9 removed outlier: 8.186A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LEU A 58 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 29 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE A 60 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 31 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL A 62 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU A 33 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 57 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE A 92 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 59 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ARG A 114 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 90 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLU A 116 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A 92 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 113 " --> pdb=" O HIS A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.689A pdb=" N THR A 168 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP A 175 " --> pdb=" O THR A 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243 removed outlier: 3.551A pdb=" N ARG A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 309 removed outlier: 3.840A pdb=" N VAL A 304 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A 327 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 306 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 329 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 308 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 309 removed outlier: 3.840A pdb=" N VAL A 304 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A 327 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 306 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 329 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 308 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS A 357 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 328 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LYS A 359 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 388 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 463 through 468 removed outlier: 6.581A pdb=" N ARG A 476 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN A 466 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 474 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N THR A 468 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 518 through 522 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 588 removed outlier: 5.669A pdb=" N ASP A 584 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS A 600 " --> pdb=" O ASP A 584 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 737 through 741 removed outlier: 3.567A pdb=" N VAL A 614 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 611 " --> pdb=" O CYS A 764 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 756 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 797 through 801 removed outlier: 3.848A pdb=" N SER A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 834 through 840 removed outlier: 3.650A pdb=" N TYR A 827 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 822 " --> pdb=" O THR A 867 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 9 removed outlier: 8.185A pdb=" N GLN B 30 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 7 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B 32 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N MET B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 5 through 9 removed outlier: 8.185A pdb=" N GLN B 30 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 7 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B 32 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N MET B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LEU B 58 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 29 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE B 60 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 31 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL B 62 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU B 33 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 57 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N PHE B 92 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 59 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG B 114 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL B 90 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLU B 116 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE B 92 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 113 " --> pdb=" O HIS B 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.690A pdb=" N THR B 168 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP B 175 " --> pdb=" O THR B 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AB9, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.552A pdb=" N ARG B 247 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 301 through 309 removed outlier: 3.839A pdb=" N VAL B 304 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 327 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 306 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 329 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR B 308 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 