Starting phenix.real_space_refine on Sat Sep 12 11:33:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e7p_9000/09_2026/6e7p_9000.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e7p_9000/09_2026/6e7p_9000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e7p_9000/09_2026/6e7p_9000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e7p_9000/09_2026/6e7p_9000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e7p_9000/09_2026/6e7p_9000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e7p_9000/09_2026/6e7p_9000.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.040 sd= 0.383 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 100 5.16 5 C 10104 2.51 5 N 2560 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15508 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'HZ7': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.39, per 1000 atoms: 0.28 Number of scatterers: 15508 At special positions: 0 Unit cell: (120.91, 120.91, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 12 15.00 O 2732 8.00 N 2560 7.00 C 10104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.04 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 630.4 milliseconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 57.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 41 through 48 removed outlier: 3.593A pdb=" N PHE A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.909A pdb=" N PHE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.835A pdb=" N MET A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.764A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 290 through 294 removed outlier: 4.231A pdb=" N GLY A 293 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A 294 " --> pdb=" O GLN A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 294' Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 301 through 326 removed outlier: 3.611A pdb=" N SER A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.552A pdb=" N VAL A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 333' Processing helix chain 'A' and resid 352 through 373 removed outlier: 3.693A pdb=" N ILE A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.584A pdb=" N LEU A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 390 " --> pdb=" O CYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 410 through 447 removed outlier: 4.265A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.756A pdb=" N CYS A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.942A pdb=" N GLU A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 4.025A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 removed outlier: 3.568A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 506 removed outlier: 3.630A pdb=" N TRP A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 526 removed outlier: 3.715A pdb=" N PHE A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 removed outlier: 3.594A pdb=" N PHE B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.909A pdb=" N PHE B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.835A pdb=" N MET B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.763A pdb=" N TYR B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 290 through 294 removed outlier: 4.232A pdb=" N GLY B 293 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP B 294 " --> pdb=" O GLN B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 290 through 294' Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 301 through 326 removed outlier: 3.611A pdb=" N SER B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.551A pdb=" N VAL B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 333' Processing helix chain 'B' and resid 352 through 373 removed outlier: 3.694A pdb=" N ILE B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.582A pdb=" N LEU B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 390 " --> pdb=" O CYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 410 through 447 removed outlier: 4.266A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.756A pdb=" N CYS B 430 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 464 removed outlier: 3.940A pdb=" N GLU B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 4.024A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 481 removed outlier: 3.567A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 506 removed outlier: 3.630A pdb=" N TRP B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 506 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 526 removed outlier: 3.714A pdb=" N PHE B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 523 " --> pdb=" O GLY B 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 48 removed outlier: 3.594A pdb=" N PHE C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.909A pdb=" N PHE C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.836A pdb=" N MET C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 138 removed outlier: 3.764A pdb=" N TYR C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 290 through 294 removed outlier: 4.232A pdb=" N GLY C 293 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP C 294 " --> pdb=" O GLN C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 294' Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 301 through 326 removed outlier: 3.610A pdb=" N SER C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 333 removed outlier: 3.552A pdb=" N VAL