Starting phenix.real_space_refine on Fri Sep 27 08:02:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/09_2024/7ssz_25417.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/09_2024/7ssz_25417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/09_2024/7ssz_25417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/09_2024/7ssz_25417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/09_2024/7ssz_25417.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/09_2024/7ssz_25417.cif" } resolution = 3.25 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= 0.003 sd= 0.062 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 60 5.16 5 C 9924 2.51 5 N 2564 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 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: 15283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2935 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 8.09, per 1000 atoms: 0.53 Number of scatterers: 15283 At special positions: 0 Unit cell: (120.132, 120.132, 152.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 60 16.00 O 2732 8.00 N 2564 7.00 C 9924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.05 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: 3.60 Conformation dependent library (CDL) restraints added in 2.0 seconds 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3520 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 20 sheets defined 52.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.879A pdb=" N ARG A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.790A pdb=" N TYR A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 256 removed outlier: 3.778A pdb=" N THR A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.302A pdb=" N GLU A 262 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 347 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.711A pdb=" N VAL A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 372 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG A 373 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 374 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 394 through 419 Processing helix chain 'A' and resid 430 through 433 removed outlier: 3.619A pdb=" N ASP A 433 " --> pdb=" O SER A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.888A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.880A pdb=" N ARG B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 216 through 226 removed outlier: 3.790A pdb=" N TYR B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 256 removed outlier: 3.778A pdb=" N THR B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.301A pdb=" N GLU B 262 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 347 Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.710A pdb=" N VAL B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 372 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 394 through 419 Processing helix chain 'B' and resid 430 through 433 removed outlier: 3.619A pdb=" N ASP B 433 " --> pdb=" O SER B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.888A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 138 removed outlier: 3.879A pdb=" N ARG C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 216 through 226 removed outlier: 3.789A pdb=" N TYR C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 256 removed outlier: 3.779A pdb=" N THR C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 4.302A pdb=" N GLU C 262 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 347 Proline residue: C 338 - end of helix Processing helix chain 'C' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 379 removed outlier: 3.710A pdb=" N VAL C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE C 372 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG C 373 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 394 through 419 Processing helix chain 'C' and resid 430 through 433 removed outlier: 3.619A pdb=" N ASP C 433 " --> pdb=" O SER C 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 430 through 433' Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.888A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.879A pdb=" N ARG D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 190 through 201 Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.790A pdb=" N TYR D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 256 removed outlier: 3.779A pdb=" N THR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 4.303A pdb=" N GLU D 262 " --> pdb=" O PHE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 347 Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.711A pdb=" N VAL D 371 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE D 372 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG D 373 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 393 Processing helix chain 'D' and resid 394 through 419 Processing helix chain 'D' and resid 430 through 433 removed outlier: 3.620A pdb=" N ASP D 433 " --> pdb=" O SER D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 433' Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'D' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.887A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 146 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 26 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 26 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.662A pdb=" N SER E 34 " --> pdb=" O TRP E 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA E 35 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG E 39 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER F 26 " --> pdb=" O GLN F 4 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER F 26 " --> pdb=" O GLN F 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.663A pdb=" N SER F 34 " --> pdb=" O TRP F 99 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA F 35 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 11 through 13 Processing sheet with id=AB1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN G 4 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER G 26 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN G 4 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER G 26 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.662A pdb=" N SER G 34 " --> pdb=" O TRP G 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA G 35 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 26 " --> pdb=" O GLN H 4 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 26 " --> pdb=" O GLN H 4 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.662A pdb=" N SER H 34 " --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA H 35 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG H 39 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AB9, first strand: chain 'B' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR B 147 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL B 107 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE B 149 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN B 109 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 146 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR C 147 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 107 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 146 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR D 147 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL D 107 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE D 149 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 146 " --> pdb=" O ASP D 141 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2364 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: 5.45 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2408 1.31 - 1.43: 4505 1.43 - 1.56: 8647 1.56 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 15652 Sorted by residual: bond pdb=" CA SER B 426 " pdb=" CB SER B 426 " ideal model delta sigma weight residual 1.528 1.451 0.077 1.61e-02 3.86e+03 2.28e+01 bond pdb=" CA SER A 426 " pdb=" CB SER A 426 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.61e-02 3.86e+03 2.23e+01 bond pdb=" CA SER D 426 " pdb=" CB SER D 426 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.61e-02 3.86e+03 2.22e+01 bond pdb=" CA SER C 426 " pdb=" CB SER C 426 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.61e-02 3.86e+03 2.21e+01 bond pdb=" N TYR C 265 " pdb=" CA TYR C 265 " ideal model delta sigma weight residual 1.453 1.491 -0.038 8.30e-03 1.45e+04 2.09e+01 ... (remaining 15647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 17387 2.13 - 4.26: 3205 4.26 - 6.39: 476 6.39 - 8.52: 98 8.52 - 10.64: 26 Bond angle restraints: 21192 Sorted by residual: angle pdb=" N VAL B 445 " pdb=" CA VAL B 445 " pdb=" C VAL B 445 " ideal model delta sigma weight residual 110.42 100.34 10.08 9.60e-01 1.09e+00 1.10e+02 angle pdb=" N VAL A 445 " pdb=" CA VAL A 445 " pdb=" C VAL A 445 " ideal model delta sigma weight residual 110.42 100.35 10.07 9.60e-01 1.09e+00 1.10e+02 angle pdb=" N VAL D 445 " pdb=" CA VAL D 445 " pdb=" C VAL D 445 " ideal model delta sigma weight residual 110.42 100.37 10.05 9.60e-01 1.09e+00 1.10e+02 angle pdb=" N VAL C 445 " pdb=" CA VAL C 445 " pdb=" C VAL C 445 " ideal model delta sigma weight residual 110.42 100.39 10.03 9.60e-01 1.09e+00 1.09e+02 angle pdb=" N GLU B 262 " pdb=" CA GLU B 262 " pdb=" C GLU B 262 " ideal model delta sigma weight residual 113.28 104.88 8.40 1.22e+00 6.72e-01 4.74e+01 ... (remaining 21187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8171 17.92 - 35.85: 801 35.85 - 53.77: 211 53.77 - 71.70: 24 71.70 - 89.62: 4 Dihedral angle restraints: 9211 sinusoidal: 3719 harmonic: 5492 Sorted by residual: dihedral pdb=" C THR D 444 " pdb=" N THR D 444 " pdb=" CA THR D 444 " pdb=" CB THR D 444 " ideal model delta harmonic sigma weight residual -122.00 -144.18 22.18 0 2.50e+00 1.60e-01 7.87e+01 dihedral pdb=" C THR B 444 " pdb=" N THR B 444 " pdb=" CA THR B 444 " pdb=" CB THR B 444 " ideal model delta harmonic sigma weight residual -122.00 -144.16 22.16 0 2.50e+00 1.60e-01 7.86e+01 dihedral pdb=" C THR C 444 " pdb=" N THR C 444 " pdb=" CA THR C 444 " pdb=" CB THR C 444 " ideal model delta harmonic sigma weight residual -122.00 -144.14 22.14 0 2.50e+00 1.60e-01 7.84e+01 ... (remaining 9208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 2014 0.167 - 0.334: 298 0.334 - 0.501: 12 0.501 - 0.669: 4 0.669 - 0.836: 4 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CA THR D 444 " pdb=" N THR D 444 " pdb=" C THR D 444 " pdb=" CB THR D 444 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA THR C 444 " pdb=" N THR C 444 " pdb=" C THR C 444 " pdb=" CB THR C 444 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" CA THR A 444 " pdb=" N THR A 444 " pdb=" C THR A 444 " pdb=" CB THR A 444 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 2329 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 201 " -0.022 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" C GLU C 201 " 0.078 2.00e-02 2.50e+03 pdb=" O GLU C 201 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY C 202 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 201 " 0.022 2.00e-02 2.50e+03 4.50e-02 2.03e+01 pdb=" C GLU A 201 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU A 201 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY A 202 