Starting phenix.real_space_refine on Wed Jul 30 01:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wr4_21876/07_2025/6wr4_21876.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wr4_21876/07_2025/6wr4_21876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wr4_21876/07_2025/6wr4_21876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wr4_21876/07_2025/6wr4_21876.map" model { file = "/net/cci-nas-00/data/ceres_data/6wr4_21876/07_2025/6wr4_21876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wr4_21876/07_2025/6wr4_21876.cif" } resolution = 2.9 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= 0.009 sd= 0.160 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7896 2.51 5 N 1941 2.21 5 O 2037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11934 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3862 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 452} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Restraints were copied for chains: C, B Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1 LMN A 901 " occ=0.50 ... (67 atoms not shown) pdb=" OCB LMN A 901 " occ=0.50 residue: pdb=" C1 LMN A 902 " occ=0.50 ... (45 atoms not shown) pdb=" OBY LMN A 902 " occ=0.50 residue: pdb=" C1 LMN B 901 " occ=0.50 ... (67 atoms not shown) pdb=" OCB LMN B 901 " occ=0.50 residue: pdb=" C1 LMN B 902 " occ=0.50 ... (45 atoms not shown) pdb=" OBY LMN B 902 " occ=0.50 residue: pdb=" C1 LMN C 901 " occ=0.50 ... (67 atoms not shown) pdb=" OCB LMN C 901 " occ=0.50 residue: pdb=" C1 LMN C 902 " occ=0.50 ... (45 atoms not shown) pdb=" OBY LMN C 902 " occ=0.50 Time building chain proxies: 8.78, per 1000 atoms: 0.74 Number of scatterers: 11934 At special positions: 0 Unit cell: (132.5, 124.02, 85.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2037 8.00 N 1941 7.00 C 7896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 6 sheets defined 69.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.671A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 86 removed outlier: 3.649A pdb=" N PHE A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 removed outlier: 3.530A pdb=" N LEU A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 129 through 167 removed outlier: 3.886A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.532A pdb=" N ALA A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 225 removed outlier: 4.044A pdb=" N MET A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.821A pdb=" N ASN A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.554A pdb=" N LYS A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 275' Processing helix chain 'A' and resid 279 through 300 removed outlier: 3.830A pdb=" N LEU A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 323 removed outlier: 3.569A pdb=" N TRP A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 346 through 355 removed outlier: 3.580A pdb=" N GLN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 365 removed outlier: 3.820A pdb=" N LYS A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 369 removed outlier: 4.030A pdb=" N LEU A 369 " --> pdb=" O ASN A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 370 through 399 removed outlier: 3.541A pdb=" N PHE A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 425 Processing helix chain 'A' and resid 437 through 445 removed outlier: 3.751A pdb=" N ALA A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.942A pdb=" N LEU A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 481 removed outlier: 3.603A pdb=" N PHE A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 492 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 508 Processing helix chain 'B' and resid 42 through 56 removed outlier: 3.671A pdb=" N PHE B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 86 removed outlier: 3.649A pdb=" N PHE B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 removed outlier: 3.529A pdb=" N LEU B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 129 through 167 removed outlier: 3.886A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.531A pdb=" N ALA B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 225 removed outlier: 4.043A pdb=" N MET B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.821A pdb=" N ASN B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.555A pdb=" N LYS B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 279 through 300 removed outlier: 3.831A pdb=" N LEU B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 323 removed outlier: 3.568A pdb=" N TRP B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.580A pdb=" N GLN B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 365 removed outlier: 3.820A pdb=" N LYS B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 369 removed outlier: 4.031A pdb=" N LEU B 369 " --> pdb=" O ASN B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 370 through 399 removed outlier: 3.541A pdb=" N PHE B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 387 