Starting phenix.real_space_refine on Fri May 16 23:21:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ysz_10911/05_2025/6ysz_10911.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ysz_10911/05_2025/6ysz_10911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ysz_10911/05_2025/6ysz_10911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ysz_10911/05_2025/6ysz_10911.map" model { file = "/net/cci-nas-00/data/ceres_data/6ysz_10911/05_2025/6ysz_10911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ysz_10911/05_2025/6ysz_10911.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.007 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 60 5.16 5 C 9348 2.51 5 N 2742 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 5.69, per 1000 atoms: 0.37 Number of scatterers: 15192 At special positions: 0 Unit cell: (101.15, 97.75, 143.65, 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 60 16.00 O 3042 8.00 N 2742 7.00 C 9348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.8 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 6 sheets defined 81.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.519A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 154 Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 removed outlier: 3.722A pdb=" N ASN B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 110 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 205 Processing helix chain 'B' and resid 216 through 231 Processing helix chain 'B' and resid 238 through 253 removed outlier: 4.346A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.638A pdb=" N ILE B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 282' Processing helix chain 'B' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA B 325 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 65 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 154 Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 205 Processing helix chain 'C' and resid 216 through 231 Processing helix chain 'C' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE C 299 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 302 " --> pdb=" O GLN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 154 Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 205 Processing helix chain 'D' and resid 216 through 231 Processing helix chain 'D' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.709A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 282' Processing helix chain 'D' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 318 removed outlier: 3.640A pdb=" N ASN D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA D 325 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA D 371 " --> pdb=" O THR D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 126 removed outlier: 3.503A pdb=" N MET E 101 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 154 Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 205 Processing helix chain 'E' and resid 216 through 231 Processing helix chain 'E' and resid 238 through 253 removed outlier: 4.346A pdb=" N GLN E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.638A pdb=" N ILE E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 282' Processing helix chain 'E' and resid 283 through 302 removed outlier: 4.530A pdb=" N GLN E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE E 299 " --> pdb=" O GLN E 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 327 " --> pdb=" O ARG E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA E 371 " --> pdb=" O THR E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.520A pdb=" N ARG F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN F 88 " --> pdb=" O ARG F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG F 110 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA F 112 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 154 Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG F 199 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL F 200 " --> pdb=" O MET F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 205 Processing helix chain 'F' and resid 216 through 231 Processing helix chain 'F' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE F 282 " --> pdb=" O TYR F 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 282' Processing helix chain 'F' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE F 299 " --> pdb=" O GLN F 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 302 " --> pdb=" O GLN F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA F 325 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA F 371 " --> pdb=" O THR F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing sheet with id=AA1, first strand: chain 'A' and resid 268 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 270 Processing sheet with id=AA3, first strand: chain 'C' and resid 268 through 270 Processing sheet with id=AA4, first strand: chain 'D' and resid 268 through 270 Processing sheet with id=AA5, first strand: chain 'E' and resid 268 through 270 Processing sheet with id=AA6, first strand: chain 'F' and resid 268 through 270 1021 hydrogen bonds defined for protein. 