301 through 309 removed outlier: 3.839A pdb=" N VAL B 304 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 327 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 306 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 329 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR B 308 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LYS B 357 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 328 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LYS B 359 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 388 " --> pdb=" O TYR B 415 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 463 through 468 removed outlier: 6.580A pdb=" N ARG B 476 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN B 466 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 474 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N THR B 468 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 518 through 522 Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 588 removed outlier: 5.669A pdb=" N ASP B 584 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS B 600 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 737 through 741 removed outlier: 3.567A pdb=" N VAL B 614 " --> pdb=" O ASP B 739 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 611 " --> pdb=" O CYS B 764 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 756 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 797 through 801 removed outlier: 3.847A pdb=" N SER B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 834 through 840 removed outlier: 3.650A pdb=" N TYR B 827 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 822 " --> pdb=" O THR B 867 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4034 1.35 - 1.48: 3074 1.48 - 1.60: 5204 1.60 - 1.73: 0 1.73 - 1.86: 80 Bond restraints: 12392 Sorted by residual: bond pdb=" CB CYS A 321 " pdb=" SG CYS A 321 " ideal model delta sigma weight residual 1.808 1.857 -0.049 3.30e-02 9.18e+02 2.21e+00 bond pdb=" CB CYS B 321 " pdb=" SG CYS B 321 " ideal model delta sigma weight residual 1.808 1.857 -0.049 3.30e-02 9.18e+02 2.20e+00 bond pdb=" CA THR B 553 " pdb=" CB THR B 553 " ideal model delta sigma weight residual 1.529 1.548 -0.019 1.58e-02 4.01e+03 1.40e+00 bond pdb=" CA THR A 553 " pdb=" CB THR A 553 " ideal model delta sigma weight residual 1.529 1.547 -0.018 1.58e-02 4.01e+03 1.34e+00 bond pdb=" C PRO A 237 " pdb=" N PRO A 238 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 ... (remaining 12387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 16511 1.62 - 3.24: 256 3.24 - 4.85: 53 4.85 - 6.47: 8 6.47 - 8.09: 6 Bond angle restraints: 16834 Sorted by residual: angle pdb=" CA CYS B 302 " pdb=" CB CYS B 302 " pdb=" SG CYS B 302 " ideal model delta sigma weight residual 114.40 122.07 -7.67 2.30e+00 1.89e-01 1.11e+01 angle pdb=" CA CYS A 302 " pdb=" CB CYS A 302 " pdb=" SG CYS A 302 " ideal model delta sigma weight residual 114.40 122.04 -7.64 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA THR B 553 " pdb=" CB THR B 553 " pdb=" CG2 THR B 553 " ideal model delta sigma weight residual 110.50 114.63 -4.13 1.70e+00 3.46e-01 5.91e+00 angle pdb=" CA THR A 553 " pdb=" CB THR A 553 " pdb=" CG2 THR A 553 " ideal model delta sigma weight residual 110.50 114.63 -4.13 1.70e+00 3.46e-01 5.90e+00 angle pdb=" C PHE A 370 " pdb=" N LYS A 371 " pdb=" CA LYS A 371 " ideal model delta sigma weight residual 120.54 123.82 -3.28 1.35e+00 5.49e-01 5.89e+00 ... (remaining 16829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 6348 16.79 - 33.58: 816 33.58 - 50.38: 228 50.38 - 67.17: 36 67.17 - 83.96: 18 Dihedral angle restraints: 7446 sinusoidal: 3006 harmonic: 4440 Sorted by residual: dihedral pdb=" CB CYS B 165 " pdb=" SG CYS B 165 " pdb=" SG CYS B 184 " pdb=" CB CYS B 184 " ideal model delta sinusoidal sigma weight residual 93.00 176.80 -83.80 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 184 " pdb=" CB CYS A 184 " ideal model delta sinusoidal sigma weight residual 93.00 176.76 -83.76 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS A 122 " pdb=" SG CYS A 122 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -25.46 -60.54 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 7443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1394 0.041 - 0.082: 308 0.082 - 0.122: 160 0.122 - 0.163: 16 0.163 - 0.204: 2 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CA PHE B 418 " pdb=" N PHE B 418 " pdb=" C PHE B 418 " pdb=" CB PHE B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE A 418 " pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CB PHE A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR A 553 " pdb=" CA THR A 553 " pdb=" OG1 THR A 553 " pdb=" CG2 THR A 553 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1877 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 778 " 0.013 2.00e-02 2.50e+03 1.69e-02 5.03e+00 pdb=" CG PHE B 778 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 778 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 778 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 778 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 778 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 778 