Starting phenix.real_space_refine on Fri Sep 27 04:33:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/09_2024/6ysz_10911.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/09_2024/6ysz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/09_2024/6ysz_10911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/09_2024/6ysz_10911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/09_2024/6ysz_10911.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/09_2024/6ysz_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-5461/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: 6.00, per 1000 atoms: 0.39 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: 3.87 Conformation dependent library (CDL) restraints added in 1.9 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: 1.68 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: 4.81 Time building geometry restraints manager: 4.45 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 0.890 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 31.800 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- 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= 0.273 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 433 time to evaluate : 1.699 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: 0.2854 time to fit residues: 179.2816 Evaluate side-chains 360 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 358 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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= 0.161 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 *********************** 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 fitting. rotamer outliers: 52 poor density : 341 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8200 (m-80) cc_final: 0.7738 (m-80) REVERT: A 125 LYS cc_start: 0.8550 (tppp) cc_final: 0.8117 (tppp) REVERT: A 135 MET cc_start: 0.7741 (tmm) cc_final: 0.7281 (tmm) REVERT: A 159 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7259 (tm-30) REVERT: A 211 MET cc_start: 0.8431 (tpp) cc_final: 0.8173 (tpp) REVERT: A 335 GLU cc_start: 0.8359 (tp30) cc_final: 0.7758 (tm-30) REVERT: A 344 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8425 (mm-40) REVERT: B 82 GLN cc_start: 0.8724 (mt0) cc_final: 0.8426 (mt0) REVERT: B 85 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 101 MET cc_start: 0.7881 (mmp) cc_final: 0.7254 (mmm) REVERT: B 125 LYS cc_start: 0.8443 (tppp) cc_final: 0.7986 (ttpt) REVERT: B 156 ILE cc_start: 0.8133 (mm) cc_final: 0.7774 (tp) REVERT: B 196 MET cc_start: 0.8092 (tpp) cc_final: 0.7861 (tmm) REVERT: B 211 MET cc_start: 0.8317 (tpp) cc_final: 0.8083 (tpt) REVERT: B 286 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7846 (mm-40) REVERT: B 321 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7276 (p0) REVERT: B 335 GLU cc_start: 0.8178 (tp30) cc_final: 0.7758 (tm-30) REVERT: B 344 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8343 (mm-40) REVERT: B 345 MET cc_start: 0.8638 (tpt) cc_final: 0.8408 (tpt) REVERT: C 85 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7685 (tm-30) REVERT: C 125 LYS cc_start: 0.8485 (tppp) cc_final: 0.7956 (ttpt) REVERT: C 135 MET cc_start: 0.7910 (tmm) cc_final: 0.7592 (tmm) REVERT: C 152 GLU cc_start: 0.7925 (tp30) cc_final: 0.7427 (tp30) REVERT: C 159 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 211 MET cc_start: 0.8344 (tpp) cc_final: 0.7818 (tpp) REVERT: C 223 LYS cc_start: 0.7933 (mmmm) cc_final: 0.7473 (mppt) REVERT: C 261 LEU cc_start: 0.7827 (mm) cc_final: 0.7573 (mm) REVERT: C 300 GLU cc_start: 0.8622 (tp30) cc_final: 0.8165 (mm-30) REVERT: C 344 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8311 (mm110) REVERT: C 345 MET cc_start: 0.8929 (tpt) cc_final: 0.8082 (tpt) REVERT: D 85 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7762 (tm-30) REVERT: D 101 MET cc_start: 0.8006 (mmp) cc_final: 0.7379 (mmm) REVERT: D 120 VAL cc_start: 0.7867 (t) cc_final: 0.7629 (p) REVERT: D 125 LYS cc_start: 0.8545 (tppp) cc_final: 0.8107 (tppp) REVERT: D 135 MET cc_start: 0.7714 (tmm) cc_final: 0.7267 (tmm) REVERT: D 196 MET cc_start: 0.8032 (tpp) cc_final: 0.7819 (tmm) REVERT: D 211 MET cc_start: 0.8482 (tpp) cc_final: 0.8219 (tpp) REVERT: D 335 GLU cc_start: 0.8303 (tp30) cc_final: 0.7693 (tm-30) REVERT: E 82 GLN cc_start: 0.8769 (mt0) cc_final: 0.8473 (mt0) REVERT: E 85 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7818 (tm-30) REVERT: E 101 MET cc_start: 0.7848 (mmp) cc_final: 0.7158 (mmm) REVERT: E 125 LYS cc_start: 0.8446 (tppp) cc_final: 0.7969 (ttpt) REVERT: E 145 GLU cc_start: 0.7919 (tp30) cc_final: 0.6992 (tp30) REVERT: E 196 MET cc_start: 0.8070 (tpp) cc_final: 0.7807 (tmm) REVERT: E 201 GLU cc_start: 0.8615 (tp30) cc_final: 0.8187 (tp30) REVERT: E 211 MET cc_start: 0.8304 (tpp) cc_final: 0.8058 (tpt) REVERT: E 321 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7283 (p0) REVERT: E 335 GLU cc_start: 0.8233 (tp30) cc_final: 0.7815 (tm-30) REVERT: E 344 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8351 (mm-40) REVERT: E 345 MET cc_start: 0.8657 (tpt) cc_final: 0.8384 (tpt) REVERT: F 85 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7703 (tm-30) REVERT: F 117 ASP cc_start: 0.7556 (t0) cc_final: 0.7283 (t0) REVERT: F 125 LYS cc_start: 0.8476 (tppp) cc_final: 0.7973 (ttpt) REVERT: F 135 MET cc_start: 0.7886 (tmm) cc_final: 0.7584 (tmm) REVERT: F 152 GLU cc_start: 0.7757 (tp30) cc_final: 0.7404 (tp30) REVERT: F 159 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7068 (tm-30) REVERT: F 206 LEU cc_start: 0.7833 (mp) cc_final: 0.7515 (mp) REVERT: F 211 MET cc_start: 0.8426 (tpp) cc_final: 0.8057 (ttp) REVERT: F 223 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7457 (mppt) REVERT: F 261 LEU cc_start: 0.7827 (mm) cc_final: 0.7556 (mm) REVERT: F 300 GLU cc_start: 0.8643 (tp30) cc_final: 0.8170 (mm-30) outliers start: 52 outliers final: 35 residues processed: 372 average time/residue: 0.2579 time to fit residues: 145.4073 Evaluate side-chains 356 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 319 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 