3045 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: 4.29 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5418 1.34 - 1.46: 1718 1.46 - 1.57: 8158 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 15414 Sorted by residual: bond pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.88e+00 bond pdb=" N GLN F 298 " pdb=" CA GLN F 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.87e+00 bond pdb=" N GLN D 298 " pdb=" CA GLN D 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.83e+00 bond pdb=" N GLN A 298 " pdb=" CA GLN A 298 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.27e-02 6.20e+03 5.70e+00 bond pdb=" N GLN B 298 " pdb=" CA GLN B 298 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.27e-02 6.20e+03 5.69e+00 ... (remaining 15409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 19133 0.95 - 1.90: 1364 1.90 - 2.85: 171 2.85 - 3.80: 80 3.80 - 4.75: 30 Bond angle restraints: 20778 Sorted by residual: angle pdb=" N THR B 276 " pdb=" CA THR B 276 " pdb=" C THR B 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.78e+00 angle pdb=" N THR E 276 " pdb=" CA THR E 276 " pdb=" C THR E 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.77e+00 angle pdb=" N THR C 276 " pdb=" CA THR C 276 " pdb=" C THR C 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.77e+00 angle pdb=" N THR F 276 " pdb=" CA THR F 276 " pdb=" C THR F 276 " ideal model delta sigma weight residual 108.34 111.48 -3.14 1.31e+00 5.83e-01 5.73e+00 angle pdb=" N THR A 276 " pdb=" CA THR A 276 " pdb=" C THR A 276 " ideal model delta sigma weight residual 108.34 111.47 -3.13 1.31e+00 5.83e-01 5.70e+00 ... (remaining 20773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 8054 15.18 - 30.35: 1084 30.35 - 45.53: 294 45.53 - 60.70: 60 60.70 - 75.88: 36 Dihedral angle restraints: 9528 sinusoidal: 4002 harmonic: 5526 Sorted by residual: dihedral pdb=" CA GLU B 126 " pdb=" C GLU B 126 " pdb=" N GLY B 127 " pdb=" CA GLY B 127 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA GLU D 126 " pdb=" C GLU D 126 " pdb=" N GLY D 127 " pdb=" CA GLY D 127 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta harmonic sigma weight residual 180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 9525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1267 0.027 - 0.054: 642 0.054 - 0.081: 193 0.081 - 0.109: 80 0.109 - 0.136: 26 Chirality restraints: 2208 Sorted by residual: chirality pdb=" CB ILE B 171 " pdb=" CA ILE B 171 " pdb=" CG1 ILE B 171 " pdb=" CG2 ILE B 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CB ILE D 171 " pdb=" CA ILE D 171 " pdb=" CG1 ILE D 171 " pdb=" CG2 ILE D 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB ILE E 171 " pdb=" CA ILE E 171 " pdb=" CG1 ILE E 171 " pdb=" CG2 ILE E 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 2205 not shown) Planarity restraints: 2826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 346 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO C 347 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO E 347 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 346 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 347 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.025 5.00e-02 4.00e+02 ... (remaining 2823 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4750 2.82 - 3.34: 15895 3.34 - 3.86: 25778 3.86 - 4.38: 27270 4.38 - 4.90: 46431 Nonbonded interactions: 120124 Sorted by model distance: nonbonded pdb=" NE2 GLN B 191 " pdb=" OE1 GLN B 239 " model vdw 2.295 3.120 nonbonded pdb=" NE2 GLN D 191 " pdb=" OE1 GLN D 239 " model vdw 2.295 3.120 nonbonded pdb=" NE2 GLN E 191 " pdb=" OE1 GLN E 239 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN A 191 " pdb=" OE1 GLN A 239 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN C 191 " pdb=" OE1 GLN C 239 " model vdw 2.296 3.120 ... (remaining 120119 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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 group one per residue 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 29.