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 418 " 0.023 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" C PHE A 418 " -0.078 2.00e-02 2.50e+03 pdb=" O PHE A 418 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 419 " 0.026 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 0.47 - 1.40: 24 1.40 - 2.34: 39 2.34 - 3.27: 15760 3.27 - 4.21: 42056 4.21 - 5.14: 83500 Warning: very small nonbonded interaction distances. Nonbonded interactions: 141379 Sorted by model distance: nonbonded pdb=" CZ ARG E 53 " pdb=" OD2 ASP B 261 " model vdw 0.467 3.270 nonbonded pdb=" OD2 ASP A 261 " pdb=" CZ ARG H 53 " model vdw 0.475 3.270 nonbonded pdb=" CZ ARG G 53 " pdb=" OD2 ASP D 261 " model vdw 0.475 3.270 nonbonded pdb=" CZ ARG F 53 " pdb=" OD2 ASP C 261 " model vdw 0.485 3.270 nonbonded pdb=" NH1 ARG E 53 " pdb=" CG ASP B 261 " model vdw 0.950 3.350 ... (remaining 141374 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 491) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 7.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 34.900 Find NCS groups from input model: 0.600 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.014 0.092 15652 Z= 0.882 Angle : 1.699 10.644 21192 Z= 1.181 Chirality : 0.119 0.836 2332 Planarity : 0.009 0.078 2700 Dihedral : 14.901 89.621 5688 Min Nonbonded Distance : 0.467 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.31 % Allowed : 10.68 % Favored : 83.01 % Cbeta Deviations : 1.14 % 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: -2.29 (0.17), residues: 1876 helix: -1.92 (0.14), residues: 928 sheet: 1.08 (0.53), residues: 120 loop : -1.26 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 436 HIS 0.009 0.004 HIS C 488 PHE 0.033 0.004 PHE C 224 TYR 0.033 0.003 TYR D 447 ARG 0.005 0.001 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 272 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7255 (pt0) REVERT: A 119 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7833 (tp) REVERT: A 147 TYR cc_start: 0.7351 (m-80) cc_final: 0.6917 (m-80) REVERT: A 170 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7194 (mmt-90) REVERT: A 187 TYR cc_start: 0.7294 (m-80) cc_final: 0.7055 (m-80) REVERT: A 198 ARG cc_start: 0.7218 (tpp-160) cc_final: 0.7014 (tpp-160) REVERT: A 218 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.5101 (ptt180) REVERT: A 328 MET cc_start: 0.7027 (mtm) cc_final: 0.6721 (mtm) REVERT: A 332 ASP cc_start: 0.7890 (m-30) cc_final: 0.7370 (m-30) REVERT: A 368 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7398 (tt) REVERT: A 395 MET cc_start: 0.7638 (mmm) cc_final: 0.7250 (mmt) REVERT: A 450 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6154 (mmt) REVERT: E 37 TRP cc_start: 0.6240 (OUTLIER) cc_final: 0.5895 (m-90) REVERT: F 37 TRP cc_start: 0.6321 (OUTLIER) cc_final: 0.5915 (m-90) REVERT: G 29 LEU cc_start: 0.7428 (mt) cc_final: 0.7193 (mp) REVERT: G 37 TRP cc_start: 0.6358 (OUTLIER) cc_final: 0.5966 (m-90) REVERT: G 78 THR cc_start: 0.7901 (p) cc_final: 0.7697 (p) REVERT: H 37 TRP cc_start: 0.6382 (OUTLIER) cc_final: 0.5963 (m-90) REVERT: H 78 THR cc_start: 0.7913 (p) cc_final: 0.7708 (p) REVERT: B 104 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7288 (pt0) REVERT: B 119 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8054 (tt) REVERT: B 147 TYR cc_start: 0.7334 (m-80) cc_final: 0.6959 (m-80) REVERT: B 170 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7494 (mmt-90) REVERT: B 218 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.5061 (ptt180) REVERT: B 328 MET cc_start: 0.7104 (mtm) cc_final: 0.6800 (mtm) REVERT: B 332 ASP cc_start: 0.7913 (m-30) cc_final: 0.7334 (m-30) REVERT: B 368 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7369 (tt) REVERT: B 395 MET cc_start: 0.7730 (mmm) cc_final: 0.7290 (mmt) REVERT: B 450 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6364 (mmt) REVERT: C 104 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7458 (tt0) REVERT: C 147 TYR cc_start: 0.7330 (m-80) cc_final: 0.7055 (m-80) REVERT: C 170 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7499 (mmt-90) REVERT: C 218 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.5059 (ptt180) REVERT: C 328 MET cc_start: 0.7057 (mtm) cc_final: 0.6706 (mtm) REVERT: C 332 ASP cc_start: 0.7762 (m-30) cc_final: 0.7189 (m-30) REVERT: C 368 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7395 (tt) REVERT: C 395 MET cc_start: 0.7692 (mmm) cc_final: 0.7275 (mmt) REVERT: C 450 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6321 (mmt) REVERT: D 104 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7452 (tt0) REVERT: D 147 TYR cc_start: 0.7338 (m-80) cc_final: 0.7070 (m-80) REVERT: D 170 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7044 (mmt-90) REVERT: D 218 ARG cc_start: 0.5561 (OUTLIER) cc_final: 0.5069 (ptt180) REVERT: D 328 MET cc_start: 0.7022 (mtm) cc_final: 0.6643 (mtm) REVERT: D 332 ASP cc_start: 0.7734 (m-30) cc_final: 0.7187 (m-30) REVERT: D 368 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7381 (tt) REVERT: D 395 MET cc_start: 0.7634 (mmm) cc_final: 0.7219 (mmt) REVERT: D 450 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6423 (mmt) outliers start: 104 outliers final: 28 residues processed: 345 average time/residue: 0.3560 time to fit residues: 168.7248 Evaluate side-chains 235 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain G residue 48 PHE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 450 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 170 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 145 ASN A 164 GLN A 217 GLN E 84 ASN F 84 ASN G 84 ASN H 84 ASN B 124 GLN B 164 GLN B 217 GLN C 124 GLN C 164 GLN C 217 GLN