93 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 169 optimal weight: 0.2980 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15414 Z= 0.174 Angle : 0.479 7.723 20778 Z= 0.243 Chirality : 0.036 0.135 2208 Planarity : 0.003 0.038 2826 Dihedral : 3.554 15.654 2094 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.01 % Allowed : 18.92 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.20), residues: 1884 helix: 1.28 (0.14), residues: 1446 sheet: None (None), residues: 0 loop : -1.52 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 B 278 ARG 0.005 0.000 ARG B 214 *********************** 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 399 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 335 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 125 LYS cc_start: 0.8551 (tppp) cc_final: 0.8124 (tppp) REVERT: A 135 MET cc_start: 0.7778 (tmm) cc_final: 0.7383 (tmm) REVERT: A 211 MET cc_start: 0.8442 (tpp) cc_final: 0.8053 (tpp) REVERT: A 318 ASN cc_start: 0.9012 (t0) cc_final: 0.7753 (t0) REVERT: A 321 ASP cc_start: 0.7568 (p0) cc_final: 0.7360 (p0) REVERT: A 335 GLU cc_start: 0.8403 (tp30) cc_final: 0.7692 (tm-30) REVERT: B 82 GLN cc_start: 0.8740 (mt0) cc_final: 0.8514 (mt0) REVERT: B 125 LYS cc_start: 0.8429 (tppp) cc_final: 0.7950 (ttpt) REVERT: B 156 ILE cc_start: 0.8231 (mm) cc_final: 0.7798 (tp) REVERT: B 196 MET cc_start: 0.8113 (tpp) cc_final: 0.7780 (tmm) REVERT: B 211 MET cc_start: 0.8262 (tpp) cc_final: 0.7990 (tpt) REVERT: B 321 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7238 (p0) REVERT: B 335 GLU cc_start: 0.8226 (tp30) cc_final: 0.7839 (tm-30) REVERT: B 344 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8369 (mm-40) REVERT: B 345 MET cc_start: 0.8717 (tpt) cc_final: 0.8305 (tpp) REVERT: C 85 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7606 (tm-30) REVERT: C 125 LYS cc_start: 0.8471 (tppp) cc_final: 0.7926 (ttpt) REVERT: C 159 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7093 (tm-30) REVERT: C 223 LYS cc_start: 0.7962 (mmmm) cc_final: 0.7514 (tppt) REVERT: C 261 LEU cc_start: 0.7935 (mm) cc_final: 0.7692 (mm) REVERT: C 300 GLU cc_start: 0.8556 (tp30) cc_final: 0.7870 (tm-30) REVERT: C 307 GLU cc_start: 0.7263 (tt0) cc_final: 0.6962 (tt0) REVERT: C 344 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8284 (mm110) REVERT: C 345 MET cc_start: 0.8961 (tpt) cc_final: 0.7945 (tpt) REVERT: D 85 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7798 (tm-30) REVERT: D 94 TYR cc_start: 0.8310 (m-80) cc_final: 0.7903 (m-80) REVERT: D 101 MET cc_start: 0.8002 (mmp) cc_final: 0.7342 (mmm) REVERT: D 120 VAL cc_start: 0.7815 (t) cc_final: 0.7581 (p) REVERT: D 135 MET cc_start: 0.7737 (tmm) cc_final: 0.7349 (tmm) REVERT: D 152 GLU cc_start: 0.7920 (tp30) cc_final: 0.7476 (tp30) REVERT: D 196 MET cc_start: 0.8043 (tpp) cc_final: 0.7670 (tmm) REVERT: D 211 MET cc_start: 0.8461 (tpp) cc_final: 0.7846 (tpt) REVERT: D 335 GLU cc_start: 0.8340 (tp30) cc_final: 0.7656 (tm-30) REVERT: E 82 GLN cc_start: 0.8761 (mt0) cc_final: 0.8526 (mt0) REVERT: E 125 LYS cc_start: 0.8441 (tppp) cc_final: 0.7939 (ttpt) REVERT: E 196 MET cc_start: 0.8078 (tpp) cc_final: 0.7693 (tmm) REVERT: E 201 GLU cc_start: 0.8585 (tp30) cc_final: 0.8127 (tp30) REVERT: E 211 MET cc_start: 0.8244 (tpp) cc_final: 0.7895 (tpt) REVERT: E 214 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7822 (mtp85) REVERT: E 300 GLU cc_start: 0.8491 (tp30) cc_final: 0.8277 (mm-30) REVERT: E 321 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7256 (p0) REVERT: E 335 GLU cc_start: 0.8352 (tp30) cc_final: 0.7753 (tm-30) REVERT: E 344 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8366 (mm-40) REVERT: E 345 MET cc_start: 0.8717 (tpt) cc_final: 0.8261 (tpt) REVERT: F 85 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7582 (tm-30) REVERT: F 125 LYS cc_start: 0.8464 (tppp) cc_final: 0.7947 (ttpt) REVERT: F 152 GLU cc_start: 0.7796 (tp30) cc_final: 0.7378 (tp30) REVERT: F 159 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7038 (tm-30) REVERT: F 206 LEU cc_start: 0.7805 (mp) cc_final: 0.7493 (mp) REVERT: F 211 MET cc_start: 0.8433 (tpp) cc_final: 0.8132 (tpp) REVERT: F 223 LYS cc_start: 0.7949 (mmmm) cc_final: 0.7489 (mppt) REVERT: F 300 GLU cc_start: 0.8582 (tp30) cc_final: 0.7880 (tm-30) REVERT: F 307 GLU cc_start: 0.7268 (tt0) cc_final: 0.6975 (tt0) outliers start: 64 outliers final: 50 residues processed: 366 average time/residue: 0.2363 time to fit residues: 132.0312 Evaluate side-chains 375 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 323 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 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 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 282 ILE 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 0.0070 chunk 179 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2199 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= 0.237 Angle : 0.490 6.164 20778 Z= 0.252 Chirality : 0.037 0.133 2208 Planarity : 0.003 0.038 2826 Dihedral : 3.573 15.831 2094 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.45 % Allowed : 20.11 % Favored : 75.44 % 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: 1.28 (0.20), residues: 1884 helix: 1.46 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.28 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.003 0.001 HIS D 182 PHE 0.010 0.001 PHE B 185 TYR 0.012 0.001 TYR C 114 ARG 0.004 0.000 ARG B 214 *********************** 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 401 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 330 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 94 TYR cc_start: 0.8260 (m-80) cc_final: 0.7845 (m-80) REVERT: A 135 MET cc_start: 0.7820 (tmm) cc_final: 0.7396 (tmm) REVERT: A 211 MET cc_start: 0.8457 (tpp) cc_final: 0.8190 (tpp) REVERT: A 318 ASN cc_start: 0.9034 (t0) cc_final: 0.7880 (t0) REVERT: A 335 GLU cc_start: 0.8427 (tp30) cc_final: 0.7745 (tm-30) REVERT: B 82 GLN cc_start: 0.8779 (mt0) cc_final: 0.8474 (mt0) REVERT: B 85 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 