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15414 Z= 0.193 Angle : 0.562 4.755 20778 Z= 0.338 Chirality : 0.038 0.136 2208 Planarity : 0.003 0.046 2826 Dihedral : 15.540 75.878 5952 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.38 % Allowed : 8.27 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 1884 helix: -0.42 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.003 0.001 HIS C 182 PHE 0.009 0.001 PHE D 185 TYR 0.009 0.001 TYR A 163 ARG 0.009 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.12087 ( 1021) hydrogen bonds : angle 4.85719 ( 3045) covalent geometry : bond 0.00420 (15414) covalent geometry : angle 0.56211 (20778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 433 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8595 (tppp) cc_final: 0.8106 (tppp) REVERT: A 135 MET cc_start: 0.7875 (tmm) cc_final: 0.7361 (tmm) REVERT: A 152 GLU cc_start: 0.8045 (tp30) cc_final: 0.7645 (tp30) REVERT: A 159 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 243 LEU cc_start: 0.7512 (tp) cc_final: 0.7223 (tp) REVERT: B 82 GLN cc_start: 0.8844 (mt0) cc_final: 0.8581 (mt0) REVERT: B 85 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 121 MET cc_start: 0.7679 (tpt) cc_final: 0.7337 (tmm) REVERT: B 125 LYS cc_start: 0.8451 (tppp) cc_final: 0.7887 (ttmm) REVERT: B 144 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7430 (mm-40) REVERT: B 145 GLU cc_start: 0.8034 (tp30) cc_final: 0.7305 (tp30) REVERT: B 196 MET cc_start: 0.8228 (tpp) cc_final: 0.7960 (tmm) REVERT: B 211 MET cc_start: 0.8295 (tpp) cc_final: 0.7928 (tpt) REVERT: B 286 GLN cc_start: 0.8324 (mm110) cc_final: 0.8122 (mm-40) REVERT: B 335 GLU cc_start: 0.8219 (tp30) cc_final: 0.7801 (tm-30) REVERT: B 344 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8301 (mm110) REVERT: C 68 ASP cc_start: 0.8048 (t70) cc_final: 0.7686 (t70) REVERT: C 94 TYR cc_start: 0.8595 (m-80) cc_final: 0.7711 (m-80) REVERT: C 121 MET cc_start: 0.7725 (tpt) cc_final: 0.7465 (tpp) REVERT: C 125 LYS cc_start: 0.8482 (tppp) cc_final: 0.8000 (tppp) REVERT: C 159 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7203 (tm-30) REVERT: C 211 MET cc_start: 0.8277 (tpp) cc_final: 0.8016 (ttp) REVERT: C 252 SER cc_start: 0.8446 (p) cc_final: 0.8083 (p) REVERT: C 291 MET cc_start: 0.8506 (tpt) cc_final: 0.8246 (tpp) REVERT: C 300 GLU cc_start: 0.8619 (tp30) cc_final: 0.8193 (mm-30) REVERT: D 95 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8570 (tp-100) REVERT: D 125 LYS cc_start: 0.8579 (tppp) cc_final: 0.8071 (tppp) REVERT: D 135 MET cc_start: 0.7809 (tmm) cc_final: 0.7279 (tmm) REVERT: D 152 GLU cc_start: 0.7999 (tp30) cc_final: 0.7549 (tp30) REVERT: D 159 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7347 (tm-30) REVERT: D 196 MET cc_start: 0.8206 (tpp) cc_final: 0.7929 (tmm) REVERT: D 243 LEU cc_start: 0.7517 (tp) cc_final: 0.7267 (tp) REVERT: D 335 GLU cc_start: 0.8309 (tp30) cc_final: 0.7729 (tm-30) REVERT: E 82 GLN cc_start: 0.8852 (mt0) cc_final: 0.8651 (mt0) REVERT: E 95 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8748 (tp40) REVERT: E 125 LYS cc_start: 0.8446 (tppp) cc_final: 0.7959 (ttmm) REVERT: E 144 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7455 (mm-40) REVERT: E 145 GLU cc_start: 0.7975 (tp30) cc_final: 0.7158 (tp30) REVERT: E 196 MET cc_start: 0.8219 (tpp) cc_final: 0.7910 (tmm) REVERT: E 211 MET cc_start: 0.8304 (tpp) cc_final: 0.7808 (tpt) REVERT: E 335 GLU cc_start: 0.8249 (tp30) cc_final: 0.7801 (tm-30) REVERT: F 82 GLN cc_start: 0.8903 (mt0) cc_final: 0.8546 (mt0) REVERT: F 94 TYR cc_start: 0.8618 (m-80) cc_final: 0.7820 (m-80) REVERT: F 117 ASP cc_start: 0.7725 (t0) cc_final: 0.7216 (t0) REVERT: F 125 LYS cc_start: 0.8505 (tppp) cc_final: 0.8043 (tppp) REVERT: F 159 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7194 (tm-30) REVERT: F 211 MET cc_start: 0.8258 (tpp) cc_final: 0.7890 (tpp) REVERT: F 252 SER cc_start: 0.8474 (p) cc_final: 0.8164 (p) REVERT: F 261 LEU cc_start: 0.7924 (mm) cc_final: 0.7667 (mm) REVERT: F 291 MET cc_start: 0.8501 (tpt) cc_final: 0.8252 (tpp) REVERT: F 300 GLU cc_start: 0.8651 (tp30) cc_final: 0.8236 (mm-30) outliers start: 6 outliers final: 2 residues processed: 437 average time/residue: 0.2853 time to fit residues: 179.4195 Evaluate side-chains 360 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 358 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain D residue 298 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 203 ASN A 298 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN B 188 GLN B 203 ASN B 286 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN C 203 ASN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN D 144 GLN D 203 ASN D 298 GLN E 188 GLN E 203 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN F 203 ASN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099857 restraints weight = 25103.