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 425 Processing helix chain 'B' and resid 437 through 445 removed outlier: 3.752A pdb=" N ALA B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.942A pdb=" N LEU B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 removed outlier: 3.603A pdb=" N PHE B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 492 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 497 through 508 Processing helix chain 'C' and resid 42 through 56 removed outlier: 3.671A pdb=" N PHE C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 86 removed outlier: 3.650A pdb=" N PHE C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 94 removed outlier: 3.528A pdb=" N LEU C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 129 through 167 removed outlier: 3.887A pdb=" N GLU C 159 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 165 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.531A pdb=" N ALA C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 225 removed outlier: 4.043A pdb=" N MET C 219 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.822A pdb=" N ASN C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.554A pdb=" N LYS C 274 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 271 through 275' Processing helix chain 'C' and resid 279 through 300 removed outlier: 3.831A pdb=" N LEU C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU C 291 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 323 removed outlier: 3.568A pdb=" N TRP C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 Processing helix chain 'C' and resid 346 through 355 removed outlier: 3.580A pdb=" N GLN C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 365 removed outlier: 3.819A pdb=" N LYS C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 369 removed outlier: 4.029A pdb=" N LEU C 369 " --> pdb=" O ASN C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 370 through 399 removed outlier: 3.541A pdb=" N PHE C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 387 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 Processing helix chain 'C' and resid 437 through 445 removed outlier: 3.752A pdb=" N ALA C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.942A pdb=" N LEU C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 481 removed outlier: 3.603A pdb=" N PHE C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 492 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 497 through 508 Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 234 removed outlier: 3.532A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.533A pdb=" N GLY B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'C' and resid 231 through 234 removed outlier: 3.532A pdb=" N GLY C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 510 through 512 597 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3471 1.34 - 1.46: 2483 1.46 - 1.58: 6173 1.58 - 1.69: 62 1.69 - 1.81: 78 Bond restraints: 12267 Sorted by residual: bond pdb=" C1 LMN A 902 " pdb=" O5 LMN A 902 " ideal model delta sigma weight residual 1.403 1.562 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" C1 LMN C 902 " pdb=" O5 LMN C 902 " ideal model delta sigma weight residual 1.403 1.562 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" C1 LMN B 902 " pdb=" O5 LMN B 902 " ideal model delta sigma weight residual 1.403 1.561 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C1 LMN A 901 " pdb=" O5 LMN A 901 " ideal model delta sigma weight residual 1.403 1.551 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C1 LMN C 901 " pdb=" O5 LMN C 901 " ideal model delta sigma weight residual 1.403 1.551 -0.148 2.00e-02 2.50e+03 5.48e+01 ... (remaining 12262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 15152 2.19 - 4.38: 1166 4.38 - 6.57: 245 6.57 - 8.76: 75 8.76 - 10.96: 18 Bond angle restraints: 16656 Sorted by residual: angle pdb=" N THR C 461 " pdb=" CA THR C 461 " pdb=" C THR C 461 " ideal model delta sigma weight residual 114.75 106.70 8.05 1.26e+00 6.30e-01 4.08e+01 angle pdb=" N THR B 461 " pdb=" CA THR B 461 " pdb=" C THR B 461 " ideal model delta sigma weight residual 114.75 106.72 8.03 1.26e+00 6.30e-01 4.07e+01 angle pdb=" N THR A 461 " pdb=" CA THR A 461 " pdb=" C THR A 461 " ideal model delta sigma weight residual 114.75 106.75 8.00 1.26e+00 6.30e-01 4.03e+01 angle pdb=" C LEU A 203 " pdb=" N THR A 204 " pdb=" CA THR A 204 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C LEU C 203 " pdb=" N THR C 204 " pdb=" CA THR C 204 " ideal model delta sigma weight residual 121.54 131.45 -9.91 1.91e+00 2.74e-01 2.69e+01 ... (remaining 16651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 6954 24.18 - 48.36: 387 48.36 - 72.54: 84 72.54 - 96.72: 57 96.72 - 120.90: 51 Dihedral angle restraints: 7533 sinusoidal: 3387 harmonic: 4146 Sorted by residual: dihedral pdb=" CA PRO B 36 " pdb=" C PRO B 36 " pdb=" N TRP B 37 " pdb=" CA TRP B 37 " ideal model delta