101 MET cc_start: 0.7967 (mmp) cc_final: 0.7217 (mmm) REVERT: B 117 ASP cc_start: 0.7552 (t0) cc_final: 0.6429 (t0) REVERT: B 125 LYS cc_start: 0.8458 (tppp) cc_final: 0.8002 (ttpt) REVERT: B 211 MET cc_start: 0.8267 (tpp) cc_final: 0.7970 (tpt) REVERT: B 286 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7887 (mm-40) REVERT: B 335 GLU cc_start: 0.8401 (tp30) cc_final: 0.7822 (tm-30) REVERT: B 344 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8520 (mm-40) REVERT: C 85 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7606 (tm-30) REVERT: C 117 ASP cc_start: 0.7403 (t0) cc_final: 0.6839 (t0) REVERT: C 125 LYS cc_start: 0.8469 (tppp) cc_final: 0.7935 (ttpt) REVERT: C 159 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7010 (tm-30) REVERT: C 223 LYS cc_start: 0.7997 (mmmm) cc_final: 0.7757 (tppt) REVERT: C 300 GLU cc_start: 0.8568 (tp30) cc_final: 0.7968 (tm-30) REVERT: C 307 GLU cc_start: 0.7431 (tt0) cc_final: 0.7101 (tt0) REVERT: C 344 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8301 (mm110) REVERT: C 345 MET cc_start: 0.8930 (tpt) cc_final: 0.8089 (tpt) REVERT: D 85 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 125 LYS cc_start: 0.8574 (tppp) cc_final: 0.8136 (tppp) REVERT: D 135 MET cc_start: 0.7817 (tmm) cc_final: 0.7396 (tmm) REVERT: D 152 GLU cc_start: 0.7972 (tp30) cc_final: 0.7523 (tp30) REVERT: D 211 MET cc_start: 0.8460 (tpp) cc_final: 0.7792 (tpt) REVERT: D 262 MET cc_start: 0.8399 (tpp) cc_final: 0.7147 (tpp) REVERT: D 321 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7209 (p0) REVERT: D 335 GLU cc_start: 0.8391 (tp30) cc_final: 0.7712 (tm-30) REVERT: E 82 GLN cc_start: 0.8764 (mt0) cc_final: 0.8453 (mt0) REVERT: E 85 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7845 (tm-30) REVERT: E 101 MET cc_start: 0.7879 (mmp) cc_final: 0.7204 (mmm) REVERT: E 125 LYS cc_start: 0.8466 (tppp) cc_final: 0.8002 (ttpt) REVERT: E 201 GLU cc_start: 0.8554 (tp30) cc_final: 0.8094 (tp30) REVERT: E 211 MET cc_start: 0.8241 (tpp) cc_final: 0.7855 (tpt) REVERT: E 214 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7764 (mtp85) REVERT: E 335 GLU cc_start: 0.8380 (tp30) cc_final: 0.7817 (tm-30) REVERT: E 344 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8502 (mm-40) REVERT: F 71 SER cc_start: 0.9019 (t) cc_final: 0.8809 (p) REVERT: F 85 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7595 (tm-30) REVERT: F 125 LYS cc_start: 0.8438 (tppp) cc_final: 0.7973 (tppp) REVERT: F 159 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6994 (tm-30) REVERT: F 211 MET cc_start: 0.8400 (tpp) cc_final: 0.7804 (tpp) REVERT: F 214 ARG cc_start: 0.7654 (mtm180) cc_final: 0.7404 (mtm180) REVERT: F 223 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7775 (tppt) REVERT: F 300 GLU cc_start: 0.8580 (tp30) cc_final: 0.8138 (mm-30) REVERT: F 307 GLU cc_start: 0.7395 (tt0) cc_final: 0.7167 (tt0) REVERT: F 344 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8322 (mm-40) outliers start: 71 outliers final: 53 residues processed: 359 average time/residue: 0.2439 time to fit residues: 132.4152 Evaluate side-chains 378 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 324 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 226 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 170 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 225 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 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 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 352 LEU 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 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 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 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 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 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15414 Z= 0.142 Angle : 0.450 5.913 20778 Z= 0.228 Chirality : 0.035 0.132 2208 Planarity : 0.003 0.035 2826 Dihedral : 3.381 14.672 2094 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.95 % Allowed : 21.62 % Favored : 74.44 % 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: 1.62 (0.20), residues: 1884 helix: 1.62 (0.14), residues: 1494 sheet: None (None), residues: 0 loop : -1.01 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 287 HIS 0.002 0.001 HIS A 182 PHE 0.009 0.001 PHE B 185 TYR 0.012 0.001 TYR F 94 ARG 0.004 0.000 ARG B 64 *********************** 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 386 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 323 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7894 (tm-30) REVERT: A 94 TYR cc_start: 0.8205 (m-80) cc_final: 0.7744 (m-80) REVERT: A 125 LYS cc_start: 0.8566 (tppp) cc_final: 0.8105 (tppp) REVERT: A 135 MET cc_start: 0.7774 (tmm) cc_final: 0.7388 (tmm) REVERT: A 152 GLU cc_start: 0.7897 (tp30) cc_final: 0.7403 (tp30) REVERT: A 211 MET cc_start: 0.8446 (tpp) cc_final: 0.8161 (tpp) REVERT: A 318 ASN cc_start: 0.9013 (t0) cc_final: 0.8668 (t0) REVERT: A 335 GLU cc_start: 0.8434 (tp30) cc_final: 0.7765 (tm-30) REVERT: B 82 GLN cc_start: 0.8705 (mt0) cc_final: 0.8389 (mt0) REVERT: B 85 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 101 MET cc_start: 0.7915 (mmp) cc_final: 0.7667 (mmp) REVERT: B 117 ASP cc_start: 0.7546 (t0) cc_final: 0.6432 (t0) REVERT: B 125 LYS cc_start: 0.8441 (tppp) cc_final: 0.8036 (ttpt) REVERT: B 211 MET cc_start: 0.8197 (tpp) cc_final: 0.7892 (tpt) REVERT: B 318 ASN cc_start: 0.9120 (t0) cc_final: 0.8237 (t0) REVERT: B 335 GLU cc_start: 0.8394 (tp30) cc_final: 0.7786 (tm-30) REVERT: B 345 MET cc_start: 0.8832 (tpt) cc_final: 0.8252 (tpt) REVERT: C 85 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 117 ASP cc_start: 0.7523 (t0) cc_final: 0.6741 (t0) REVERT: C 125 LYS cc_start: 0.8455 (tppp) cc_final: 0.8007 (tppp) REVERT: C 152 GLU cc_start: 0.7843 (tp30) cc_final: 0.7334 (tp30) REVERT: C 223 LYS cc_start: 0.7978 (mmmm) cc_final: 0.7752 (tppt) REVERT: C 291 MET cc_start: 0.8468 (tpp) cc_final: 0.7870 (tpp) REVERT: C 300 GLU cc_start: 0.8521 (tp30) cc_final: 0.7827 (tm-30) REVERT: C 307 