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.103482 restraints weight = 13182.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105833 restraints weight = 8030.278| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15414 Z= 0.117 Angle : 0.520 9.907 20778 Z= 0.260 Chirality : 0.037 0.142 2208 Planarity : 0.004 0.042 2826 Dihedral : 3.774 15.926 2100 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.26 % Allowed : 14.41 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 1884 helix: 0.80 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -1.85 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.002 0.001 HIS A 182 PHE 0.009 0.001 PHE E 185 TYR 0.010 0.001 TYR C 114 ARG 0.007 0.000 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 1021) hydrogen bonds : angle 3.40685 ( 3045) covalent geometry : bond 0.00250 (15414) covalent geometry : angle 0.51988 (20778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 341 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8170 (m-80) cc_final: 0.7746 (m-80) REVERT: A 125 LYS cc_start: 0.8539 (tppp) cc_final: 0.8107 (tppp) REVERT: A 135 MET cc_start: 0.7767 (tmm) cc_final: 0.7314 (tmm) REVERT: A 159 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7220 (tm-30) REVERT: A 211 MET cc_start: 0.8413 (tpp) cc_final: 0.8173 (tpp) REVERT: A 335 GLU cc_start: 0.8311 (tp30) cc_final: 0.7731 (tm-30) REVERT: B 82 GLN cc_start: 0.8732 (mt0) cc_final: 0.8438 (mt0) REVERT: B 85 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 101 MET cc_start: 0.7872 (mmp) cc_final: 0.7240 (mmm) REVERT: B 125 LYS cc_start: 0.8425 (tppp) cc_final: 0.7979 (ttpt) REVERT: B 156 ILE cc_start: 0.8160 (mm) cc_final: 0.7819 (tp) REVERT: B 196 MET cc_start: 0.8121 (tpp) cc_final: 0.7920 (tmm) REVERT: B 211 MET cc_start: 0.8315 (tpp) cc_final: 0.8108 (tpt) REVERT: B 286 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7817 (mm-40) REVERT: B 321 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7320 (p0) REVERT: B 335 GLU cc_start: 0.8118 (tp30) cc_final: 0.7722 (tm-30) REVERT: B 344 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8364 (mm-40) REVERT: B 345 MET cc_start: 0.8600 (tpt) cc_final: 0.8383 (tpt) REVERT: C 85 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 125 LYS cc_start: 0.8457 (tppp) cc_final: 0.7975 (ttpt) REVERT: C 135 MET cc_start: 0.7914 (tmm) cc_final: 0.7595 (tmm) REVERT: C 152 GLU cc_start: 0.7900 (tp30) cc_final: 0.7409 (tp30) REVERT: C 159 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7049 (tm-30) REVERT: C 211 MET cc_start: 0.8277 (tpp) cc_final: 0.7803 (tpp) REVERT: C 223 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7577 (mppt) REVERT: C 261 LEU cc_start: 0.7875 (mm) cc_final: 0.7619 (mm) REVERT: C 300 GLU cc_start: 0.8592 (tp30) cc_final: 0.8148 (mm-30) REVERT: C 344 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8322 (mm110) REVERT: C 345 MET cc_start: 0.8893 (tpt) cc_final: 0.8074 (tpt) REVERT: D 85 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7783 (tm-30) REVERT: D 101 MET cc_start: 0.8022 (mmp) cc_final: 0.7383 (mmm) REVERT: D 120 VAL cc_start: 0.8022 (t) cc_final: 0.7780 (p) REVERT: D 125 LYS cc_start: 0.8541 (tppp) cc_final: 0.8102 (tppp) REVERT: D 135 MET cc_start: 0.7735 (tmm) cc_final: 0.7298 (tmm) REVERT: D 211 MET cc_start: 0.8469 (tpp) cc_final: 0.8224 (tpp) REVERT: D 335 GLU cc_start: 0.8262 (tp30) cc_final: 0.7666 (tm-30) REVERT: E 82 GLN cc_start: 0.8773 (mt0) cc_final: 0.8479 (mt0) REVERT: E 85 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7845 (tm-30) REVERT: E 101 MET cc_start: 0.7842 (mmp) cc_final: 0.7146 (mmm) REVERT: E 125 LYS cc_start: 0.8435 (tppp) cc_final: 0.7966 (ttpt) REVERT: E 145 GLU cc_start: 0.7908 (tp30) cc_final: 0.6996 (tp30) REVERT: E 196 MET cc_start: 0.8101 (tpp) cc_final: 0.7865 (tmm) REVERT: E 201 GLU cc_start: 0.8604 (tp30) cc_final: 0.8178 (tp30) REVERT: E 211 MET cc_start: 0.8288 (tpp) cc_final: 0.8070 (tpt) REVERT: E 321 