D 124 GLN D 145 ASN D 217 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15652 Z= 0.222 Angle : 0.663 6.858 21192 Z= 0.362 Chirality : 0.046 0.212 2332 Planarity : 0.006 0.055 2700 Dihedral : 8.803 59.825 2240 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.13 % Allowed : 14.32 % Favored : 81.55 % 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: -0.58 (0.19), residues: 1876 helix: -0.02 (0.17), residues: 956 sheet: 1.30 (0.45), residues: 136 loop : -1.05 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 99 HIS 0.002 0.001 HIS C 488 PHE 0.016 0.001 PHE F 68 TYR 0.016 0.002 TYR B 447 ARG 0.004 0.000 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 194 time to evaluate : 1.806 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7290 (tt0) REVERT: A 170 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7029 (mmt-90) REVERT: A 332 ASP cc_start: 0.7771 (m-30) cc_final: 0.7297 (m-30) REVERT: A 368 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7497 (tt) REVERT: A 395 MET cc_start: 0.7257 (mmm) cc_final: 0.6863 (mmt) REVERT: A 450 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5676 (mmt) REVERT: A 469 VAL cc_start: 0.7695 (p) cc_final: 0.7286 (t) REVERT: E 26 SER cc_start: 0.7751 (m) cc_final: 0.7029 (p) REVERT: F 26 SER cc_start: 0.7670 (m) cc_final: 0.7040 (p) REVERT: G 26 SER cc_start: 0.7659 (m) cc_final: 0.7001 (p) REVERT: H 26 SER cc_start: 0.7674 (m) cc_final: 0.7008 (p) REVERT: H 53 ARG cc_start: 0.5813 (ttp-170) cc_final: 0.5400 (ttp80) REVERT: B 104 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7328 (tt0) REVERT: B 218 ARG cc_start: 0.5393 (OUTLIER) cc_final: 0.4841 (ptt180) REVERT: B 309 GLU cc_start: 0.6796 (tt0) cc_final: 0.6389 (tt0) REVERT: B 328 MET cc_start: 0.6554 (mtm) cc_final: 0.6266 (mtt) REVERT: B 332 ASP cc_start: 0.7729 (m-30) cc_final: 0.7251 (m-30) REVERT: B 368 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7501 (tt) REVERT: B 395 MET cc_start: 0.7332 (mmm) cc_final: 0.6890 (mmt) REVERT: B 450 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5817 (mmt) REVERT: B 469 VAL cc_start: 0.7794 (p) cc_final: 0.7401 (t) REVERT: C 104 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7331 (tt0) REVERT: C 170 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6767 (mmt-90) REVERT: C 218 ARG cc_start: 0.5411 (OUTLIER) cc_final: 0.4847 (ptt180) REVERT: C 328 MET cc_start: 0.6533 (mtm) cc_final: 0.6265 (mtt) REVERT: C 332 ASP cc_start: 0.7771 (m-30) cc_final: 0.7246 (m-30) REVERT: C 368 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7380 (tt) REVERT: C 395 MET cc_start: 0.7291 (mmm) cc_final: 0.6871 (mmt) REVERT: C 450 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.5722 (mmt) REVERT: C 469 VAL cc_start: 0.7783 (p) cc_final: 0.7394 (t) REVERT: D 104 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7311 (tt0) REVERT: D 170 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6782 (mmt-90) REVERT: D 218 ARG cc_start: 0.5447 (OUTLIER) cc_final: 0.4901 (ptt180) REVERT: D 328 MET cc_start: 0.6535 (mtm) cc_final: 0.6300 (mtt) REVERT: D 332 ASP cc_start: 0.7710 (m-30) cc_final: 0.7210 (m-30) REVERT: D 368 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7432 (tt) REVERT: D 395 MET cc_start: 0.7249 (mmm) cc_final: 0.6856 (mmt) REVERT: D 469 VAL cc_start: 0.7799 (p) cc_final: 0.7422 (t) outliers start: 68 outliers final: 34 residues processed: 243 average time/residue: 0.3004 time to fit residues: 106.1684 Evaluate side-chains 208 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain G residue 48 PHE Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 169 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15652 Z= 0.195 Angle : 0.576 5.947 21192 Z= 0.311 Chirality : 0.043 0.211 2332 Planarity : 0.005 0.051 2700 Dihedral : 7.540 59.582 2201 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.88 % Allowed : 15.41 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.20), residues: 1876 helix: 0.77 (0.18), residues: 944 sheet: 1.28 (0.38), residues: 176 loop : -1.07 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 221 HIS 0.002 0.001 HIS D 451 PHE 0.010 0.001 PHE C 406 TYR 0.018 0.001 TYR D 447 ARG 0.007 0.001 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 161 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7263 (tt0) REVERT: A 218 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.5150 (ptt180) REVERT: A 332 ASP cc_start: 0.7710 (m-30) cc_final: 0.7401 (m-30) REVERT: A 368 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7526 (tt) REVERT: A 395 MET cc_start: 0.7185 (mmm) cc_final: 0.6834 (mmt) REVERT: A 450 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5723 (mmt) REVERT: A 469 VAL cc_start: 0.7729 (p) cc_final: 0.7344 (t) REVERT: E 26 SER cc_start: 0.7639 (m) cc_final: 0.7159 (p) REVERT: G 26 SER cc_start: 0.7652 (m) cc_final: 0.7200 (p) REVERT: H 26 SER cc_start: 0.7673 (m) cc_final: 0.7211 (p) REVERT: B 104 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7302 (tt0) REVERT: B 332 ASP cc_start: 0.7652 (m-30) cc_final: 0.7326 (m-30) REVERT: B 368 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7541 (tt) REVERT: B 395 MET cc_start: 0.7255 (mmm) cc_final: 0.6852 (mmt) REVERT: B 423 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7467 (t70) REVERT: B 450 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.6076 (mpp) REVERT: B 469 VAL cc_start: 0.7767 (p) cc_final: 0.7416 (t) REVERT: C 104 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7323 (tt0) REVERT: C 187 TYR cc_start: 0.7241 (m-80) cc_final: 0.6787 (m-80) REVERT: C 332 ASP cc_start: 0.7667 (m-30) cc_final: 0.7329 (m-30) REVERT: C 368 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7430 (tt) REVERT: C 395 MET cc_start: 0.7210 (mmm) cc_final: 0.6831 (mmt) REVERT: C 450 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5726 (mmt) REVERT: C 469 VAL cc_start: 0.7770 (p) cc_final: 0.7417 (t) REVERT: D 104 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7273 (tt0) REVERT: D 332 ASP cc_start: 0.7636 (m-30) cc_final: 0.7294 (m-30) REVERT: D 368 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7484 (tt) REVERT: D 395 MET cc_start: 0.7206 (mmm) cc_final: 0.6848 (mmt) REVERT: D 450 MET cc_start: 0.6840 (mtm) cc_final: 0.6386 (mtt) REVERT: D 469 VAL cc_start: 0.7741 (p) cc_final: 0.7367 (t) outliers start: 64 outliers final: 36 residues processed: 209 average time/residue: 0.2694 time to fit residues: 83.6313 Evaluate side-chains 197 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain G residue 48 PHE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 6.9990 chunk 128 optimal weight: 0.0980 chunk 88 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 0.0050 chunk 162 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15652 Z= 0.176 Angle : 0.530 5.121 21192 Z= 0.285 Chirality : 0.042 0.156 2332 Planarity : 0.005 0.048 2700 Dihedral : 6.706 59.010 2177 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.67 % Allowed : 16.69 % Favored : 80.64 % 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: 0.54 (0.20), residues: 1876 helix: 1.26 (0.18), residues: 928 sheet: 0.66 (0.34), residues: 232 loop : -0.92 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 107 HIS 0.003 0.001 HIS D 451 PHE 0.009 0.001 PHE B 406 TYR 0.017 0.001 TYR B 447 ARG 0.006 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 162 time to evaluate : 1.816 Fit side-chains REVERT: A 104 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7305 (tt0) REVERT: A 218 ARG cc_start: 0.5744 (ptt180) cc_final: 0.5163 (ptt180) REVERT: A 332 ASP cc_start: 0.7575 (m-30) cc_final: 0.7300 (m-30) REVERT: A 368 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 395 MET cc_start: 0.7118 (mmm) cc_final: 0.6799 (mmt) REVERT: A 469 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7374 (t) REVERT: B 104 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7358 (tt0) REVERT: B 218 ARG cc_start: 0.5649 (ptt180) cc_final: 0.5083 (ptt180) REVERT: B 328 MET cc_start: 0.6339 (mtt) cc_final: 0.6108 (mtt) REVERT: B 332 ASP cc_start: 0.7540 (m-30) cc_final: 0.7267 (m-30) REVERT: B 368 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7503 (tt) REVERT: B 395 MET cc_start: 0.7170 (mmm) cc_final: 0.6832 (mmt) REVERT: B 423 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7421 (t70) REVERT: B 450 MET cc_start: 0.6026 (mmt) cc_final: 0.5638 (mmt) REVERT: B 469 VAL cc_start: 0.7762 (p) cc_final: 0.7417 (t) REVERT: C 104 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7400 (tt0) REVERT: C 218 ARG cc_start: 0.5668 (ptt180) cc_final: 0.5107 (ptt180) REVERT: C 328 MET cc_start: 0.6317 (mtt) cc_final: 0.6084 (mtt) REVERT: C 332 ASP cc_start: 0.7550 (m-30) cc_final: 0.7276 (m-30) REVERT: C 368 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7476 (tt) REVERT: C 395 MET cc_start: 0.7155 (mmm) cc_final: 0.6817 (mmt) REVERT: C 423 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7385 (t70) REVERT: C 450 MET cc_start: 0.5967 (mmt) cc_final: 0.5625 (mmt) REVERT: C 469 VAL cc_start: 0.7768 (p) cc_final: 0.7415 (t) REVERT: D 104 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7369 (tt0) REVERT: D 218 ARG cc_start: 0.5716 (ptt180) cc_final: 0.5159 (ptt180) REVERT: D 328 MET cc_start: 0.6305 (mtt) cc_final: 0.6058 (mtt) REVERT: D 332 ASP cc_start: 0.7545 (m-30) cc_final: 0.7266 (m-30) REVERT: D 368 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7501 (tt) REVERT: D 395 MET cc_start: 0.7097 (mmm) cc_final: 0.6778 (mmt) REVERT: D 450 MET cc_start: 0.6724 (mtm) cc_final: 0.6303 (mtt) REVERT: D 469 VAL cc_start: 0.7764 (p) cc_final: 0.7410 (t) outliers start: 44 outliers final: 27 residues processed: 194 average time/residue: 0.2729 time to fit residues: 78.5616 Evaluate side-chains 179 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.7980 chunk 103 optimal weight: 0.0980 chunk 2 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 155 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 163 optimal weight: 0.0060 chunk 45 optimal weight: 4.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN D 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15652 Z= 0.231 Angle : 0.548 4.964 21192 Z= 0.295 Chirality : 0.042 0.127 2332 Planarity : 0.005 0.047 2700 Dihedral : 6.199 59.815 2148 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.52 % Allowed : 16.50 % Favored : 79.98 % 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: 0.60 (0.20), residues: 1876 helix: 1.28 (0.18), residues: 932 sheet: 0.71 (0.33), residues: 232 loop : -0.87 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 107 HIS 0.003 0.001 HIS D 451 PHE 0.012 0.001 PHE A 406 TYR 0.018 0.001 TYR B 447 ARG 0.004 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 156 time to evaluate : 1.726 Fit side-chains REVERT: A 104 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7296 (tt0) REVERT: A 218 ARG cc_start: 0.5791 (ptt180) cc_final: 0.5226 (ptt180) REVERT: A 332 ASP cc_start: 0.7576 (m-30) cc_final: 0.7305 (m-30) REVERT: A 368 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7510 (tt) REVERT: A 395 MET cc_start: 0.7259 (mmm) cc_final: 0.6936 (mmt) REVERT: A 450 MET cc_start: 0.6555 (mtm) cc_final: 0.6232 (mtt) REVERT: A 469 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7398 (t) REVERT: B 104 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7358 (tt0) REVERT: B 218 