harmonic sigma weight residual -180.00 -138.41 -41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" CA PRO C 36 " pdb=" C PRO C 36 " pdb=" N TRP C 37 " pdb=" CA TRP C 37 " ideal model delta harmonic sigma weight residual -180.00 -138.42 -41.58 0 5.00e+00 4.00e-02 6.91e+01 dihedral pdb=" CA GLN C 436 " pdb=" C GLN C 436 " pdb=" N LEU C 437 " pdb=" CA LEU C 437 " ideal model delta harmonic sigma weight residual 180.00 138.43 41.57 0 5.00e+00 4.00e-02 6.91e+01 ... (remaining 7530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1658 0.096 - 0.191: 223 0.191 - 0.287: 12 0.287 - 0.382: 12 0.382 - 0.478: 3 Chirality restraints: 1908 Sorted by residual: chirality pdb=" CA ARG C 279 " pdb=" N ARG C 279 " pdb=" C ARG C 279 " pdb=" CB ARG C 279 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA ARG B 279 " pdb=" N ARG B 279 " pdb=" C ARG B 279 " pdb=" CB ARG B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA ARG A 279 " pdb=" N ARG A 279 " pdb=" C ARG A 279 " pdb=" CB ARG A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 1905 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 448 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO C 449 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 449 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 449 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 448 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO B 449 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 448 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO A 449 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " 0.035 5.00e-02 4.00e+02 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3124 2.80 - 3.32: 10383 3.32 - 3.85: 19091 3.85 - 4.37: 23463 4.37 - 4.90: 38289 Nonbonded interactions: 94350 Sorted by model distance: nonbonded pdb=" OG SER B 261 " pdb=" O LEU B 262 " model vdw 2.272 3.040 nonbonded pdb=" OG SER C 261 " pdb=" O LEU C 262 " model vdw 2.272 3.040 nonbonded pdb=" OG SER A 261 " pdb=" O LEU A 262 " model vdw 2.272 3.040 nonbonded pdb=" O ILE C 254 " pdb=" NH1 ARG C 289 " model vdw 2.298 3.120 nonbonded pdb=" O ILE B 254 " pdb=" NH1 ARG B 289 " model vdw 2.298 3.120 ... (remaining 94345 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 30.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.570 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:133.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.012 0.159 12267 Z= 0.558 Angle : 1.398 10.956 16656 Z= 0.735 Chirality : 0.070 0.478 1908 Planarity : 0.007 0.065 2013 Dihedral : 20.663 120.896 4845 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.17 % Favored : 94.40 % Rotamer: Outliers : 5.53 % Allowed : 2.64 % Favored : 91.83 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -6.12 (0.14), residues: 1392 helix: -4.16 (0.08), residues: 921 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 257 HIS 0.011 0.002 HIS C 406 PHE 0.034 0.003 PHE A 243 TYR 0.020 0.003 TYR B 218 ARG 0.027 0.002 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.30275 ( 597) hydrogen bonds : angle 10.16717 ( 1755) covalent geometry : bond 0.01174 (12267) covalent geometry : angle 1.39823 (16656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 1.503 Fit side-chains REVERT: A 172 MET cc_start: 0.6909 (mmp) cc_final: 0.6696 (mmt) REVERT: A 245 ARG cc_start: 0.7000 (ttt-90) cc_final: 0.6784 (ttt180) REVERT: A 448 MET cc_start: 0.6421 (mmt) cc_final: 0.5882 (mmt) REVERT: B 504 PHE cc_start: 0.7359 (t80) cc_final: 0.7081 (t80) REVERT: C 245 ARG cc_start: 0.6834 (ttt-90) cc_final: 0.6544 (ttt180) outliers start: 69 outliers final: 4 residues processed: 312 average time/residue: 1.6532 time to fit residues: 559.5653 Evaluate side-chains 153 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 288 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 217 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 348 HIS A 428 GLN A 451 HIS A 457 HIS B 191 GLN B 217 ASN ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 348 HIS ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 455 ASN B 457 HIS C 57 ASN C 191 GLN C 217 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN C 348 HIS ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 457 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.184806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.157958 restraints weight = 13436.075| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.10 r_work: 0.3512 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12267 Z= 0.154 Angle : 0.814 8.334 16656 Z= 0.400 Chirality : 0.047 0.230 1908 Planarity : 0.006 0.058 2013 Dihedral : 18.551 105.877 2153 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.96 % Allowed : 10.18 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -3.56 (0.19), residues: 1392 helix: -1.83 (0.15), residues: 939 sheet: -4.53 (0.56), residues: 30 loop : -3.09 (0.24), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 180 HIS 0.005 0.001 HIS B 406 PHE 