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7310 (p0) REVERT: E 335 GLU cc_start: 0.8175 (tp30) cc_final: 0.7780 (tm-30) REVERT: E 344 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8369 (mm-40) REVERT: E 345 MET cc_start: 0.8622 (tpt) cc_final: 0.8357 (tpt) REVERT: F 85 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7745 (tm-30) REVERT: F 117 ASP cc_start: 0.7582 (t0) cc_final: 0.7298 (t0) REVERT: F 125 LYS cc_start: 0.8453 (tppp) cc_final: 0.7989 (ttpt) REVERT: F 135 MET cc_start: 0.7889 (tmm) cc_final: 0.7586 (tmm) REVERT: F 152 GLU cc_start: 0.7736 (tp30) cc_final: 0.7389 (tp30) REVERT: F 159 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7025 (tm-30) REVERT: F 206 LEU cc_start: 0.7888 (mp) cc_final: 0.7581 (mp) REVERT: F 211 MET cc_start: 0.8378 (tpp) cc_final: 0.7978 (ttp) REVERT: F 223 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7574 (mppt) REVERT: F 261 LEU cc_start: 0.7870 (mm) cc_final: 0.7596 (mm) REVERT: F 300 GLU cc_start: 0.8612 (tp30) cc_final: 0.8153 (mm-30) outliers start: 52 outliers final: 35 residues processed: 372 average time/residue: 0.2374 time to fit residues: 133.5553 Evaluate side-chains 357 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 164 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.0020 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100911 restraints weight = 25194.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104469 restraints weight = 13240.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106853 restraints weight = 8130.037| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15414 Z= 0.111 Angle : 0.473 7.718 20778 Z= 0.239 Chirality : 0.035 0.136 2208 Planarity : 0.003 0.038 2826 Dihedral : 3.503 15.389 2094 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.95 % Allowed : 18.73 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1884 helix: 1.22 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.002 0.001 HIS D 182 PHE 0.009 0.001 PHE D 185 TYR 0.011 0.001 TYR A 114 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 1021) hydrogen bonds : angle 3.13581 ( 3045) covalent geometry : bond 0.00239 (15414) covalent geometry : angle 0.47271 (20778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 339 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 135 MET cc_start: 0.7781 (tmm) cc_final: 0.7395 (tmm) REVERT: A 152 GLU cc_start: 0.7923 (tp30) cc_final: 0.7488 (tp30) REVERT: A 211 MET cc_start: 0.8399 (tpp) cc_final: 0.8011 (tpp) REVERT: A 318 ASN cc_start: 0.9036 (t0) cc_final: 0.7782 (t0) REVERT: A 335 GLU cc_start: 0.8359 (tp30) cc_final: 0.7654 (tm-30) REVERT: B 82 GLN cc_start: 0.8740 (mt0) cc_final: 0.8516 (mt0) REVERT: B 125 LYS cc_start: 0.8414 (tppp) cc_final: 0.7954 (ttpt) REVERT: B 196 MET cc_start: 0.8147 (tpp) cc_final: 0.7819 (tmm) REVERT: B 211 MET cc_start: 0.8243 (tpp) cc_final: 0.8004 (tpt) REVERT: B 321 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7267 (p0) REVERT: B 335 GLU cc_start: 0.8168 (tp30) cc_final: 0.7797 (tm-30) REVERT: B 344 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8373 (mm-40) REVERT: B 345 MET cc_start: 0.8697 (tpt) cc_final: 0.8287 (tpp) REVERT: C 85 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 125 LYS cc_start: 0.8459 (tppp) cc_final: 0.7927 (ttpt) REVERT: C 152 GLU cc_start: 0.7888 (tp30) cc_final: 0.7351 (tp30) REVERT: C 159 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7020 (tm-30) REVERT: C 223 LYS cc_start: 0.8000 (mmmm) cc_final: 0.7581 (tppt) REVERT: C 261 LEU cc_start: 0.7967 (mm) cc_final: 0.7697 (mm) REVERT: C 300 GLU cc_start: 0.8523 (tp30) cc_final: 0.7858 (tm-30) REVERT: C 307 GLU cc_start: 0.7135 (tt0) cc_final: 0.6870 (tt0) REVERT: C 335 GLU cc_start: 0.8370 (tp30) cc_final: 0.7837 (tm-30) REVERT: C 344 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8289 (mm110) REVERT: D 85 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7759 (tm-30) REVERT: D 94 TYR cc_start: 0.8237 (m-80) cc_final: 0.7897 (m-80) REVERT: D 101 MET cc_start: 0.7997 (mmp) cc_final: 0.7316 (mmm) REVERT: D 120 VAL cc_start: 0.7886 (t) cc_final: 0.7653 (p) REVERT: D 135 MET cc_start: 0.7769 (tmm) cc_final: 0.7414 (tmm) REVERT: D 152 GLU cc_start: 0.7904 (tp30) cc_final: 0.7435 (tp30) REVERT: D 211 MET cc_start: 0.8416 (tpp) cc_final: 0.7854 (tpt) REVERT: D 300 GLU cc_start: 0.8558 (tp30) cc_final: 0.8035 (mm-30) REVERT: D 318 ASN cc_start: 0.9041 (t0) cc_final: 0.8562 (t0) REVERT: D 335 GLU cc_start: 0.8292 (tp30) cc_final: 0.7611 (tm-30) REVERT: E 82 