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 778 " 0.012 2.00e-02 2.50e+03 1.69e-02 4.99e+00 pdb=" CG PHE A 778 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 778 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 778 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 778 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 778 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 778 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 418 " -0.023 2.00e-02 2.50e+03 1.52e-02 4.03e+00 pdb=" CG PHE B 418 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 418 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 418 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 418 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 418 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 418 " -0.014 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 454 2.72 - 3.27: 11367 3.27 - 3.81: 18708 3.81 - 4.36: 22710 4.36 - 4.90: 40028 Nonbonded interactions: 93267 Sorted by model distance: nonbonded pdb=" O GLY B 347 " pdb=" ND2 ASN B 372 " model vdw 2.175 3.120 nonbonded pdb=" O GLY A 347 " pdb=" ND2 ASN A 372 " model vdw 2.175 3.120 nonbonded pdb=" OG SER B 801 " pdb=" OG SER B 805 " model vdw 2.226 3.040 nonbonded pdb=" OG SER A 801 " pdb=" OG SER A 805 " model vdw 2.226 3.040 nonbonded pdb=" O LEU A 430 " pdb=" OG1 THR A 434 " model vdw 2.230 3.040 ... (remaining 93262 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.820 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.002 0.049 12420 Z= 0.104 Angle : 0.544 8.091 16890 Z= 0.281 Chirality : 0.043 0.204 1880 Planarity : 0.004 0.040 2176 Dihedral : 15.938 83.961 4502 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.09 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 22.87 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.22), residues: 1510 helix: 1.00 (0.53), residues: 112 sheet: -0.10 (0.26), residues: 376 loop : -1.52 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 377 TYR 0.009 0.001 TYR B 176 PHE 0.039 0.001 PHE B 778 TRP 0.008 0.001 TRP B 402 HIS 0.004 0.001 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00230 (12392) covalent geometry : angle 0.54064 (16834) SS BOND : bond 0.00329 ( 28) SS BOND : angle 1.19985 ( 56) hydrogen bonds : bond 0.14143 ( 250) hydrogen bonds : angle 6.10491 ( 636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.383 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1027 time to fit residues: 12.1399 Evaluate side-chains 77 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN B 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.131613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100537 restraints weight = 19087.748| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.97 r_work: 0.3155 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12420 Z= 0.140 Angle : 0.538 6.224 16890 Z= 0.278 Chirality : 0.044 0.141 1880 Planarity : 0.004 0.043 2176 Dihedral : 4.339 24.346 1688 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.52 % Allowed : 20.73 % Favored : 76.75 % 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: -1.32 (0.22), residues: 1510 helix: 1.52 (0.54), residues: 100 sheet: -0.12 (0.26), residues: 376 loop : -1.51 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 377 TYR 0.009 0.001 TYR A 56 PHE 0.034 0.001 PHE B 418 TRP 0.006 0.001 TRP B 599 HIS 0.006 0.001 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00335 (12392) covalent geometry : angle 0.53640 (16834) SS BOND : bond 0.00266 ( 28) SS BOND : angle 0.85934 ( 56) hydrogen bonds : bond 0.02678 ( 250) hydrogen bonds : angle 5.16118 ( 636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.8193 (mt0) cc_final: 0.7908 (mm110) REVERT: A 307 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7240 (tttp) REVERT: A 377 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7507 (mtm110) REVERT: B 229 GLN cc_start: 0.8168 (mt0) cc_final: 0.7875 (mm110) REVERT: B 307 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7099 (tttp) REVERT: B 377 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7514 (mtm110) outliers start: 33 outliers final: 17 residues processed: 120 average time/residue: 0.0957 time to fit residues: 17.7482 Evaluate side-chains 99 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 480 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 113 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.0370 chunk 25 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 overall best weight: 1.0464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099758 restraints weight = 19217.576| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.97 r_work: 0.3144 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12420 Z= 0.128 Angle : 0.527 9.013 16890 Z= 0.269 Chirality : 0.044 0.180 1880 Planarity : 0.004 0.041 2176 Dihedral : 4.338 23.494 1688 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.59 % Allowed : 22.33 % Favored : 75.08 % 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: -1.38 (0.21), residues: 1510 helix: 1.60 (0.54), residues: 100 sheet: -0.17 (0.26), residues: 376 loop : -1.56 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.009 0.001 TYR A 56 PHE 0.024 0.001 PHE B 418 TRP 0.006 0.001 