0.014 0.001 PHE A 79 TYR 0.016 0.001 TYR A 177 ARG 0.005 0.001 ARG B 353 Details of bonding type rmsd hydrogen bonds : bond 0.05657 ( 597) hydrogen bonds : angle 4.96530 ( 1755) covalent geometry : bond 0.00322 (12267) covalent geometry : angle 0.81421 (16656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 1.193 Fit side-chains REVERT: A 43 LEU cc_start: 0.7988 (mt) cc_final: 0.7689 (tp) REVERT: A 292 TRP cc_start: 0.6891 (m100) cc_final: 0.6426 (m-10) REVERT: B 292 TRP cc_start: 0.7114 (m100) cc_final: 0.6679 (m-10) REVERT: B 422 ARG cc_start: 0.7825 (mmt-90) cc_final: 0.7601 (mmt180) REVERT: C 292 TRP cc_start: 0.6983 (m100) cc_final: 0.6527 (m-10) outliers start: 37 outliers final: 11 residues processed: 198 average time/residue: 1.0463 time to fit residues: 227.9310 Evaluate side-chains 136 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PRO Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 36 PRO Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 36 PRO Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 124 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 250 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN B 57 ASN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.184841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.157396 restraints weight = 13511.586| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.18 r_work: 0.3585 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12267 Z= 0.131 Angle : 0.712 8.112 16656 Z= 0.348 Chirality : 0.047 0.350 1908 Planarity : 0.004 0.049 2013 Dihedral : 13.697 75.170 2145 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.96 % Allowed : 14.34 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.21), residues: 1392 helix: -0.55 (0.17), residues: 912 sheet: -4.22 (0.63), residues: 30 loop : -2.91 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 180 HIS 0.005 0.001 HIS B 406 PHE 0.012 0.001 PHE C 79 TYR 0.017 0.001 TYR A 177 ARG 0.007 0.001 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 597) hydrogen bonds : angle 4.43936 ( 1755) covalent geometry : bond 0.00281 (12267) covalent geometry : angle 0.71225 (16656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.311 Fit side-chains REVERT: A 43 LEU cc_start: 0.8057 (mt) cc_final: 0.7770 (tp) REVERT: A 69 GLU cc_start: 0.7966 (mp0) cc_final: 0.7440 (mp0) REVERT: A 292 TRP cc_start: 0.6831 (m100) cc_final: 0.6377 (m-10) REVERT: B 69 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: B 292 TRP cc_start: 0.6843 (m100) cc_final: 0.6342 (m-10) REVERT: B 477 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7516 (tp) REVERT: C 69 GLU cc_start: 0.8146 (mp0) cc_final: 0.7347 (mp0) REVERT: C 291 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7107 (tp) REVERT: C 292 TRP cc_start: 0.6861 (m100) cc_final: 0.6455 (m-10) outliers start: 37 outliers final: 14 residues processed: 172 average time/residue: 0.8740 time to fit residues: 168.4598 Evaluate side-chains 146 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PRO Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 36 PRO Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 36 PRO Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 0.0070 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 406 HIS ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.184397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.155684 restraints weight = 13548.735| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.30 r_work: 0.3629 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12267 Z= 0.121 Angle : 0.663 7.784 16656 Z= 0.324 Chirality : 0.045 0.333 1908 Planarity : 0.004 0.050 2013 Dihedral : 12.331 71.036 2145 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.21 % Allowed : 15.30 % Favored : 81.49 % 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: -1.56 (0.22), residues: 1392 helix: -0.12 (0.17), residues: 924 sheet: -4.00 (0.68), residues: 30 loop : -2.71 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 180 HIS 0.005 0.001 HIS B 406 PHE 0.010 0.001 PHE B 298 TYR 0.013 0.001 TYR A 177 ARG 0.004 0.001 ARG C 353 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 597) hydrogen bonds : angle 4.29182 ( 1755) covalent geometry : bond 0.00264 (12267) covalent geometry : angle 0.66256 (16656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 1.297 Fit side-chains REVERT: A 43 LEU cc_start: 0.8063 (mt) cc_final: 0.7790 (tp) REVERT: A 69 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: A 292 TRP cc_start: 0.6844 (m100) cc_final: 0.6309 (m-10) REVERT: B 69 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: B 245 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7101 (mtp85) REVERT: B 266 GLU cc_start: 0.7316 (tt0) cc_final: 0.6988 (tp30) REVERT: B 292 TRP cc_start: 0.6875 (m100) cc_final: 0.6353 (m-10) REVERT: B 477 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7411 (tp) REVERT: C 69 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: C 292 