C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY C 332 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 327 through 333' Processing helix chain 'C' and resid 352 through 373 removed outlier: 3.694A pdb=" N ILE C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 398 removed outlier: 3.583A pdb=" N LEU C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 390 " --> pdb=" O CYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 410 through 447 removed outlier: 4.266A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.756A pdb=" N CYS C 430 " --> pdb=" O MET C 426 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 464 removed outlier: 3.940A pdb=" N GLU C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 removed outlier: 4.024A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 481 removed outlier: 3.567A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 506 removed outlier: 3.629A pdb=" N TRP C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU C 504 " --> pdb=" O SER C 500 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 506 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 526 removed outlier: 3.715A pdb=" N PHE C 513 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR C 523 " --> pdb=" O GLY C 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 48 removed outlier: 3.593A pdb=" N PHE D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 removed outlier: 3.910A pdb=" N PHE D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.835A pdb=" N MET D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.764A pdb=" N TYR D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 290 through 294 removed outlier: 4.231A pdb=" N GLY D 293 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP D 294 " --> pdb=" O GLN D 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 290 through 294' Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 301 through 326 removed outlier: 3.610A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 317 " --> pdb=" O PHE D 313 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.551A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 333' Processing helix chain 'D' and resid 352 through 373 removed outlier: 3.693A pdb=" N ILE D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 398 removed outlier: 3.583A pdb=" N LEU D 389 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 390 " --> pdb=" O CYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 410 through 447 removed outlier: 4.265A pdb=" N LEU D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.756A pdb=" N CYS D 430 " --> pdb=" O MET D 426 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 464 removed outlier: 3.940A pdb=" N GLU D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 4.025A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 481 removed outlier: 3.568A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 506 removed outlier: 3.629A pdb=" N TRP D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 492 " --> pdb=" O SER D 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 504 " --> pdb=" O SER D 500 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 506 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 526 removed outlier: 3.715A pdb=" N PHE D 513 " --> pdb=" O VAL D 509 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR D 523 " --> pdb=" O GLY D 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.518A pdb=" N THR A 261 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.518A pdb=" N THR A 261 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.519A pdb=" N THR B 261 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.519A pdb=" N THR B 261 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.519A pdb=" N THR C 261 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.519A pdb=" N THR C 261 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.518A pdb=" N THR D 261 " --> pdb=" O SER D 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.518A pdb=" N THR D 261 " --> pdb=" O SER D 274 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2112 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: 2.81 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4764 1.34 - 1.47: 4245 1.47 - 1.60: 6723 1.60 - 1.72: 16 1.72 - 1.85: 140 Bond restraints: 15888 Sorted by residual: bond pdb=" O4 HZ7 C 801 " pdb=" P3 HZ7 C 801 " ideal model delta sigma weight residual 1.707 1.608 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" O4 HZ7 D 801 " pdb=" P3 HZ7 D 801 " ideal model delta sigma weight residual 1.707 1.608 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" O4 HZ7 B 801 " pdb=" P3 HZ7 B 801 " ideal model delta sigma weight residual 1.707 1.608 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O2 HZ7 D 801 " pdb=" P2 HZ7 D 801 " ideal model delta sigma weight residual 1.713 1.615 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O2 HZ7 B 801 " pdb=" P2 HZ7 B 801 " ideal model delta sigma weight residual 1.713 1.615 0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 15883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 20760 2.53 - 5.05: 667 5.05 - 7.58: 97 7.58 - 10.11: 28 10.11 - 12.63: 12 Bond angle restraints: 21564 Sorted by residual: angle pdb=" CA SER B 488 " pdb=" C SER B 488 " pdb=" N LEU B 489 " ideal model delta sigma weight residual 116.84 124.22 -7.38 1.71e+00 3.42e-01 1.86e+01 angle pdb=" CA SER A 488 " pdb=" C