ARG cc_start: 0.5666 (ptt180) cc_final: 0.5111 (ptt180) REVERT: B 332 ASP cc_start: 0.7556 (m-30) cc_final: 0.7285 (m-30) REVERT: B 368 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7572 (tt) REVERT: B 395 MET cc_start: 0.7287 (mmm) cc_final: 0.6963 (mmt) REVERT: B 469 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7467 (t) REVERT: C 104 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7448 (tt0) REVERT: C 218 ARG cc_start: 0.5794 (ptt180) cc_final: 0.5233 (ptt180) REVERT: C 332 ASP cc_start: 0.7572 (m-30) cc_final: 0.7302 (m-30) REVERT: C 368 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7509 (tt) REVERT: C 395 MET cc_start: 0.7260 (mmm) cc_final: 0.6943 (mmt) REVERT: C 423 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7360 (t70) REVERT: C 450 MET cc_start: 0.6079 (mmt) cc_final: 0.5725 (mmt) REVERT: C 469 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7457 (t) REVERT: D 104 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7392 (tt0) REVERT: D 218 ARG cc_start: 0.5787 (ptt180) cc_final: 0.5205 (ptt180) REVERT: D 332 ASP cc_start: 0.7559 (m-30) cc_final: 0.7287 (m-30) REVERT: D 368 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7516 (tt) REVERT: D 395 MET cc_start: 0.7262 (mmm) cc_final: 0.6895 (mmt) REVERT: D 450 MET cc_start: 0.6807 (mtm) cc_final: 0.6427 (mtt) REVERT: D 469 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7468 (t) outliers start: 58 outliers final: 43 residues processed: 197 average time/residue: 0.2927 time to fit residues: 86.3998 Evaluate side-chains 200 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 148 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 5.9990 chunk 163 optimal weight: 0.0040 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 60 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN F 33 ASN H 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15652 Z= 0.150 Angle : 0.498 4.835 21192 Z= 0.267 Chirality : 0.040 0.125 2332 Planarity : 0.005 0.045 2700 Dihedral : 6.066 58.971 2148 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.61 % Allowed : 17.29 % Favored : 80.10 % 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: 0.85 (0.20), residues: 1876 helix: 1.53 (0.18), residues: 928 sheet: 0.81 (0.33), residues: 240 loop : -0.81 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 99 HIS 0.003 0.001 HIS A 451 PHE 0.008 0.001 PHE A 406 TYR 0.014 0.001 TYR B 447 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 1.678 Fit side-chains REVERT: A 104 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7246 (tt0) REVERT: A 218 ARG cc_start: 0.5788 (ptt180) cc_final: 0.5221 (ptt180) REVERT: A 332 ASP cc_start: 0.7522 (m-30) cc_final: 0.7251 (m-30) REVERT: A 368 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7526 (tt) REVERT: A 395 MET cc_start: 0.7030 (mmm) cc_final: 0.6787 (mmt) REVERT: A 450 MET cc_start: 0.6475 (mtm) cc_final: 0.6217 (mtt) REVERT: A 469 VAL cc_start: 0.7747 (p) cc_final: 0.7396 (t) REVERT: B 104 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7307 (tt0) REVERT: B 119 LEU cc_start: 0.8528 (mt) cc_final: 0.8243 (mt) REVERT: B 218 ARG cc_start: 0.5789 (ptt180) cc_final: 0.5216 (ptt180) REVERT: B 332 ASP cc_start: 0.7541 (m-30) cc_final: 0.7265 (m-30) REVERT: B 368 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7485 (tt) REVERT: B 395 MET cc_start: 0.7044 (mmm) cc_final: 0.6800 (mmt) REVERT: B 450 MET cc_start: 0.6429 (mtm) cc_final: 0.6060 (mtt) REVERT: B 469 VAL cc_start: 0.7774 (p) cc_final: 0.7427 (t) REVERT: C 104 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7405 (tt0) REVERT: C 218 ARG cc_start: 0.5804 (ptt180) cc_final: 0.5199 (ptt180) REVERT: C 332 ASP cc_start: 0.7546 (m-30) cc_final: 0.7271 (m-30) REVERT: C 368 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7456 (tt) REVERT: C 395 MET cc_start: 0.7035 (mmm) cc_final: 0.6792 (mmt) REVERT: C 450 MET cc_start: 0.5914 (mmt) cc_final: 0.5591 (mmt) REVERT: C 469 VAL cc_start: 0.7772 (p) cc_final: 0.7423 (t) REVERT: D 104 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7381 (tt0) REVERT: D 218 ARG cc_start: 0.5788 (ptt180) cc_final: 0.5186 (ptt180) REVERT: D 332 ASP cc_start: 0.7543 (m-30) cc_final: 0.7264 (m-30) REVERT: D 368 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7477 (tt) REVERT: D 395 MET cc_start: 0.7080 (mmm) cc_final: 0.6810 (mmt) REVERT: D 450 MET cc_start: 0.6533 (mtm) cc_final: 0.6169 (mtt) REVERT: D 469 VAL cc_start: 0.7777 (p) cc_final: 0.7426 (t) outliers start: 43 outliers final: 32 residues processed: 182 average time/residue: 0.2588 time to fit residues: 70.8692 Evaluate side-chains 177 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.0040 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 0.0270 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN F 33 ASN C 164 GLN D 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15652 Z= 0.140 Angle : 0.484 4.792 21192 Z= 0.259 Chirality : 0.040 0.120 2332 Planarity : 0.004 0.045 2700 Dihedral : 5.953 59.381 2148 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.37 % Allowed : 17.96 % Favored : 79.67 % 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: 1.00 (0.20), residues: 1876 helix: 1.61 (0.18), residues: 932 sheet: 0.82 (0.33), residues: 244 loop : -0.65 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 107 HIS 0.004 0.001 HIS D 451 PHE 0.007 0.001 PHE A 406 TYR 0.016 0.001 TYR B 447 ARG 0.003 0.000 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 1.528 Fit side-chains REVERT: A 104 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7245 (tt0) REVERT: A 119 LEU cc_start: 0.8462 (mt) cc_final: 0.8227 (mt) REVERT: A 218 ARG cc_start: 0.5818 (ptt180) cc_final: 0.5212 (ptt180) REVERT: A 332 ASP cc_start: 0.7531 (m-30) cc_final: 0.7286 (m-30) REVERT: A 368 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7540 (tt) REVERT: A 450 MET cc_start: 0.6381 (mtm) cc_final: 0.6170 (mtt) REVERT: A 469 VAL cc_start: 0.7745 (p) cc_final: 0.7403 (t) REVERT: B 104 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7319 (tt0) REVERT: B 218 ARG cc_start: 0.5756 (ptt180) cc_final: 0.5150 (ptt180) REVERT: B 262 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: B 332 ASP cc_start: 0.7501 (m-30) cc_final: 0.7263 (m-30) REVERT: B 368 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7489 (tt) REVERT: B 395 MET cc_start: 0.6954 (mmm) cc_final: 0.6739 (mmt) REVERT: B 469 VAL cc_start: 0.7742 (p) cc_final: 0.7401 (t) REVERT: C 104 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7426 (tt0) REVERT: C 218 ARG cc_start: 0.5821 (ptt180) cc_final: 0.5209 (ptt180) REVERT: C 262 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: C 332 ASP cc_start: 0.7503 (m-30) cc_final: 0.7267 (m-30) REVERT: C 368 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7470 (tt) REVERT: C 450 MET cc_start: 0.5836 (mmt) cc_final: 0.5633 (mmt) REVERT: C 469 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7406 (t) REVERT: D 104 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7332 (tt0) REVERT: D 119 LEU cc_start: 0.8459 (mt) cc_final: 0.8244 (mt) REVERT: D 218 ARG cc_start: 0.5809 (ptt180) cc_final: 0.5191 (ptt180) REVERT: D 332 ASP cc_start: 0.7496 (m-30) cc_final: 0.7257 (m-30) REVERT: D 368 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7471 (tt) REVERT: D 469 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7406 (t) outliers start: 39 outliers final: 28 residues processed: 170 average time/residue: 0.2682 time to fit residues: 68.1381 Evaluate side-chains 175 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 123 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN C 164 GLN D 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15652 Z= 0.189 Angle : 0.509 9.150 21192 Z= 0.271 Chirality : 0.041 0.122 2332 Planarity : 0.005 0.046 2700 Dihedral : 5.961 59.836 2148 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.67 % Allowed : 17.84 % Favored : 79.49 % 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: 1876 helix: 1.53 (0.18), residues: 936 sheet: 0.69 (0.33), residues: 252 loop : -0.61 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 99 HIS 0.004 0.001 HIS D 451 PHE 0.010 0.001 PHE B 406 TYR 0.014 0.001 TYR B 447 ARG 0.002 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 1.706 Fit side-chains REVERT: A 104 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7276 (tt0) REVERT: A 218 ARG cc_start: 0.5825 (ptt180) cc_final: 0.5211 (ptt180) REVERT: A 332 ASP cc_start: 0.7526 (m-30) cc_final: 0.7261 (m-30) REVERT: A 368 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7499 (tt) REVERT: A 450 MET cc_start: 0.6505 (mtm) cc_final: 0.6265 (mtt) REVERT: A 469 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7420 (t) REVERT: B 104 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7284 (tt0) REVERT: B 218 ARG cc_start: 0.5766 (ptt180) cc_final: 0.5160 (ptt180) REVERT: B 262 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7153 (pm20) REVERT: B 332 ASP cc_start: 0.7514 (m-30) cc_final: 0.7256 (m-30) REVERT: B 368 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7538 (tt) REVERT: B 469 VAL cc_start: 0.7819 (p) cc_final: 0.7427 (t) REVERT: C 104 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7418 (tt0) REVERT: C 218 ARG cc_start: 0.5828 (ptt180) cc_final: 0.5225 (ptt180) REVERT: C 262 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: C 332 ASP cc_start: 0.7529 (m-30) cc_final: 0.7272 (m-30) REVERT: C 368 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7498 (tt) REVERT: C 469 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7460 (t) REVERT: D 104 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7317 (tt0) REVERT: D 119 LEU cc_start: 0.8385 (mt) cc_final: 0.8150 (mt) REVERT: D 218 ARG cc_start: 0.5814 (ptt180) cc_final: 0.5209 (ptt180) REVERT: D 332 ASP cc_start: 0.7519 (m-30) cc_final: 0.7257 (m-30) REVERT: D 368 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7508 (tt) REVERT: D 469 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7463 (t) outliers start: 44 outliers final: 34 residues processed: 175 average time/residue: 0.2593 time to fit residues: 68.2635 Evaluate side-chains 182 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 139 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 101 optimal weight: 0.0030 chunk 73 optimal weight: 0.0050 chunk 132 optimal weight: 0.0870 chunk 51 optimal weight: 0.4980 chunk 152 optimal weight: 0.0870 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 178 optimal weight: 0.7980 overall best weight: 0.