TRP cc_start: 0.6789 (m100) cc_final: 0.6349 (m-10) outliers start: 40 outliers final: 15 residues processed: 178 average time/residue: 1.0105 time to fit residues: 204.8539 Evaluate side-chains 152 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 117 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.183110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.154307 restraints weight = 13448.030| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.32 r_work: 0.3527 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12267 Z= 0.127 Angle : 0.660 7.593 16656 Z= 0.323 Chirality : 0.045 0.303 1908 Planarity : 0.004 0.052 2013 Dihedral : 11.359 67.180 2145 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 3.04 % Allowed : 16.51 % Favored : 80.45 % 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: -1.22 (0.22), residues: 1392 helix: 0.13 (0.18), residues: 924 sheet: -4.07 (0.66), residues: 30 loop : -2.53 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 180 HIS 0.005 0.001 HIS B 348 PHE 0.010 0.001 PHE A 79 TYR 0.014 0.001 TYR C 177 ARG 0.004 0.000 ARG C 353 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 597) hydrogen bonds : angle 4.24938 ( 1755) covalent geometry : bond 0.00282 (12267) covalent geometry : angle 0.66044 (16656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 1.309 Fit side-chains REVERT: A 43 LEU cc_start: 0.8057 (mt) cc_final: 0.7807 (tp) REVERT: A 69 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: A 128 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6162 (pm20) REVERT: A 292 TRP cc_start: 0.6911 (m100) cc_final: 0.6363 (m-10) REVERT: B 69 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: B 245 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7190 (mtp85) REVERT: B 266 GLU cc_start: 0.7370 (tt0) cc_final: 0.7002 (tp30) REVERT: B 292 TRP cc_start: 0.6974 (m100) cc_final: 0.6392 (m-10) REVERT: B 477 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7382 (tp) REVERT: C 69 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: C 128 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: C 292 TRP cc_start: 0.6945 (m100) cc_final: 0.6382 (m-10) outliers start: 38 outliers final: 16 residues processed: 163 average time/residue: 0.9178 time to fit residues: 166.7721 Evaluate side-chains 154 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 21 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 355 ASN B 429 HIS C 355 ASN C 455 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.178591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149309 restraints weight = 13626.243| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.28 r_work: 0.3437 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12267 Z= 0.181 Angle : 0.734 7.031 16656 Z= 0.358 Chirality : 0.048 0.273 1908 Planarity : 0.004 0.051 2013 Dihedral : 11.228 70.064 2145 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.37 % Allowed : 16.83 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.22), residues: 1392 helix: -0.05 (0.17), residues: 942 sheet: -4.15 (0.63), residues: 30 loop : -2.50 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 180 HIS 0.006 0.001 HIS B 348 PHE 0.022 0.002 PHE C 298 TYR 0.017 0.002 TYR C 177 ARG 0.006 0.001 ARG C 341 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 597) hydrogen bonds : angle 4.43151 ( 1755) covalent geometry : bond 0.00432 (12267) covalent geometry : angle 0.73438 (16656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.253 Fit side-chains REVERT: A 43 LEU cc_start: 0.8351 (mt) cc_final: 0.8091 (tp) REVERT: A 69 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: A 128 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6131 (pm20) REVERT: A 239 GLU cc_start: 0.7608 (tt0) cc_final: 0.7379 (tt0) REVERT: A 292 TRP cc_start: 0.7177 (m100) cc_final: 0.6521 (m-10) REVERT: B 69 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: B 128 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: B 266 GLU cc_start: 0.7440 (tt0) cc_final: 0.7069 (tp30) REVERT: B 439 ARG cc_start: 0.7724 (ptp90) cc_final: 0.7404 (ptm-80) REVERT: B 477 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7459 (tp) REVERT: C 69 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: C 128 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: C 291 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6977 (tp) REVERT: C 292 TRP cc_start: 0.7118 (m100) cc_final: 0.6411 (m-10) REVERT: C 508 PHE cc_start: 0.7511 (m-80) cc_final: 0.7242 (m-80) outliers start: 42 outliers final: 22 residues processed: 166 average time/residue: 1.0225 time to fit residues: 187.4453 Evaluate side-chains 153 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PRO Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 36 PRO Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 121 optimal weight: 0.0000 chunk 85 optimal weight: 7.9990 chunk 7 optimal weight: 0.0570 chunk 140 optimal weight: 0.0040 chunk 10 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 overall best weight: 0.