GLU cc_start: 0.7225 (tt0) cc_final: 0.6928 (tt0) REVERT: C 318 ASN cc_start: 0.9067 (t0) cc_final: 0.8438 (t0) REVERT: C 344 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8215 (mm110) REVERT: D 85 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7859 (tm-30) REVERT: D 94 TYR cc_start: 0.8128 (m-80) cc_final: 0.7716 (m-80) REVERT: D 101 MET cc_start: 0.7897 (mmp) cc_final: 0.7293 (mmm) REVERT: D 120 VAL cc_start: 0.7756 (t) cc_final: 0.7491 (p) REVERT: D 135 MET cc_start: 0.7746 (tmm) cc_final: 0.7386 (tmm) REVERT: D 152 GLU cc_start: 0.7894 (tp30) cc_final: 0.7394 (tp30) REVERT: D 211 MET cc_start: 0.8454 (tpp) cc_final: 0.8120 (tpp) REVERT: D 318 ASN cc_start: 0.9027 (t0) cc_final: 0.8651 (t0) REVERT: D 335 GLU cc_start: 0.8349 (tp30) cc_final: 0.7693 (tm-30) REVERT: E 82 GLN cc_start: 0.8718 (mt0) cc_final: 0.8394 (mt0) REVERT: E 85 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7840 (tm-30) REVERT: E 125 LYS cc_start: 0.8454 (tppp) cc_final: 0.8022 (ttpt) REVERT: E 145 GLU cc_start: 0.7787 (tp30) cc_final: 0.6943 (tp30) REVERT: E 160 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7427 (t0) REVERT: E 201 GLU cc_start: 0.8509 (tp30) cc_final: 0.8005 (tp30) REVERT: E 214 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7657 (ttm-80) REVERT: E 318 ASN cc_start: 0.9133 (t0) cc_final: 0.8248 (t0) REVERT: E 335 GLU cc_start: 0.8373 (tp30) cc_final: 0.7790 (tm-30) REVERT: E 345 MET cc_start: 0.8866 (tpt) cc_final: 0.8229 (tpt) REVERT: F 85 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7612 (tm-30) REVERT: F 121 MET cc_start: 0.7530 (tpp) cc_final: 0.7291 (tpp) REVERT: F 125 LYS cc_start: 0.8436 (tppp) cc_final: 0.7976 (tppp) REVERT: F 152 GLU cc_start: 0.7884 (tp30) cc_final: 0.7373 (tp30) REVERT: F 211 MET cc_start: 0.8369 (tpp) cc_final: 0.7908 (tpp) REVERT: F 223 LYS cc_start: 0.7963 (mmmm) cc_final: 0.7726 (tppt) REVERT: F 261 LEU cc_start: 0.7850 (mm) cc_final: 0.7583 (mm) REVERT: F 291 MET cc_start: 0.8445 (tpp) cc_final: 0.7893 (tpp) REVERT: F 300 GLU cc_start: 0.8538 (tp30) cc_final: 0.8105 (mm-30) REVERT: F 318 ASN cc_start: 0.9074 (t0) cc_final: 0.8431 (t0) REVERT: F 344 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8207 (mm-40) REVERT: F 345 MET cc_start: 0.8931 (tpt) cc_final: 0.8033 (tpt) outliers start: 63 outliers final: 50 residues processed: 357 average time/residue: 0.2529 time to fit residues: 136.3537 Evaluate side-chains 360 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 309 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 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 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 264 VAL 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 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 326 TRP 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 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 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 ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** 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 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 189 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2692 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= 0.158 Angle : 0.462 6.215 20778 Z= 0.234 Chirality : 0.035 0.129 2208 Planarity : 0.003 0.037 2826 Dihedral : 3.349 15.669 2094 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.07 % Allowed : 21.87 % Favored : 74.06 % 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: 1.97 (0.20), residues: 1884 helix: 1.91 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -0.87 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 366 HIS 0.002 0.001 HIS A 182 PHE 0.010 0.001 PHE C 185 TYR 0.013 0.001 TYR E 94 ARG 0.008 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 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 395 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 330 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 94 TYR cc_start: 0.8181 (m-80) cc_final: 0.7754 (m-80) REVERT: A 125 LYS cc_start: 0.8583 (tppp) cc_final: 0.8072 (tppp) REVERT: A 135 MET cc_start: 0.7782 (tmm) cc_final: 0.7394 (tmm) REVERT: A 152 GLU cc_start: 0.7883 (tp30) cc_final: 0.7361 (tp30) REVERT: A 211 MET cc_start: 0.8437 (tpp) cc_final: 0.8069 (tpp) REVERT: A 318 ASN cc_start: 0.8995 (t0) cc_final: 0.8674 (t0) REVERT: A 335 GLU cc_start: 0.8467 (tp30) cc_final: 0.7766 (tm-30) REVERT: B 82 GLN cc_start: 0.8702 (mt0) cc_final: 0.8369 (mt0) REVERT: B 85 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7848 (tm-30) REVERT: B 101 MET cc_start: 0.7885 (mmp) cc_final: 0.7404 (mmm) REVERT: B 117 ASP cc_start: 0.7551 (t0) cc_final: 0.6508 (t0) REVERT: B 125 LYS cc_start: 0.8443 (tppp) cc_final: 0.8029 (ttpt) REVERT: B 211 MET cc_start: 0.8190 (tpp) cc_final: 0.7884 (tpt) REVERT: B 318 ASN cc_start: 0.9098 (t0) cc_final: 0.8195 (t0) REVERT: B 335 GLU cc_start: 0.8394 (tp30) cc_final: 0.7798 (tm-30) REVERT: B 345 MET cc_start: 0.8841 (tpt) cc_final: 0.8257 (tpt) REVERT: C 85 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 117 ASP cc_start: 0.7566 (t0) cc_final: 0.6794 (t0) REVERT: C 125 LYS cc_start: 0.8421 (tppp) cc_final: 0.7965 (tppp) REVERT: C 152 GLU cc_start: 0.7904 (tp30) cc_final: 0.7356 (tp30) REVERT: C 223 LYS cc_start: 0.7987 (mmmm) cc_final: 0.7767 (tppt) REVERT: C 300 GLU cc_start: 0.8511 (tp30) cc_final: 0.7823 (tm-30) REVERT: C 307 GLU cc_start: 0.7297 (tt0) cc_final: 0.6995 (tt0) REVERT: C 318 ASN cc_start: 0.9056 (t0) cc_final: 0.8417 (t0) REVERT: C 344 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8226 (mm-40) REVERT: C 345 MET cc_start: 0.8883 (tpt) cc_final: 0.8678 (tpt) REVERT: D 85 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 101 MET cc_start: 0.7921 (mmp) cc_final: 0.7275 (mmm) REVERT: D 135 MET cc_start: 0.7749 (tmm) cc_final: 0.7397 (tmm) REVERT: D 152 GLU cc_start: 0.7877 (tp30) cc_final: 0.7351 (tp30) REVERT: D 211 MET cc_start: 0.8482 (tpp) cc_final: 0.8153 (tpp) REVERT: D 318 ASN cc_start: 0.8975 (t0) cc_final: 0.8666 (t0) REVERT: D 335 GLU cc_start: 0.8356 (tp30) cc_final: 0.7716 (tm-30) REVERT: E 82 GLN cc_start: 0.8732 (mt0) cc_final: 0.8397 (mt0) REVERT: E 85 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7841 (tm-30) REVERT: E 125 LYS cc_start: 0.8481 (tppp) cc_final: 0.8133 (ttpt) REVERT: E 160 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7417 (t0) REVERT: E 201 GLU cc_start: 0.8457 (tp30) cc_final: 0.7951 (tp30) REVERT: E 214 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7626 (ttm-80) REVERT: E 318 ASN cc_start: 0.9118 (t0) cc_final: 0.8215 (t0) REVERT: E 335 GLU cc_start: 0.8387 (tp30) cc_final: 0.7813 (tm-30) REVERT: E 345 MET cc_start: 0.8825 (tpt) cc_final: 0.8236 (tpt) REVERT: F 85 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7624 (tm-30) REVERT: F 121 MET cc_start: 0.7511 (tpp) cc_final: 0.7246 (tpp) REVERT: F 125 LYS cc_start: 0.8441 (tppp) cc_final: 0.8003 (tppp) REVERT: F 152 GLU cc_start: 0.7934 (tp30) cc_final: 0.7383 (tp30) REVERT: F 223 LYS cc_start: 0.7999 (mmmm) cc_final: 0.7778 (tppt) REVERT: F 262 MET cc_start: 0.8192 (tpp) cc_final: 0.7912 (tpp) REVERT: F 318 ASN cc_start: 0.9062 (t0) cc_final: 0.8432 (t0) REVERT: F 344 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8230 (mm-40) REVERT: F 345 MET cc_start: 0.8936 (tpt) cc_final: 0.8083 (tpt) outliers start: 65 outliers final: 53 residues processed: 365 average time/residue: 0.2394 time to fit residues: 132.2924 Evaluate side-chains 377 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 323 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 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 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 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 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 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 326 TRP 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 170 ASP 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 189 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** 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 189 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15414 Z= 0.169 Angle : 0.472 8.228 20778 Z= 0.241 Chirality : 0.035 0.137 2208 Planarity : 0.003 0.034 2826 Dihedral : 3.370 15.646 2094 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.07 % Allowed : 22.56 % Favored : 73.37 % 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: 2.13 (0.20), residues: 1884 helix: 2.09 (0.14), residues: 1446 sheet: None (None), residues: 0 loop : -0.95 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 366 HIS 0.002 0.001 HIS D 182 PHE 0.013 0.001 PHE F 129 TYR 0.013 0.001 TYR E 94 ARG 0.005 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 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 396 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 331 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 94 TYR cc_start: 0.8216 (m-80) cc_final: 0.7848 (m-80) REVERT: A 135 MET cc_start: 0.7795 (tmm) cc_final: 0.7387 (tmm) REVERT: A 152 GLU cc_start: 0.7869 (tp30) cc_final: 0.7349 (tp30) REVERT: A 318 ASN cc_start: 0.8977 (t0) cc_final: 0.8692 (t0) REVERT: A 335 GLU cc_start: 0.8449 (tp30) cc_final: 0.7758 (tm-30) REVERT: B 82 GLN cc_start: 0.8716 (mt0) cc_final: 0.8392 (mt0) REVERT: B 85 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 101 MET cc_start: 0.7884 (mmp) cc_final: 0.7401 (mmm) REVERT: B 117 ASP cc_start: 0.7575 (t0) cc_final: 0.6559 (t0) REVERT: B 125 LYS cc_start: 0.8436 (tppp) cc_final: 0.8120 (ttpt) REVERT: B 211 MET cc_start: 0.8245 (tpp) cc_final: 0.7684 (ttp) REVERT: B 318 ASN cc_start: 0.9080 (t0) cc_final: 0.8200 (t0) REVERT: B 335 GLU cc_start: 0.8417 (tp30) cc_final: 0.7863 (tm-30) REVERT: B 345 MET cc_start: 0.8877 (tpt) cc_final: 0.8605 (ttm) REVERT: C 85 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 117 ASP cc_start: 0.7512 (t0) cc_final: 0.6750 (t0) REVERT: C 125 LYS cc_start: 0.8215 (tppp) cc_final: 0.7836 (tppp) REVERT: C 152 GLU cc_start: 0.7913 (tp30) cc_final: 0.7356 (tp30) REVERT: C 223 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7760 (tppt) REVERT: C 300 GLU cc_start: 0.8503 (tp30) cc_final: 0.7829 (tm-30) REVERT: C 307 GLU cc_start: 0.7358 (tt0) cc_final: 0.7033 (tt0) REVERT: C 318 ASN cc_start: 0.9050 (t0) cc_final: 0.8435 (t0) REVERT: C 344 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8281 (mm-40) REVERT: D 85 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7894 (tm-30) REVERT: D 101 MET cc_start: 0.7901 (mmp) cc_final: 0.7257 (mmm) REVERT: D 135 MET cc_start: 0.7778 (tmm) cc_final: 0.7390 (tmm) REVERT: D 152 GLU cc_start: 0.7856 (tp30) cc_final: 0.7335 (tp30) REVERT: D 211 MET cc_start: 0.8466 (tpp) cc_final: 0.8150 (tpp) REVERT: D 318 ASN cc_start: 0.8955 (t0) cc_final: 0.7798 (t0) REVERT: D 335 GLU cc_start: 0.8371 (tp30) cc_final: 0.7711 (tm-30) REVERT: E 82 GLN cc_start: 0.8737 (mt0) cc_final: 0.8400 (mt0) REVERT: E 85 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7852 (tm-30) REVERT: E 125 LYS cc_start: 0.8518 (tppp) cc_final: 0.8243 (ttpt) REVERT: E 145 GLU cc_start: 0.7774 (tp30) cc_final: 0.6955 (tp30) REVERT: E 160 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7407 (t70) REVERT: E 201 GLU cc_start: 0.8431 (tp30) cc_final: 0.7932 (tp30) REVERT: E 214 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7716 (ttm-80) REVERT: E 318 ASN cc_start: 0.9107 (t0) cc_final: 0.8202 (t0) REVERT: E 335 GLU cc_start: 0.8406 (tp30) cc_final: 0.7851 (tm-30) REVERT: E 345 MET cc_start: 0.8871 (tpt) cc_final: 0.8609 (ttm) REVERT: F 85 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7584 (tm-30) REVERT: F 125 LYS cc_start: 0.8389 (tppp) cc_final: 0.7838 (tppp) REVERT: F 135 MET cc_start: 0.8022 (tmm) cc_final: 0.7144 (tmm) REVERT: F 152 GLU cc_start: 0.7932 (tp30) cc_final: 0.7370 (tp30) REVERT: F 223 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7773 (tppt) REVERT: F 318 ASN cc_start: 0.9048 (t0) cc_final: 0.8390 (t0) REVERT: F 344 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8351 (mm-40) REVERT: F 345 MET cc_start: 0.8958 (tpt) cc_final: 0.8110 (tpt) outliers start: 65 outliers final: 56 residues processed: 368 