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN B 164 GLN D 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15652 Z= 0.120 Angle : 0.472 7.897 21192 Z= 0.249 Chirality : 0.039 0.124 2332 Planarity : 0.004 0.045 2700 Dihedral : 5.791 59.568 2148 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.70 % Allowed : 18.93 % Favored : 79.37 % 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: 1.13 (0.20), residues: 1876 helix: 1.75 (0.18), residues: 932 sheet: 0.38 (0.32), residues: 272 loop : -0.47 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 107 HIS 0.007 0.001 HIS B 451 PHE 0.006 0.001 PHE C 412 TYR 0.012 0.001 TYR D 447 ARG 0.003 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.598 Fit side-chains REVERT: A 104 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7241 (tt0) REVERT: A 218 ARG cc_start: 0.5816 (ptt180) cc_final: 0.5222 (ptt180) REVERT: A 332 ASP cc_start: 0.7386 (m-30) cc_final: 0.7120 (m-30) REVERT: A 368 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7512 (tt) REVERT: A 469 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7384 (t) REVERT: A 490 GLU cc_start: 0.5562 (pp20) cc_final: 0.5149 (mm-30) REVERT: B 104 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7343 (tt0) REVERT: B 218 ARG cc_start: 0.5778 (ptt180) cc_final: 0.5191 (ptt180) REVERT: B 332 ASP cc_start: 0.7373 (m-30) cc_final: 0.7110 (m-30) REVERT: B 368 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7536 (tt) REVERT: B 469 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7415 (t) REVERT: B 490 GLU cc_start: 0.5408 (pp20) cc_final: 0.5043 (mm-30) REVERT: C 104 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7376 (tt0) REVERT: C 119 LEU cc_start: 0.8530 (tp) cc_final: 0.8328 (mt) REVERT: C 218 ARG cc_start: 0.5753 (ptt180) cc_final: 0.5166 (ptt180) REVERT: C 332 ASP cc_start: 0.7371 (m-30) cc_final: 0.7111 (m-30) REVERT: C 368 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7488 (tt) REVERT: C 469 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7405 (t) REVERT: C 490 GLU cc_start: 0.5404 (pp20) cc_final: 0.5040 (mm-30) REVERT: D 104 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7348 (tt0) REVERT: D 218 ARG cc_start: 0.5809 (ptt180) cc_final: 0.5221 (ptt180) REVERT: D 332 ASP cc_start: 0.7379 (m-30) cc_final: 0.7120 (m-30) REVERT: D 368 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7502 (tt) REVERT: D 469 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7403 (t) REVERT: D 490 GLU cc_start: 0.5372 (pp20) cc_final: 0.5038 (mm-30) outliers start: 28 outliers final: 15 residues processed: 161 average time/residue: 0.2657 time to fit residues: 63.7152 Evaluate side-chains 163 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 158 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN B 164 GLN C 164 GLN D 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15652 Z= 0.193 Angle : 0.513 9.237 21192 Z= 0.269 Chirality : 0.041 0.123 2332 Planarity : 0.005 0.046 2700 Dihedral : 5.764 59.965 2144 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.46 % Allowed : 18.87 % Favored : 79.67 % 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: 1.09 (0.21), residues: 1876 helix: 1.68 (0.18), residues: 932 sheet: 0.48 (0.32), residues: 272 loop : -0.48 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 107 HIS 0.006 0.001 HIS A 451 PHE 0.010 0.001 PHE B 406 TYR 0.015 0.001 TYR D 447 ARG 0.003 0.000 ARG H 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 2.058 Fit side-chains REVERT: A 104 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7228 (tt0) REVERT: A 218 ARG cc_start: 0.5783 (ptt180) cc_final: 0.5181 (ptt180) REVERT: A 332 ASP cc_start: 0.7444 (m-30) cc_final: 0.7192 (m-30) REVERT: A 368 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7511 (tt) REVERT: A 469 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7410 (t) REVERT: H 54 MET cc_start: 0.6956 (ptm) cc_final: 0.6558 (ptm) REVERT: B 104 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7240 (tt0) REVERT: B 218 ARG cc_start: 0.5791 (ptt180) cc_final: 0.5204 (ptt180) REVERT: B 332 ASP cc_start: 0.7431 (m-30) cc_final: 0.7183 (m-30) REVERT: B 368 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7483 (tt) REVERT: B 469 VAL cc_start: 0.7802 (p) cc_final: 0.7445 (t) REVERT: B 490 GLU cc_start: 0.5388 (pp20) cc_final: 0.5049 (mm-30) REVERT: C 104 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7395 (tt0) REVERT: C 218 ARG cc_start: 0.5782 (ptt180) cc_final: 0.5174 (ptt180) REVERT: C 332 ASP cc_start: 0.7436 (m-30) cc_final: 0.7190 (m-30) REVERT: C 368 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7450 (tt) REVERT: C 469 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7416 (t) REVERT: C 490 GLU cc_start: 0.5387 (pp20) cc_final: 0.5047 (mm-30) REVERT: D 104 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7342 (tt0) REVERT: D 218 ARG cc_start: 0.5838 (ptt180) cc_final: 0.5229 (ptt180) REVERT: D 332 ASP cc_start: 0.7441 (m-30) cc_final: 0.7190 (m-30) REVERT: D 368 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7491 (tt) REVERT: D 469 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7427 (t) REVERT: D 490 GLU cc_start: 0.5433 (pp20) cc_final: 0.5086 (mm-30) outliers start: 24 outliers final: 15 residues processed: 154 average time/residue: 0.2899 time to fit residues: 67.2258 Evaluate side-chains 157 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 3.9990 chunk 137 optimal weight: 0.0970 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN B 164 GLN C 164 GLN D 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.213842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.187045 restraints weight = 17567.715| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.30 r_work: 0.3733 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15652 Z= 0.168 Angle : 0.502 8.080 21192 Z= 0.264 Chirality : 0.041 0.122 2332 Planarity : 0.004 0.045 2700 Dihedral : 5.705 59.929 2142 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.52 % Allowed : 18.99 % Favored : 79.49 % 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: 1.15 (0.20), residues: 1876 helix: 1.73 (0.18), residues: 932 sheet: 0.80 (0.33), residues: 252 loop : -0.55 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 107 HIS 0.004 0.001 HIS B 451 PHE 0.009 0.001 PHE B 406 TYR 0.014 0.001 TYR D 447 ARG 0.003 0.000 ARG B 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.91 seconds wall clock time: 59 minutes 13.56 seconds (3553.56 seconds total)