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.185915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.158491 restraints weight = 13528.398| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.16 r_work: 0.3574 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12267 Z= 0.109 Angle : 0.608 8.473 16656 Z= 0.302 Chirality : 0.041 0.180 1908 Planarity : 0.004 0.048 2013 Dihedral : 10.813 66.399 2145 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.48 % Allowed : 18.27 % Favored : 79.25 % 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: -0.78 (0.22), residues: 1392 helix: 0.45 (0.17), residues: 924 sheet: -4.12 (0.66), residues: 30 loop : -2.32 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 180 HIS 0.004 0.001 HIS B 444 PHE 0.025 0.001 PHE C 298 TYR 0.012 0.001 TYR C 177 ARG 0.006 0.000 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 597) hydrogen bonds : angle 4.14139 ( 1755) covalent geometry : bond 0.00227 (12267) covalent geometry : angle 0.60807 (16656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.269 Fit side-chains REVERT: A 69 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: A 128 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6149 (pm20) REVERT: A 159 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8221 (tm-30) REVERT: A 292 TRP cc_start: 0.7001 (m100) cc_final: 0.6375 (m-10) REVERT: B 69 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: B 128 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.5454 (pm20) REVERT: B 266 GLU cc_start: 0.7341 (tt0) cc_final: 0.7024 (tp30) REVERT: B 422 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.7428 (mmt180) REVERT: B 477 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7459 (tp) REVERT: C 69 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: C 159 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8252 (tm-30) REVERT: C 203 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.2035 (mt) REVERT: C 292 TRP cc_start: 0.6967 (m100) cc_final: 0.6353 (m-10) outliers start: 31 outliers final: 9 residues processed: 163 average time/residue: 0.8565 time to fit residues: 156.6122 Evaluate side-chains 141 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.185470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.158084 restraints weight = 13620.117| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.12 r_work: 0.3572 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12267 Z= 0.115 Angle : 0.622 6.593 16656 Z= 0.306 Chirality : 0.043 0.182 1908 Planarity : 0.004 0.043 2013 Dihedral : 10.731 69.948 2145 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.40 % Allowed : 18.91 % Favored : 78.69 % 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: -0.55 (0.23), residues: 1392 helix: 0.57 (0.17), residues: 945 sheet: -4.06 (0.66), residues: 30 loop : -2.19 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 180 HIS 0.004 0.001 HIS B 348 PHE 0.029 0.001 PHE C 298 TYR 0.017 0.001 TYR C 177 ARG 0.005 0.000 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 597) hydrogen bonds : angle 4.13015 ( 1755) covalent geometry : bond 0.00256 (12267) covalent geometry : angle 0.62220 (16656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.278 Fit side-chains REVERT: A 63 LEU cc_start: 0.7789 (mm) cc_final: 0.7587 (tp) REVERT: A 69 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: A 128 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6342 (pm20) REVERT: A 159 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 188 VAL cc_start: 0.7660 (p) cc_final: 0.7176 (t) REVERT: A 292 TRP cc_start: 0.6956 (m100) cc_final: 0.6321 (m-10) REVERT: B 69 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: B 128 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.5458 (pm20) REVERT: B 188 VAL cc_start: 0.7565 (p) cc_final: 0.7089 (t) REVERT: B 266 GLU cc_start: 0.7329 (tt0) cc_final: 0.7088 (tp30) REVERT: B 477 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7468 (tp) REVERT: B 508 PHE cc_start: 0.7434 (m-80) cc_final: 0.7209 (m-80) REVERT: C 69 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: C 159 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 292 TRP cc_start: 0.6958 (m100) cc_final: 0.6342 (m-10) outliers start: 30 outliers final: 13 residues processed: 162 average time/residue: 0.8815 time to fit residues: 160.5220 Evaluate side-chains 159 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.180649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.151678 restraints weight = 13558.241| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.26 r_work: 0.3476 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12267 Z= 0.161 Angle : 0.691 6.539 16656 Z= 0.338 Chirality : 0.046 0.255 1908 Planarity : 0.004 0.049 2013 Dihedral : 10.855 70.920 2145 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.24 % Allowed : 18.99 % Favored : 78.77 % 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: -0.78 (0.22), residues: 1392 helix: 0.39 (0.17), residues: 945 sheet: -4.08 (0.64), residues: 30 loop : -2.28 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 180 HIS 0.006 0.001 HIS B 348 PHE 0.029 0.002 PHE C 298 TYR 0.020 0.002 TYR B 249 ARG 0.005 0.001 ARG C 341 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 597) hydrogen bonds : angle 4.30671 ( 1755) covalent geometry : bond 0.00384 (12267) covalent geometry : angle 0.69056 (16656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.272 Fit side-chains REVERT: A 69 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 128 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6228 (pm20) REVERT: A 159 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 292 TRP cc_start: 0.7135 (m100) cc_final: 0.6416 (m-10) REVERT: B 69 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: B 128 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: B 266 GLU cc_start: 0.7395 (tt0) cc_final: 0.7058 (tp30) REVERT: B 477 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7477 (tp) REVERT: C 69 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: C 128 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: C 159 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 292 TRP cc_start: 0.7034 (m100) cc_final: 0.6357 (m-10) outliers start: 28 outliers final: 13 residues processed: 162 average time/residue: 0.9411 time to fit residues: 169.5715 Evaluate side-chains 156 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.183274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.154616 restraints weight = 13536.138| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.31 r_work: 0.3527 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12267 Z= 0.125 Angle : 0.646 8.805 16656 Z= 0.318 Chirality : 0.043 0.212 1908 Planarity : 0.004 0.043 2013 Dihedral : 10.777 69.231 2145 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.00 % Allowed : 19.39 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.61 (0.22), residues: 1392 helix: 0.52 (0.17), residues: 945 sheet: -4.04 (0.65), residues: 30 loop : -2.21 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 180 HIS 0.004 0.001 HIS B 348 PHE 0.029 0.001 PHE C 298 TYR 0.019 0.001 TYR B 249 ARG 0.006 0.000 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 597) hydrogen bonds : angle 4.21920 ( 1755) covalent geometry : bond 0.00283 (12267) covalent geometry : angle 0.64629 (16656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.364 Fit side-chains REVERT: A 69 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: A 128 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6255 (pm20) REVERT: A 159 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8196 (tm-30) REVERT: A 188 VAL cc_start: 0.7601 (p) cc_final: 0.7031 (t) REVERT: A 292 TRP cc_start: 0.6999 (m100) cc_final: 0.6256 (m-10) REVERT: B 69 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: B 128 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: B 159 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8122 (tm-30) REVERT: B 182 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6510 (mt-10) REVERT: B 188 VAL cc_start: 0.7232 (p) cc_final: 0.6755 (t) REVERT: B 266 GLU cc_start: 0.7362 (tt0) cc_final: 0.7093 (tp30) REVERT: B 477 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7466 (tp) REVERT: C 69 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: C 128 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: C 159 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8231 (tm-30) REVERT: C 506 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7662 (ttp-110) outliers start: 25 outliers final: 15 residues processed: 161 average time/residue: 0.9574 time to fit residues: 171.7593 Evaluate side-chains 160 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 117 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.180716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.153116 restraints weight = 13509.830| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.12 r_work: 0.3445 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12267 Z= 0.156 Angle : 0.689 7.786 16656 Z= 0.337 Chirality : 0.045 0.257 1908 Planarity : 0.004 0.047 2013 Dihedral : 10.863 70.861 2145 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.92 % Allowed : 19.39 % Favored : 78.69 % 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: -0.74 (0.22), residues: 1392 helix: 0.40 (0.17), residues: 945 sheet: -4.08 (0.63), residues: 30 loop : -2.21 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 180 HIS 0.007 0.001 HIS B 348 PHE 0.030 0.002 PHE C 298 TYR 0.020 0.002 TYR B 249 ARG 0.006 0.001 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 597) hydrogen bonds : angle 4.31066 ( 1755) covalent geometry : bond 0.00371 (12267) covalent geometry : angle 0.68877 (16656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8190.38 seconds wall clock time: 143 minutes 49.65 seconds (8629.65 seconds total)