average time/residue: 0.2577 time to fit residues: 145.2017 Evaluate side-chains 375 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 318 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 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 170 ASP Chi-restraints excluded: chain B residue 225 ILE 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 337 ASP 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 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 326 TRP 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 225 ILE 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 337 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 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 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 ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN ** D 164 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** ** E 361 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15414 Z= 0.204 Angle : 0.498 7.390 20778 Z= 0.253 Chirality : 0.036 0.126 2208 Planarity : 0.003 0.033 2826 Dihedral : 3.454 16.628 2094 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.01 % Allowed : 22.81 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.20), residues: 1884 helix: 2.01 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : -0.77 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 366 HIS 0.002 0.001 HIS A 182 PHE 0.021 0.001 PHE C 129 TYR 0.014 0.001 TYR E 94 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 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 381 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 317 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7929 (tm-30) REVERT: A 125 LYS cc_start: 0.8572 (tppp) cc_final: 0.8045 (tppp) REVERT: A 135 MET cc_start: 0.7792 (tmm) cc_final: 0.7379 (tmm) REVERT: A 152 GLU cc_start: 0.7876 (tp30) cc_final: 0.7357 (tp30) REVERT: A 211 MET cc_start: 0.8443 (tpp) cc_final: 0.8178 (tpp) REVERT: A 300 GLU cc_start: 0.8526 (tp30) cc_final: 0.8216 (tp30) REVERT: A 307 GLU cc_start: 0.7327 (tt0) cc_final: 0.7082 (tt0) REVERT: A 318 ASN cc_start: 0.8971 (t0) cc_final: 0.7807 (t0) REVERT: A 335 GLU cc_start: 0.8487 (tp30) cc_final: 0.7794 (tm-30) REVERT: B 82 GLN cc_start: 0.8748 (mt0) cc_final: 0.8433 (mt0) REVERT: B 85 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 101 MET cc_start: 0.7912 (mmp) cc_final: 0.7476 (mmm) REVERT: B 117 ASP cc_start: 0.7606 (t0) cc_final: 0.6839 (t0) REVERT: B 125 LYS cc_start: 0.8516 (tppp) cc_final: 0.8117 (ttpp) REVERT: B 145 GLU cc_start: 0.7932 (tp30) cc_final: 0.7090 (tp30) REVERT: B 211 MET cc_start: 0.8247 (tpp) cc_final: 0.7691 (ttp) REVERT: B 318 ASN cc_start: 0.9041 (t160) cc_final: 0.8057 (t0) REVERT: B 335 GLU cc_start: 0.8454 (tp30) cc_final: 0.7863 (tm-30) REVERT: B 345 MET cc_start: 0.8874 (tpt) cc_final: 0.8293 (tpt) REVERT: C 85 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7614 (tm-30) REVERT: C 117 ASP cc_start: 0.7515 (t0) cc_final: 0.6753 (t0) REVERT: C 125 LYS cc_start: 0.8219 (tppp) cc_final: 0.7818 (tppp) REVERT: C 152 GLU cc_start: 0.7933 (tp30) cc_final: 0.7381 (tp30) REVERT: C 307 GLU cc_start: 0.7441 (tt0) cc_final: 0.7093 (tt0) REVERT: C 318 ASN cc_start: 0.9051 (t0) cc_final: 0.8428 (t0) REVERT: C 335 GLU cc_start: 0.8505 (tp30) cc_final: 0.8041 (tm-30) REVERT: D 85 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7952 (tm-30) REVERT: D 94 TYR cc_start: 0.8066 (m-80) cc_final: 0.7693 (m-80) REVERT: D 101 MET cc_start: 0.7897 (mmp) cc_final: 0.7292 (mmm) REVERT: D 125 LYS cc_start: 0.8557 (tppp) cc_final: 0.8100 (tppp) REVERT: D 135 MET cc_start: 0.7781 (tmm) cc_final: 0.7373 (tmm) REVERT: D 152 GLU cc_start: 0.7868 (tp30) cc_final: 0.7351 (tp30) REVERT: D 211 MET cc_start: 0.8497 (tpp) cc_final: 0.8170 (tpp) REVERT: D 298 GLN cc_start: 0.8468 (mt0) cc_final: 0.8212 (mt0) REVERT: D 307 GLU cc_start: 0.7317 (tt0) cc_final: 0.7078 (tt0) REVERT: D 318 ASN cc_start: 0.8950 (t0) cc_final: 0.7802 (t0) REVERT: D 335 GLU cc_start: 0.8391 (tp30) cc_final: 0.7755 (tm-30) REVERT: E 82 GLN cc_start: 0.8752 (mt0) cc_final: 0.8429 (mt0) REVERT: E 85 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7860 (tm-30) REVERT: E 125 LYS cc_start: 0.8532 (tppp) cc_final: 0.8294 (ttpt) REVERT: E 145 GLU cc_start: 0.7776 (tp30) cc_final: 0.6918 (tp30) REVERT: E 160 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7437 (t70) REVERT: E 214 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7729 (ttm-80) REVERT: E 318 ASN cc_start: 0.9106 (t0) cc_final: 0.8194 (t0) REVERT: E 335 GLU cc_start: 0.8402 (tp30) cc_final: 0.7854 (tm-30) REVERT: E 345 MET cc_start: 0.8863 (tpt) cc_final: 0.8351 (tpt) REVERT: F 85 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7585 (tm-30) REVERT: F 125 LYS cc_start: 0.8199 (tppp) cc_final: 0.7656 (tppp) REVERT: F 152 GLU cc_start: 0.7954 (tp30) cc_final: 0.7406 (tp30) REVERT: F 318 ASN cc_start: 0.9045 (t0) cc_final: 0.8428 (t0) REVERT: F 337 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.6988 (t70) REVERT: F 345 MET cc_start: 0.8984 (tpt) cc_final: 0.8147 (tpt) outliers start: 64 outliers final: 58 residues processed: 353 average time/residue: 0.2329 time to fit residues: 124.9520 Evaluate side-chains 374 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 314 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 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 337 ASP 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 170 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 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 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 326 TRP 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 170 ASP Chi-restraints excluded: chain E residue 225 ILE 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 337 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 170 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 337 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 131 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 189 GLN ** 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 