GLN cc_start: 0.8755 (mt0) cc_final: 0.8520 (mt0) REVERT: E 125 LYS cc_start: 0.8432 (tppp) cc_final: 0.7956 (ttpt) REVERT: E 201 GLU cc_start: 0.8569 (tp30) cc_final: 0.8118 (tp30) REVERT: E 211 MET cc_start: 0.8215 (tpp) cc_final: 0.7897 (tpt) REVERT: E 214 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7806 (mtp85) REVERT: E 321 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7279 (p0) REVERT: E 335 GLU cc_start: 0.8280 (tp30) cc_final: 0.7700 (tm-30) REVERT: E 344 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8388 (mm-40) REVERT: E 345 MET cc_start: 0.8696 (tpt) cc_final: 0.8002 (tpt) REVERT: F 85 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7607 (tm-30) REVERT: F 125 LYS cc_start: 0.8441 (tppp) cc_final: 0.7946 (ttpt) REVERT: F 152 GLU cc_start: 0.7769 (tp30) cc_final: 0.7344 (tp30) REVERT: F 159 GLU cc_start: 0.7455 (tm-30) cc_final: 0.6969 (tm-30) REVERT: F 211 MET cc_start: 0.8354 (tpp) cc_final: 0.7894 (ttp) REVERT: F 223 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7598 (mppt) REVERT: F 300 GLU cc_start: 0.8570 (tp30) cc_final: 0.8119 (mm-30) REVERT: F 344 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8225 (mm110) outliers start: 63 outliers final: 49 residues processed: 371 average time/residue: 0.2436 time to fit residues: 137.7605 Evaluate side-chains 378 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 327 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 125 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 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 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100865 restraints weight = 25286.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.104495 restraints weight = 13339.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106790 restraints weight = 8171.155| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15414 Z= 0.114 Angle : 0.459 6.112 20778 Z= 0.233 Chirality : 0.035 0.134 2208 Planarity : 0.003 0.036 2826 Dihedral : 3.411 15.085 2094 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.26 % Allowed : 20.36 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1884 helix: 1.54 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -1.25 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 366 HIS 0.002 0.001 HIS D 182 PHE 0.009 0.001 PHE E 185 TYR 0.012 0.001 TYR B 94 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 1021) hydrogen bonds : angle 3.00611 ( 3045) covalent geometry : bond 0.00250 (15414) covalent geometry : angle 0.45905 (20778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 94 TYR cc_start: 0.8118 (m-80) cc_final: 0.7708 (m-80) REVERT: A 125 LYS cc_start: 0.8598 (tppp) cc_final: 0.8148 (tppp) REVERT: A 135 MET cc_start: 0.7822 (tmm) cc_final: 0.7452 (tmm) REVERT: A 152 GLU cc_start: 0.7898 (tp30) cc_final: 0.7401 (tp30) REVERT: A 211 MET cc_start: 0.8377 (tpp) cc_final: 0.8123 (tpp) REVERT: A 262 MET cc_start: 0.8448 (tpp) cc_final: 0.7377 (tpp) REVERT: A 307 GLU cc_start: 0.7142 (tt0) cc_final: 0.6895 (tt0) REVERT: A 318 ASN cc_start: 0.9062 (t0) cc_final: 0.8665 (t0) REVERT: A 335 GLU cc_start: 0.8340 (tp30) cc_final: 0.7683 (tm-30) REVERT: B 82 GLN cc_start: 0.8741 (mt0) cc_final: 0.8443 (mt0) REVERT: B 85 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 101 MET cc_start: 0.7927 (mmp) cc_final: 0.7169 (mmm) REVERT: B 117 ASP cc_start: 0.7551 (t0) cc_final: 0.7152 (t0) REVERT: B 125 LYS cc_start: 0.8437 (tppp) cc_final: 0.7976 (ttpt) REVERT: B 211 MET cc_start: 0.8186 (tpp) cc_final: 0.7932 (tpt) REVERT: B 318 ASN cc_start: 0.9167 (t0) cc_final: 0.8284 (t0) REVERT: B 335 GLU cc_start: 0.8330 (tp30) cc_final: 0.7745 (tm-30) REVERT: B 345 MET cc_start: 0.8776 (tpt) cc_final: 0.8287 (tpt) REVERT: C 85 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7589 (tm-30) REVERT: C 117 ASP cc_start: 0.7406 (t0) cc_final: 0.6662 (t0) REVERT: C 125 LYS cc_start: 0.8454 (tppp) cc_final: 0.8026 (tppp) REVERT: C 135 MET cc_start: 0.8017 (tmm) cc_final: 0.7810 (tmm) REVERT: C 223 LYS cc_start: 0.8014 (mmmm) cc_final: 0.7584 (mppt) REVERT: C 300 GLU cc_start: 0.8509 (tp30) cc_final: 0.7955 (tm-30) REVERT: C 307 GLU cc_start: 0.7189 (tt0) cc_final: 0.6903 (tt0) REVERT: C 318 ASN cc_start: 0.9081 (t0) cc_final: 0.8417 (t0) REVERT: C 344 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8219 (mm-40) REVERT: C 345 MET cc_start: 0.8854 (tpt) cc_final: 0.8002 (tpt) REVERT: D 85 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7855 (tm-30) REVERT: D 120 VAL cc_start: 