TRP A 599 HIS 0.005 0.001 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00309 (12392) covalent geometry : angle 0.52560 (16834) SS BOND : bond 0.00279 ( 28) SS BOND : angle 0.76430 ( 56) hydrogen bonds : bond 0.02615 ( 250) hydrogen bonds : angle 5.06553 ( 636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.494 Fit side-chains REVERT: A 7 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8359 (pp) REVERT: A 229 GLN cc_start: 0.8177 (mt0) cc_final: 0.7899 (mm110) REVERT: A 307 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7206 (tttp) REVERT: A 377 ARG cc_start: 0.7758 (mtm110) cc_final: 0.7482 (mtm110) REVERT: A 402 TRP cc_start: 0.7556 (OUTLIER) cc_final: 0.6050 (p-90) REVERT: B 7 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8351 (pp) REVERT: B 229 GLN cc_start: 0.8148 (mt0) cc_final: 0.7865 (mm110) REVERT: B 377 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7486 (mtm110) REVERT: B 402 TRP cc_start: 0.7545 (OUTLIER) cc_final: 0.6048 (p-90) outliers start: 34 outliers final: 16 residues processed: 123 average time/residue: 0.1027 time to fit residues: 19.0235 Evaluate side-chains 105 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 480 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 480 TYR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 774 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 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 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 419 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN B 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.129117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097434 restraints weight = 19116.378| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.01 r_work: 0.3111 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12420 Z= 0.164 Angle : 0.553 7.211 16890 Z= 0.285 Chirality : 0.045 0.202 1880 Planarity : 0.004 0.041 2176 Dihedral : 4.561 23.747 1688 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.51 % Allowed : 20.43 % Favored : 76.07 % 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: -1.53 (0.21), residues: 1510 helix: 1.53 (0.54), residues: 100 sheet: -0.33 (0.26), residues: 378 loop : -1.64 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 743 TYR 0.009 0.001 TYR B 630 PHE 0.051 0.002 PHE B 418 TRP 0.007 0.001 TRP A 599 HIS 0.005 0.001 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00399 (12392) covalent geometry : angle 0.55169 (16834) SS BOND : bond 0.00309 ( 28) SS BOND : angle 0.81943 ( 56) hydrogen bonds : bond 0.02644 ( 250) hydrogen bonds : angle 5.09618 ( 636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8462 (pp) REVERT: A 229 GLN cc_start: 0.8189 (mt0) cc_final: 0.7917 (mm110) REVERT: A 307 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7302 (tttp) REVERT: A 402 TRP cc_start: 0.7753 (OUTLIER) cc_final: 0.6222 (p-90) REVERT: B 7 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8460 (pp) REVERT: B 229 GLN cc_start: 0.8190 (mt0) cc_final: 0.7911 (mm110) REVERT: B 402 TRP cc_start: 0.7741 (OUTLIER) cc_final: 0.6223 (p-90) outliers start: 46 outliers final: 33 residues processed: 123 average time/residue: 0.0955 time to fit residues: 18.0110 Evaluate side-chains 116 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 480 TYR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 480 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 62 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 151 optimal weight: 0.0470 chunk 117 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 42 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 overall best weight: 0.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 337 ASN ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 271 GLN B 337 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101054 restraints weight = 19064.236| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.97 r_work: 0.3158 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12420 Z= 0.095 Angle : 0.514 6.958 16890 Z= 0.264 Chirality : 0.043 0.187 1880 Planarity : 0.004 0.041 2176 Dihedral : 4.306 25.323 1688 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.36 % Allowed : 23.02 % Favored : 74.62 % 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: -1.39 (0.21), residues: 1510 helix: 1.60 (0.55), residues: 100 sheet: -0.20 (0.26), residues: 374 loop : -1.56 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.008 0.001 TYR B 415 PHE 0.043 0.001 PHE B 418 TRP 0.007 0.001 TRP A 616 HIS 0.004 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00221 (12392) covalent geometry : angle 0.51368 (16834) SS BOND : bond 0.00219 ( 28) SS BOND : angle 0.65448 ( 56) hydrogen bonds : bond 0.02249 ( 250) hydrogen bonds : angle 4.83514 ( 636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.343 Fit side-chains REVERT: A 229 GLN cc_start: 0.8160 (mt0) cc_final: 0.7889 (mm110) REVERT: A 307 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7191 (tttp) REVERT: A 402 TRP cc_start: 0.7516 (OUTLIER) cc_final: 0.6309 (p-90) REVERT: B 229 GLN cc_start: 0.8185 (mt0) cc_final: 0.7906 (mm110) REVERT: B 402 TRP cc_start: 0.7510 (OUTLIER) cc_final: 0.6311 (p-90) outliers start: 31 outliers final: 20 