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15414 Z= 0.168 Angle : 0.483 7.469 20778 Z= 0.245 Chirality : 0.035 0.128 2208 Planarity : 0.003 0.032 2826 Dihedral : 3.394 16.284 2094 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.70 % Allowed : 23.43 % Favored : 72.87 % 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: 2.21 (0.20), residues: 1884 helix: 2.07 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : -0.76 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 287 HIS 0.003 0.001 HIS A 182 PHE 0.018 0.001 PHE C 129 TYR 0.014 0.001 TYR E 94 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 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 372 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 313 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 94 TYR cc_start: 0.8168 (m-80) cc_final: 0.7708 (m-80) REVERT: A 135 MET cc_start: 0.7751 (tmm) cc_final: 0.7347 (tmm) REVERT: A 152 GLU cc_start: 0.7816 (tp30) cc_final: 0.7303 (tp30) REVERT: A 211 MET cc_start: 0.8412 (tpp) cc_final: 0.8186 (tpp) REVERT: A 307 GLU cc_start: 0.7293 (tt0) cc_final: 0.7028 (tt0) REVERT: A 318 ASN cc_start: 0.8959 (t0) cc_final: 0.7785 (t0) REVERT: A 335 GLU cc_start: 0.8477 (tp30) cc_final: 0.7796 (tm-30) REVERT: B 82 GLN cc_start: 0.8723 (mt0) cc_final: 0.8392 (mt0) REVERT: B 85 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 94 TYR cc_start: 0.8168 (m-80) cc_final: 0.7781 (m-80) REVERT: B 101 MET cc_start: 0.7879 (mmp) cc_final: 0.7386 (mmm) REVERT: B 117 ASP cc_start: 0.7590 (t0) cc_final: 0.7191 (t0) REVERT: B 125 LYS cc_start: 0.8484 (tppp) cc_final: 0.8193 (ttpt) REVERT: B 145 GLU cc_start: 0.7891 (tp30) cc_final: 0.7057 (tp30) REVERT: B 160 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7375 (t0) REVERT: B 211 MET cc_start: 0.8235 (tpp) cc_final: 0.7681 (ttp) REVERT: B 318 ASN cc_start: 0.8984 (t160) cc_final: 0.7993 (t0) REVERT: B 335 GLU cc_start: 0.8440 (tp30) cc_final: 0.7872 (tm-30) REVERT: B 345 MET cc_start: 0.8927 (tpt) cc_final: 0.8423 (tpt) REVERT: C 85 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7576 (tm-30) REVERT: C 94 TYR cc_start: 0.8114 (m-80) cc_final: 0.7545 (m-80) REVERT: C 117 ASP cc_start: 0.7501 (t0) cc_final: 0.6745 (t0) REVERT: C 125 LYS cc_start: 0.8140 (tppp) cc_final: 0.7795 (tppp) REVERT: C 152 GLU cc_start: 0.7909 (tp30) cc_final: 0.7355 (tp30) REVERT: C 307 GLU cc_start: 0.7384 (tt0) cc_final: 0.7054 (tt0) REVERT: C 318 ASN cc_start: 0.9026 (t0) cc_final: 0.8422 (t0) REVERT: C 335 GLU cc_start: 0.8491 (tp30) cc_final: 0.8032 (tm-30) REVERT: C 344 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8386 (mp10) REVERT: D 85 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7956 (tm-30) REVERT: D 94 TYR cc_start: 0.7992 (m-80) cc_final: 0.7639 (m-80) REVERT: D 101 MET cc_start: 0.7870 (mmp) cc_final: 0.7307 (mmm) REVERT: D 125 LYS cc_start: 0.8570 (tppp) cc_final: 0.8112 (tppp) REVERT: D 135 MET cc_start: 0.7729 (tmm) cc_final: 0.7353 (tmm) REVERT: D 152 GLU cc_start: 0.7820 (tp30) cc_final: 0.7306 (tp30) REVERT: D 211 MET cc_start: 0.8456 (tpp) cc_final: 0.8157 (tpp) REVERT: D 307 GLU cc_start: 0.7271 (tt0) cc_final: 0.7015 (tt0) REVERT: D 318 ASN cc_start: 0.8932 (t0) cc_final: 0.7781 (t0) REVERT: D 335 GLU cc_start: 0.8382 (tp30) cc_final: 0.7757 (tm-30) REVERT: E 82 GLN cc_start: 0.8738 (mt0) cc_final: 0.8412 (mt0) REVERT: E 85 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7864 (tm-30) REVERT: E 94 TYR cc_start: 0.8084 (m-80) cc_final: 0.7582 (m-80) REVERT: E 125 LYS cc_start: 0.8463 (tppp) cc_final: 0.8140 (ttpp) REVERT: E 145 GLU cc_start: 0.7748 (tp30) cc_final: 0.6912 (tp30) REVERT: E 160 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7434 (t70) REVERT: E 214 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7708 (ttm-80) REVERT: E 318 ASN cc_start: 0.9084 (t0) cc_final: 0.8187 (t0) REVERT: E 335 GLU cc_start: 0.8391 (tp30) cc_final: 0.7837 (tm-30) REVERT: E 345 MET cc_start: 0.8882 (tpt) cc_final: 0.8343 (tpt) REVERT: F 85 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7568 (tm-30) REVERT: F 94 TYR cc_start: 0.8139 (m-80) cc_final: 0.7589 (m-80) REVERT: F 125 LYS cc_start: 0.8150 (tppp) cc_final: 0.7658 (tppp) REVERT: F 152 GLU cc_start: 0.7925 (tp30) cc_final: 0.7382 (tp30) REVERT: F 318 ASN cc_start: 0.9036 (t0) cc_final: 0.8405 (t0) REVERT: F 335 GLU cc_start: 0.8507 (tp30) cc_final: 0.8020 (tm-30) REVERT: F 345 MET cc_start: 0.8833 (tpt) cc_final: 0.8144 (tpt) outliers start: 59 outliers final: 52 residues processed: 347 average time/residue: 0.2347 time to fit residues: 123.2224 Evaluate side-chains 369 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 315 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 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 337 ASP 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 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 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 214 ARG 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 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 282 ILE Chi-restraints excluded: chain D residue 326 TRP 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 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 337 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 170 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 337 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN C 189 GLN C 298 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN ** 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 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15414 Z= 0.151 Angle : 0.503 8.899 20778 Z= 0.251 Chirality : 0.035 0.138 2208 Planarity : 0.003 0.030 2826 Dihedral : 3.374 17.315 2094 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.51 % Allowed : 23.75 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.33 (0.19), residues: 1884 helix: 2.24 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -0.87 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 287 HIS 0.003 0.001 HIS A 182 PHE 0.018 0.001 PHE C 129 TYR 0.014 0.001 TYR E 94 ARG 0.002 