0.7902 (t) cc_final: 0.7634 (p) REVERT: D 135 MET cc_start: 0.7787 (tmm) cc_final: 0.7436 (tmm) REVERT: D 152 GLU cc_start: 0.7885 (tp30) cc_final: 0.7363 (tp30) REVERT: D 211 MET cc_start: 0.8419 (tpp) cc_final: 0.8071 (tpt) REVERT: D 307 GLU cc_start: 0.7163 (tt0) cc_final: 0.6908 (tt0) REVERT: D 321 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7224 (p0) REVERT: D 335 GLU cc_start: 0.8288 (tp30) cc_final: 0.7638 (tm-30) REVERT: E 82 GLN cc_start: 0.8734 (mt0) cc_final: 0.8479 (mt0) REVERT: E 101 MET cc_start: 0.7795 (mmp) cc_final: 0.7108 (mmm) REVERT: E 125 LYS cc_start: 0.8448 (tppp) cc_final: 0.7960 (ttpt) REVERT: E 201 GLU cc_start: 0.8542 (tp30) cc_final: 0.8076 (tp30) REVERT: E 214 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7729 (ttm-80) REVERT: E 335 GLU cc_start: 0.8302 (tp30) cc_final: 0.7711 (tm-30) REVERT: E 345 MET cc_start: 0.8767 (tpt) cc_final: 0.8228 (tpt) REVERT: F 85 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7633 (tm-30) REVERT: F 125 LYS cc_start: 0.8450 (tppp) cc_final: 0.7946 (ttpt) REVERT: F 152 GLU cc_start: 0.7740 (tp30) cc_final: 0.7297 (tp30) REVERT: F 223 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7807 (tppt) REVERT: F 261 LEU cc_start: 0.7935 (mm) cc_final: 0.7666 (mm) REVERT: F 300 GLU cc_start: 0.8513 (tp30) cc_final: 0.8083 (mm-30) REVERT: F 335 GLU cc_start: 0.8406 (tp30) cc_final: 0.7957 (tm-30) REVERT: F 344 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8234 (mm-40) REVERT: F 345 MET cc_start: 0.8853 (tpt) cc_final: 0.7974 (tpt) outliers start: 52 outliers final: 42 residues processed: 347 average time/residue: 0.2482 time to fit residues: 130.9495 Evaluate side-chains 363 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 77 optimal weight: 0.0050 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.097260 restraints weight = 25557.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100833 restraints weight = 13624.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.103167 restraints weight = 8410.558| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15414 Z= 0.167 Angle : 0.482 5.746 20778 Z= 0.250 Chirality : 0.037 0.128 2208 Planarity : 0.003 0.036 2826 Dihedral : 3.534 15.527 2094 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.76 % Allowed : 20.36 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.20), residues: 1884 helix: 1.62 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.10 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 366 HIS 0.003 0.001 HIS D 182 PHE 0.011 0.001 PHE B 185 TYR 0.012 0.001 TYR F 114 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 1021) hydrogen bonds : angle 3.07289 ( 3045) covalent geometry : bond 0.00386 (15414) covalent geometry : angle 0.48229 (20778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 334 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 94 TYR cc_start: 0.8268 (m-80) cc_final: 0.7857 (m-80) REVERT: A 135 MET cc_start: 0.7869 (tmm) cc_final: 0.7454 (tmm) REVERT: A 152 GLU cc_start: 0.7977 (tp30) cc_final: 0.7525 (tp30) REVERT: A 211 MET cc_start: 0.8422 (tpp) cc_final: 0.8088 (tpp) REVERT: A 298 GLN cc_start: 0.8465 (mt0) cc_final: 0.8219 (mt0) REVERT: A 318 ASN cc_start: 0.9030 (t0) cc_final: 0.7902 (t0) REVERT: A 321 ASP cc_start: 0.7639 (p0) cc_final: 0.7396 (p0) REVERT: A 335 GLU cc_start: 0.8416 (tp30) cc_final: 0.7751 (tm-30) REVERT: B 82 GLN cc_start: 0.8794 (mt0) cc_final: 0.8474 (mt0) REVERT: B 85 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7895 (tm-30) REVERT: B 101 MET cc_start: 0.7996 (mmp) cc_final: 0.7718 (mmp) REVERT: B 117 ASP cc_start: 0.7597 (t0) cc_final: 0.6535 (t0) REVERT: B 125 LYS cc_start: 0.8449 (tppp) cc_final: 0.8043 (ttpt) REVERT: B 211 MET cc_start: 0.8244 (tpp) cc_final: 0.7952 (tpt) REVERT: B 286 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7842 (mm-40) REVERT: B 318 ASN cc_start: 0.9136 (t0) cc_final: 0.8060 (t0) REVERT: B 335 GLU cc_start: 0.8369 (tp30) cc_final: 0.7787 (tm-30) REVERT: B 345 MET cc_start: 0.8753 (tpt) cc_final: 0.8238 (tpt) REVERT: C 85 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7671 (tm-30) REVERT: C 117 ASP cc_start: 0.7506 (t0) cc_final: 0.7018 (t0) REVERT: C 125 LYS cc_start: 0.8440 (tppp) cc_final: 0.8014 (tppp) REVERT: C 152 GLU cc_start: 0.7879 (tp30) cc_final: 0.7370 (tp30) REVERT: C 223 LYS cc_start: 0.8043 (mmmm) cc_final: 0.7821 (tppt) REVERT: C 300 GLU cc_start: 0.8516 (tp30) cc_final: 0.7858 (tm-30) REVERT: C 307 GLU cc_start: 0.7384 (tt0) cc_final: 0.7083 (tt0) REVERT: C 318 ASN cc_start: 0.9076 (t0) cc_final: 0.8364 (t0) REVERT: C 344 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8261 (mm-40) REVERT: C 345 MET cc_start: 0.8882 (tpt) cc_final: 0.8116 (tpt) REVERT: D 85 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 94 TYR cc_start: 0.8182 (m-80) cc_final: 0.7894 (m-80) REVERT: D 120 VAL cc_start: 0.7967 (t) cc_final: 0.7612 (p) REVERT: D 135 MET cc_start: 0.7848 (tmm) cc_final: 0.7480 (tmm) REVERT: D 152 GLU cc_start: 0.7933 (tp30) cc_final: 0.7445 (tp30) REVERT: D 211 MET cc_start: 0.8404 (tpp) cc_final: 0.8003 (tpt) REVERT: D 318 ASN cc_start: 0.9043 (t0) cc_final: 0.7888 (t0) REVERT: D 321 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7279 (p0) REVERT: D 335 GLU cc_start: 0.8336 (tp30) cc_final: 0.7712 (tm-30) REVERT: E 82 GLN cc_start: 0.8798 (mt0) cc_final: 0.8463 (mt0) REVERT: E 85 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7893 (tm-30) REVERT: E 101 MET cc_start: 0.7922 (mmp) cc_final: 0.7289 (mmm) REVERT: E 125 LYS cc_start: 0.8466 (tppp) cc_final: 0.7987 (ttpt) REVERT: E 145 GLU cc_start: 0.7864 (tp30) cc_final: 0.7063 (tp30) REVERT: E 160 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7389 (t0) REVERT: E 201 GLU cc_start: 0.8491 (tp30) cc_final: 0.7999 (tp30) REVERT: E 214 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7746 (mtp85) REVERT: E 318 ASN cc_start: 0.9143 (t0) cc_final: 0.8059 (t0) REVERT: E 335 GLU cc_start: 0.8368 (tp30) cc_final: 0.7817 (tm-30) REVERT: F 85 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7635 (tm-30) REVERT: F 125 LYS cc_start: 0.8427 (tppp) cc_final: 0.7936 (tppp) REVERT: F 223 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7842 (tppt) REVERT: F 275 THR cc_start: 0.8394 (t) cc_final: 0.7979 (m) REVERT: F 300 GLU cc_start: 0.8534 (tp30) cc_final: 0.7852 (tm-30) REVERT: F 318 ASN cc_start: 0.9081 (t0) cc_final: 0.8364 (t0) REVERT: F 345 MET cc_start: 0.8890 (tpt) cc_final: 0.8036 (tpt) outliers start: 76 outliers final: 60 residues processed: 371 average time/residue: 0.2334 time to fit residues: 131.3510 Evaluate side-chains 394 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 332 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1257 > 50: distance: 14 - 18: 24.935 distance: 18 - 19: 16.279 distance: 19 - 20: 7.393 distance: 19 - 22: 19.720 distance: 20 - 21: 28.593 distance: 20 - 26: 15.007 distance: 22 - 23: 10.318 distance: 23 - 24: 23.058 distance: 23 - 25: 16.079 distance: 26 - 27: 13.248 distance: 27 - 28: 26.807 distance: 27 - 30: 29.391 distance: 28 - 29: 22.414 distance: 28 - 33: 34.377 distance: 30 - 31: 14.117 distance: 30 - 32: 23.246 distance: 33 - 34: 11.573 distance: 33 - 39: 18.708 distance: 34 - 35: 10.744 distance: 34 - 37: 17.615 distance: 35 - 36: 26.309 distance: 35 - 40: 29.618 distance: 37 - 38: 9.784 distance: 38 - 39: 12.684 distance: 40 - 41: 10.310 distance: 41 - 42: 25.190 distance: 41 - 44: 12.157 distance: 42 - 43: 8.758 distance: 42 - 49: 5.869 distance: 43 - 80: 12.793 distance: 44 - 45: 17.095 distance: 45 - 46: 25.287 distance: 46 - 47: 24.676 distance: 46 - 48: 22.548 distance: 49 - 50: 22.868 distance: 50 - 51: 12.115 distance: 50 - 53: 6.372 distance: 51 - 52: 4.423 distance: 51 - 58: 11.329 distance: 52 - 89: 22.208 distance: 53 - 54: 17.091 distance: 54 - 55: 5.420 distance: 55 - 56: 6.146 distance: 55 - 57: 11.595 distance: 58 - 59: 10.740 distance: 59 - 60: 5.561 distance: 59 - 62: 11.959 distance: 60 - 61: 6.643 distance: 60 - 69: 3.977 distance: 61 - 94: 15.592 distance: 62 - 63: 17.681 distance: 63 - 64: 14.077 distance: 64 - 65: 6.244 distance: 65 - 66: 7.619 distance: 66 - 67: 5.140 distance: 66 - 68: 6.285 distance: 70 - 71: 9.232 distance: 70 - 73: 12.001 distance: 71 - 72: 19.492 distance: 71 - 80: 10.732 distance: 73 - 74: 20.401 distance: 74 - 75: 4.819 distance: 75 - 76: 6.121 distance: 76 - 77: 11.577 distance: 77 - 78: 3.856 distance: 77 - 79: 8.129 distance: 80 - 81: 7.710 distance: 81 - 82: 12.676 distance: 81 - 84: 12.661 distance: 82 - 83: 4.634 distance: 82 - 89: 25.494 distance: 84 - 85: 29.159 distance: 85 - 86: 40.974 distance: 86 - 87: 15.926 distance: 86 - 88: 8.235 distance: 89 - 90: 19.606 distance: 90 - 91: 14.760 distance: 90 - 93: 21.723 distance: 91 - 92: 7.038 distance: 91 - 94: 12.034 distance: 94 - 95: 18.479 distance: 95 - 96: 18.224 distance: 95 - 98: 38.482 distance: 96 - 97: 23.796 distance: 96 - 102: 23.191 distance: 98 - 99: 22.006 distance: 99 - 100: 25.764 distance: 99 - 101: 19.221