residues processed: 113 average time/residue: 0.1111 time to fit residues: 18.1643 Evaluate side-chains 105 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 480 TYR Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 480 TYR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 825 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 24 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 617 GLN B 28 HIS B 183 HIS B 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097309 restraints weight = 19512.945| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.35 r_work: 0.3014 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 12420 Z= 0.362 Angle : 0.718 6.465 16890 Z= 0.372 Chirality : 0.050 0.222 1880 Planarity : 0.005 0.040 2176 Dihedral : 5.357 25.385 1688 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.26 % Favored : 88.61 % Rotamer: Outliers : 3.43 % Allowed : 22.10 % Favored : 74.47 % 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: -1.94 (0.21), residues: 1510 helix: 1.08 (0.54), residues: 100 sheet: -0.60 (0.26), residues: 356 loop : -1.91 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 377 TYR 0.014 0.002 TYR A 389 PHE 0.059 0.003 PHE B 418 TRP 0.014 0.002 TRP B 599 HIS 0.008 0.002 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00873 (12392) covalent geometry : angle 0.71481 (16834) SS BOND : bond 0.00544 ( 28) SS BOND : angle 1.30548 ( 56) hydrogen bonds : bond 0.03430 ( 250) hydrogen bonds : angle 5.65015 ( 636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8576 (pp) REVERT: A 229 GLN cc_start: 0.8204 (mt0) cc_final: 0.7975 (mm110) REVERT: B 7 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8574 (pp) REVERT: B 229 GLN cc_start: 0.8204 (mt0) cc_final: 0.7965 (mm110) outliers start: 45 outliers final: 36 residues processed: 121 average time/residue: 0.0873 time to fit residues: 16.8046 Evaluate side-chains 115 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 150 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 106 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 617 GLN B 337 ASN B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.128483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100922 restraints weight = 19125.349| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.38 r_work: 0.3087 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12420 Z= 0.121 Angle : 0.554 7.289 16890 Z= 0.285 Chirality : 0.044 0.196 1880 Planarity : 0.004 0.037 2176 Dihedral : 4.772 27.750 1688 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.82 % Allowed : 23.02 % Favored : 74.16 % 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: -1.78 (0.21), residues: 1510 helix: 1.18 (0.54), residues: 100 sheet: -0.62 (0.25), residues: 384 loop : -1.75 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 377 TYR 0.007 0.001 TYR A 56 PHE 0.038 0.001 PHE B 418 TRP 0.008 0.001 TRP A 179 HIS 0.005 0.001 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00284 (12392) covalent geometry : angle 0.55327 (16834) SS BOND : bond 0.00239 ( 28) SS BOND : angle 0.72478 ( 56) hydrogen bonds : bond 0.02532 ( 250) hydrogen bonds : angle 5.12666 ( 636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.458 Fit side-chains REVERT: A 229 GLN cc_start: 0.8212 (mt0) cc_final: 0.7948 (mm110) REVERT: B 229 GLN cc_start: 0.8217 (mt0) cc_final: 0.7946 (mm110) outliers start: 37 outliers final: 31 residues processed: 118 average time/residue: 0.0944 time to fit residues: 17.4049 Evaluate side-chains 111 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 480 TYR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 883 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 133 optimal weight: 0.2980 chunk 116 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.0070 chunk 12 optimal weight: 0.0070 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 617 GLN B 337 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099952 restraints weight = 19051.710| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.97 r_work: 0.3154 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12420 Z= 0.094 Angle : 0.532 9.536 16890 Z= 0.270 Chirality : 0.043 0.185 1880 Planarity : 0.004 0.039 2176 Dihedral : 4.399 28.237 1688 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.44 % Allowed : 23.63 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.21), residues: 1510 helix: 0.81 (0.52), residues: 112 sheet: -0.44 (0.25), residues: 384 loop : -1.69 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 377 TYR 0.009 0.001 TYR A 415 PHE 0.032 0.001 PHE A 418 TRP 0.010 0.001 TRP B 616 HIS 0.004 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00213 (12392) covalent geometry : angle 0.53186 (16834) SS BOND : bond 0.00208 ( 28) SS BOND : angle 0.67629 ( 56) hydrogen bonds : bond 0.02170 ( 250) hydrogen bonds : angle 4.82275 ( 636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.442 Fit side-chains REVERT: A 229 GLN cc_start: 0.8156 (mt0) cc_final: 0.7933 (mm110) REVERT: A 316 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: B 229 GLN cc_start: 0.8168 (mt0) cc_final: 0.7938 (mm110) REVERT: B 316 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7420 (mp10) outliers start: 32 outliers final: 