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 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 368 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 312 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 94 TYR cc_start: 0.8091 (m-80) cc_final: 0.7689 (m-80) REVERT: A 101 MET cc_start: 0.7858 (mmp) cc_final: 0.7150 (mmm) REVERT: A 135 MET cc_start: 0.7738 (tmm) cc_final: 0.7403 (tmm) REVERT: A 152 GLU cc_start: 0.7791 (tp30) cc_final: 0.7264 (tp30) REVERT: A 211 MET cc_start: 0.8394 (tpp) cc_final: 0.8076 (tpt) REVERT: A 300 GLU cc_start: 0.8517 (tp30) cc_final: 0.8199 (tp30) REVERT: A 307 GLU cc_start: 0.7220 (tt0) cc_final: 0.6939 (tt0) REVERT: A 318 ASN cc_start: 0.8909 (t0) cc_final: 0.7761 (t0) REVERT: A 335 GLU cc_start: 0.8465 (tp30) cc_final: 0.7774 (tm-30) REVERT: B 82 GLN cc_start: 0.8720 (mt0) cc_final: 0.8398 (mt0) REVERT: B 85 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 94 TYR cc_start: 0.8137 (m-80) cc_final: 0.7793 (m-80) REVERT: B 101 MET cc_start: 0.7828 (mmp) cc_final: 0.7336 (mmm) REVERT: B 117 ASP cc_start: 0.7558 (t0) cc_final: 0.7163 (t0) REVERT: B 125 LYS cc_start: 0.8452 (tppp) cc_final: 0.8063 (ttpp) REVERT: B 145 GLU cc_start: 0.7883 (tp30) cc_final: 0.7038 (tp30) REVERT: B 160 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7369 (t0) REVERT: B 211 MET cc_start: 0.8222 (tpp) cc_final: 0.7679 (ttp) REVERT: B 318 ASN cc_start: 0.8946 (t160) cc_final: 0.7983 (t0) REVERT: B 335 GLU cc_start: 0.8434 (tp30) cc_final: 0.7848 (tm-30) REVERT: B 345 MET cc_start: 0.8897 (tpt) cc_final: 0.8538 (ttm) REVERT: C 85 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 94 TYR cc_start: 0.8023 (m-80) cc_final: 0.7519 (m-80) REVERT: C 117 ASP cc_start: 0.7488 (t0) cc_final: 0.6748 (t0) REVERT: C 125 LYS cc_start: 0.8144 (tppp) cc_final: 0.7815 (tppp) REVERT: C 152 GLU cc_start: 0.7899 (tp30) cc_final: 0.7352 (tp30) REVERT: C 307 GLU cc_start: 0.7308 (tt0) cc_final: 0.6994 (tt0) REVERT: C 318 ASN cc_start: 0.8996 (t0) cc_final: 0.8437 (t0) REVERT: C 335 GLU cc_start: 0.8483 (tp30) cc_final: 0.8009 (tm-30) REVERT: D 85 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7937 (tm-30) REVERT: D 94 TYR cc_start: 0.7817 (m-80) cc_final: 0.7562 (m-80) REVERT: D 101 MET cc_start: 0.7851 (mmp) cc_final: 0.7283 (mmm) REVERT: D 125 LYS cc_start: 0.8564 (tppp) cc_final: 0.8114 (tppp) REVERT: D 135 MET cc_start: 0.7690 (tmm) cc_final: 0.7356 (tmm) REVERT: D 152 GLU cc_start: 0.7798 (tp30) cc_final: 0.7265 (tp30) REVERT: D 157 ASP cc_start: 0.8120 (t0) cc_final: 0.7898 (t0) REVERT: D 211 MET cc_start: 0.8393 (tpp) cc_final: 0.8133 (tpp) REVERT: D 307 GLU cc_start: 0.7216 (tt0) cc_final: 0.6945 (tt0) REVERT: D 318 ASN cc_start: 0.8892 (t0) cc_final: 0.7760 (t0) REVERT: D 328 MET cc_start: 0.6935 (ttp) cc_final: 0.6703 (ttp) REVERT: D 335 GLU cc_start: 0.8369 (tp30) cc_final: 0.7749 (tm-30) REVERT: E 82 GLN cc_start: 0.8735 (mt0) cc_final: 0.8411 (mt0) REVERT: E 85 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7861 (tm-30) REVERT: E 94 TYR cc_start: 0.8051 (m-80) cc_final: 0.7605 (m-80) REVERT: E 125 LYS cc_start: 0.8456 (tppp) cc_final: 0.8124 (ttpp) REVERT: E 145 GLU cc_start: 0.7696 (tp30) cc_final: 0.6914 (tp30) REVERT: E 160 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7429 (t70) REVERT: E 201 GLU cc_start: 0.8373 (tp30) cc_final: 0.7900 (tp30) REVERT: E 214 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7677 (ttm-80) REVERT: E 318 ASN cc_start: 0.9078 (t0) cc_final: 0.8163 (t0) REVERT: E 335 GLU cc_start: 0.8376 (tp30) cc_final: 0.7839 (tm-30) REVERT: E 345 MET cc_start: 0.8864 (tpt) cc_final: 0.8318 (tpt) REVERT: F 85 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7560 (tm-30) REVERT: F 94 TYR cc_start: 0.8090 (m-80) cc_final: 0.7582 (m-80) REVERT: F 125 LYS cc_start: 0.8100 (tppp) cc_final: 0.7719 (tppp) REVERT: F 152 GLU cc_start: 0.7893 (tp30) cc_final: 0.7336 (tp30) REVERT: F 318 ASN cc_start: 0.9021 (t0) cc_final: 0.8414 (t0) REVERT: F 335 GLU cc_start: 0.8500 (tp30) cc_final: 0.8016 (tm-30) REVERT: F 337 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.6950 (t70) outliers start: 56 outliers final: 47 residues processed: 350 average time/residue: 0.2456 time to fit residues: 130.7562 Evaluate side-chains 356 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 306 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 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 225 ILE 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 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 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 82 GLN 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 282 ILE Chi-restraints excluded: chain D residue 326 TRP 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 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP 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 282 ILE Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.0970 chunk 157 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** C 318 ASN ** 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 298 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 298 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104089 restraints weight = 25225.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107749 restraints weight = 13378.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110124 restraints weight = 8218.222| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15414 Z= 0.139 Angle : 0.496 8.814 20778 Z= 0.248 Chirality : 0.035 0.133 2208 Planarity : 0.003 0.031 2826 Dihedral : 3.321 17.111 2094 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.01 % Allowed : 24.56 % Favored : 72.43 % 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: 2.42 (0.19), residues: 1884 helix: 2.28 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.82 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 287 HIS 0.003 0.001 HIS A 182 PHE 0.026 0.001 PHE C 129 TYR 0.014 0.001 TYR E 94 ARG 0.009 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.02 seconds wall clock time: 55 minutes 40.33 seconds (3340.33 seconds total)