25 residues processed: 112 average time/residue: 0.0913 time to fit residues: 16.1512 Evaluate side-chains 105 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 480 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 480 TYR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 883 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 140 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 419 ASN B 337 ASN B 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098343 restraints weight = 19156.999| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.02 r_work: 0.3124 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12420 Z= 0.122 Angle : 0.551 10.559 16890 Z= 0.278 Chirality : 0.044 0.197 1880 Planarity : 0.004 0.040 2176 Dihedral : 4.434 25.760 1688 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.59 % Allowed : 23.63 % Favored : 73.78 % 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: -1.62 (0.21), residues: 1510 helix: 1.27 (0.54), residues: 100 sheet: -0.46 (0.25), residues: 384 loop : -1.66 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 377 TYR 0.007 0.001 TYR A 56 PHE 0.034 0.001 PHE A 418 TRP 0.006 0.001 TRP B 179 HIS 0.005 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00293 (12392) covalent geometry : angle 0.55061 (16834) SS BOND : bond 0.00238 ( 28) SS BOND : angle 0.72708 ( 56) hydrogen bonds : bond 0.02336 ( 250) hydrogen bonds : angle 4.88139 ( 636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.483 Fit side-chains REVERT: A 229 GLN cc_start: 0.8124 (mt0) cc_final: 0.7907 (mm110) REVERT: A 316 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7409 (mp10) REVERT: B 229 GLN cc_start: 0.8136 (mt0) cc_final: 0.7915 (mm110) REVERT: B 316 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7413 (mp10) outliers start: 34 outliers final: 29 residues processed: 113 average time/residue: 0.0966 time to fit residues: 16.9812 Evaluate side-chains 110 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 480 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 883 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 147 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 108 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.128681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096774 restraints weight = 19167.659| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.03 r_work: 0.3096 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12420 Z= 0.151 Angle : 0.575 10.795 16890 Z= 0.290 Chirality : 0.045 0.196 1880 Planarity : 0.004 0.040 2176 Dihedral : 4.588 25.323 1688 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.59 % Allowed : 23.17 % Favored : 74.24 % 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: -1.68 (0.21), residues: 1510 helix: 1.28 (0.54), residues: 100 sheet: -0.51 (0.25), residues: 384 loop : -1.70 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 377 TYR 0.009 0.001 TYR A 56 PHE 0.039 0.001 PHE A 418 TRP 0.007 0.001 TRP A 599 HIS 0.006 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00365 (12392) covalent geometry : angle 0.57364 (16834) SS BOND : bond 0.00277 ( 28) SS BOND : angle 0.80046 ( 56) hydrogen bonds : bond 0.02520 ( 250) hydrogen bonds : angle 5.00917 ( 636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.493 Fit side-chains REVERT: A 229 GLN cc_start: 0.8115 (mt0) cc_final: 0.7892 (mm110) REVERT: A 316 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: A 377 ARG cc_start: 0.7516 (mtm110) cc_final: 0.6796 (ttp-110) REVERT: B 229 GLN cc_start: 0.8119 (mt0) cc_final: 0.7893 (mm110) REVERT: B 316 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: B 377 ARG cc_start: 0.7524 (mtm110) cc_final: 0.6833 (ttp-110) outliers start: 34 outliers final: 31 residues processed: 110 average time/residue: 0.0925 time to fit residues: 16.0043 Evaluate side-chains 106 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 883 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 106 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 0.4980 chunk 46 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 139 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100495 restraints weight = 19285.814| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.38 r_work: 0.3081 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12420 Z= 0.160 Angle : 0.581 11.142 16890 Z= 0.294 Chirality : 0.045 0.273 1880 Planarity : 0.004 0.039 2176 Dihedral : 4.685 26.921 1688 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.74 % Allowed : 23.17 % Favored : 74.09 % 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: -1.73 (0.21), residues: 1510 helix: 1.13 (0.54), residues: 100 sheet: -0.52 (0.25), residues: 384 loop : -1.75 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 377 TYR 0.009 0.001 TYR A 56 PHE 0.042 0.002 PHE A 418 TRP 0.008 0.001 TRP B 599 HIS 0.006 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00388 (12392) covalent geometry : angle 0.58049 (16834) SS BOND : bond 0.00281 ( 28) SS BOND : angle 0.82605 ( 56) hydrogen bonds : bond 0.02565 ( 250) hydrogen bonds : angle 5.04937 ( 636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2788.57 seconds wall clock time: 48 minutes 30.32 seconds (2910.32 seconds total)