SER A 488 " pdb=" N LEU A 489 " ideal model delta sigma weight residual 116.84 124.20 -7.36 1.71e+00 3.42e-01 1.85e+01 angle pdb=" CA SER D 488 " pdb=" C SER D 488 " pdb=" N LEU D 489 " ideal model delta sigma weight residual 116.84 124.20 -7.36 1.71e+00 3.42e-01 1.85e+01 angle pdb=" CA SER C 488 " pdb=" C SER C 488 " pdb=" N LEU C 489 " ideal model delta sigma weight residual 116.84 124.17 -7.33 1.71e+00 3.42e-01 1.84e+01 angle pdb=" C PRO C 177 " pdb=" N ALA C 178 " pdb=" CA ALA C 178 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 ... (remaining 21559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.21: 8618 14.21 - 28.42: 619 28.42 - 42.62: 191 42.62 - 56.83: 24 56.83 - 71.04: 20 Dihedral angle restraints: 9472 sinusoidal: 3908 harmonic: 5564 Sorted by residual: dihedral pdb=" CA TRP D 335 " pdb=" C TRP D 335 " pdb=" N ARG D 336 " pdb=" CA ARG D 336 " ideal model delta harmonic sigma weight residual -180.00 -130.54 -49.46 0 5.00e+00 4.00e-02 9.79e+01 dihedral pdb=" CA TRP A 335 " pdb=" C TRP A 335 " pdb=" N ARG A 336 " pdb=" CA ARG A 336 " ideal model delta harmonic sigma weight residual -180.00 -130.58 -49.42 0 5.00e+00 4.00e-02 9.77e+01 dihedral pdb=" CA TRP C 335 " pdb=" C TRP C 335 " pdb=" N ARG C 336 " pdb=" CA ARG C 336 " ideal model delta harmonic sigma weight residual 180.00 -130.58 -49.42 0 5.00e+00 4.00e-02 9.77e+01 ... (remaining 9469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2089 0.077 - 0.153: 360 0.153 - 0.230: 12 0.230 - 0.306: 3 0.306 - 0.383: 4 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CB VAL B 289 " pdb=" CA VAL B 289 " pdb=" CG1 VAL B 289 " pdb=" CG2 VAL B 289 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB VAL D 289 " pdb=" CA VAL D 289 " pdb=" CG1 VAL D 289 " pdb=" CG2 VAL D 289 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CB VAL A 289 " pdb=" CA VAL A 289 " pdb=" CG1 VAL A 289 " pdb=" CG2 VAL A 289 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 2465 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 422 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO C 423 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 423 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 423 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 422 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO D 423 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 422 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO A 423 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " 0.034 5.00e-02 4.00e+02 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4614 2.81 - 3.33: 13860 3.33 - 3.86: 23264 3.86 - 4.38: 27061 4.38 - 4.90: 45604 Nonbonded interactions: 114403 Sorted by model distance: nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.289 3.040 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.290 3.040 nonbonded pdb=" O TYR D 439 " pdb=" OH TYR D 497 " model vdw 2.290 3.040 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.291 3.040 nonbonded pdb=" O THR B 158 " pdb=" OG SER B 161 " model vdw 2.323 3.040 ... (remaining 114398 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.460 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.011 0.385 15900 Z= 0.737 Angle : 1.121 12.634 21580 Z= 0.568 Chirality : 0.057 0.383 2468 Planarity : 0.006 0.059 2648 Dihedral : 11.515 71.038 5864 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.01 % Favored : 91.77 % Rotamer: Outliers : 0.24 % Allowed : 2.84 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.15 (0.15), residues: 1884 helix: -3.95 (0.09), residues: 880 sheet: -2.39 (0.34), residues: 212 loop : -2.85 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 200 TYR 0.022 0.003 TYR C 404 PHE 0.024 0.003 PHE A 235 TRP 0.020 0.003 TRP B 491 HIS 0.008 0.003 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00927 / 0.42 (15888) covalent geometry : angle 1.11958 / 0.57 (21564) SS BOND : bond 0.00601 / 0.32 ( 8) SS BOND : angle 2.46724 / 1.30 ( 16) hydrogen bonds : bond 0.32880 / 21.16 ( 672) hydrogen bonds : angle 9.45455 / 6.59 ( 2112) Misc. bond : bond 0.38415 / 19.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 262 time to evaluate : 0.606 Fit side-chains REVERT: A 57 ARG cc_start: 0.7281 (mtt180) cc_final: 0.5892 (mmt180) REVERT: A 295 ASN cc_start: 0.7073 (t0) cc_final: 0.6855 (m-40) REVERT: A 349 GLU cc_start: 0.8529 (pp20) cc_final: 0.8261 (pp20) REVERT: A 422 LEU cc_start: 0.9205 (tt) cc_final: 0.8990 (tp) REVERT: A 451 HIS cc_start: 0.7117 (m-70) cc_final: 0.6349 (m-70) REVERT: A 480 MET cc_start: 0.8259 (mmp) cc_final: 0.7890 (mmp) REVERT: B 57 ARG cc_start: 0.7286 (mtt180) cc_final: 0.5857 (mmt180) REVERT: B 295 ASN cc_start: 0.7217 (t0) cc_final: 0.6958 (m-40) REVERT: B 349 GLU cc_start: 0.8558 (pp20) cc_final: 0.8247 (pp20) REVERT: B 422 LEU cc_start: 0.9239 (tt) cc_final: 0.9037 (tp) REVERT: B 451 HIS cc_start: 0.7095 (m-70) cc_final: 0.6354 (m-70) REVERT: B 480 MET cc_start: 0.8266 (mmp) cc_final: 0.7884 (mmp) REVERT: C 57 ARG cc_start: 0.7284 (mtt180) cc_final: 0.5875 (mmt180) REVERT: C 295 ASN cc_start: 0.7237 (t0) cc_final: 0.6986 (m-40) REVERT: C 349 GLU cc_start: 0.8568 (pp20) cc_final: 0.8330 (pp20) REVERT: C 451 HIS cc_start: 0.7122 (m-70) cc_final: 0.6361 (m-70) REVERT: C 480 MET cc_start: 0.8259 (mmp) cc_final: 0.7881 (mmp) REVERT: D 57 ARG cc_start: 0.7171 (mtt180) cc_final: 0.5829 (mmt180) REVERT: D 295 ASN cc_start: 0.7222 (t0) cc_final: 0.6970 (m-40) REVERT: D 321 LEU cc_start: 0.8103 (mt) cc_final: 0.7890 (mt) REVERT: D 422 LEU cc_start: 0.9191 (tt) cc_final: 0.8968 (tp) REVERT: D 451 HIS cc_start: 0.7117 (m-70) cc_final: 0.6288 (m-70) REVERT: D 480 MET cc_start: 0.8285 (mmp) cc_final: 0.7891 (mmp) outliers start: 4 outliers final: 0 residues processed: 266 average time/residue: 0.1189 time to fit residues: 48.1987 Evaluate side-chains 148 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 79 GLN A 97 ASN A 234 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS A 327 GLN B 69 GLN B 79 GLN B 97 ASN B 234 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 327 GLN C 69 GLN C 79 GLN C 97 ASN C 234 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS D 69 GLN D 79 GLN D 97 ASN D 234 HIS D 292 HIS D 327 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.121086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096647 restraints weight = 35338.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099340 restraints weight = 19175.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101212 restraints weight = 12931.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102459 restraints weight = 10009.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.103084 restraints weight = 8465.422| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15900 Z= 0.147 Angle : 0.684 9.693 21580 Z= 0.348 Chirality : 0.042 0.141 2468 Planarity : 0.005 0.048 2648 Dihedral : 8.233 45.953 2360 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.24 % Allowed : 9.75 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.17), residues: 1884 helix: -1.69 (0.14), residues: 976 sheet: -1.57 (0.35), residues: 212 loop : -3.11 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.011 0.001 TYR A 126 PHE 0.016 0.002 PHE C 493 TRP 0.012 0.001 TRP A 491 HIS 0.005 0.001 HIS D 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (15888) covalent geometry : angle 0.68347 / 0.35 (21564) SS BOND : bond 0.00248 / 0.12 ( 8) SS BOND : angle 0.95146 / 0.50 ( 16) hydrogen bonds : bond 0.06507 / 4.12 ( 672) hydrogen bonds : angle 4.82208 / 3.32 ( 2112) Misc. bond : bond 0.00262 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6045 (tpt170) REVERT: A 295 ASN cc_start: 0.7345 (t0) cc_final: 0.7043 (m-40) REVERT: A 371 MET cc_start: 0.8632 (mtp) cc_final: 0.8422 (mtp) REVERT: A 451 HIS cc_start: 0.7101 (m-70) cc_final: 0.6460 (m-70) REVERT: A 459 MET cc_start: 0.8667 (mtp) cc_final: 0.8390 (mtm) REVERT: B 57 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6004 (tpt170) REVERT: B 295 ASN cc_start: 0.7220 (t0) cc_final: 0.6888 (m-40) REVERT: B 459 MET cc_start: 0.8666 (mtp) cc_final: 0.8380 (mtm) REVERT: C 57 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6051 (tpt170) REVERT: C 295 ASN cc_start: 0.7279 (t0) cc_final: 0.6982 (m-40) REVERT: C 451 HIS cc_start: 0.7094 (m-70) cc_final: 0.6532 (m-70) REVERT: C 459 MET cc_start: 0.8676 (mtp) cc_final: 0.8386 (mtm) REVERT: D 57 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6041 (tpt170) REVERT: D 295 ASN cc_start: 0.7174 (t0) cc_final: 0.6866 (m-40) REVERT: D 334 MET cc_start: 0.2601 (mtm) cc_final: 0.1757 (ttm) REVERT: D 459 MET cc_start: 0.8653 (mtp) cc_final: 0.8297 (mtp) outliers start: 21 outliers final: 4 residues processed: 223 average time/residue: 0.1095 time to fit residues: 38.1713 Evaluate side-chains 142 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 359 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 185 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 286 HIS A 327 GLN B 286 HIS B 327 GLN C 280 HIS C 286 HIS D 286 HIS D 327 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.119884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095363 restraints weight = 35628.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.098076 restraints weight = 19463.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099895 restraints weight = 13157.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.100816 restraints weight = 10247.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101745 restraints weight = 8859.297| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15900 Z= 0.163 Angle : 0.661 7.896 21580 Z= 0.332 Chirality : 0.041 0.132 2468 Planarity : 0.004 0.046 2648 Dihedral : 7.634 44.783 2360 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.01 % Allowed : 9.34 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.18), residues: 1884 helix: -0.74 (0.16), residues: 944 sheet: -1.43 (0.36), residues: 212 loop : -2.73 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 146 TYR 0.013 0.001 TYR D 169 PHE 0.013 0.002 PHE C 493 TRP 0.007 0.001 TRP A 491 HIS 0.007 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (15888) covalent geometry : angle 0.66001 / 0.33 (21564) SS BOND : bond 0.00236 / 0.12 ( 8) SS BOND : angle 1.59783 / 0.78 ( 16) hydrogen bonds : bond 0.05687 / 3.59 ( 672) hydrogen bonds : angle 4.40365 / 3.02 ( 2112) Misc. bond : bond 0.00272 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6874 (t80) REVERT: A 50 MET cc_start: 0.6953 (mmm) cc_final: 0.6228 (mtt) REVERT: A 57 ARG cc_start: 0.7216 (mtt180) cc_final: 0.5991 (tpt170) REVERT: A 67 MET cc_start: 0.7624 (tmm) cc_final: 0.7312 (tmm) REVERT: A 295 ASN cc_start: 0.7140 (t0) cc_final: 0.6837 (m-40) REVERT: B 47 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7005 (t80) REVERT: B 50 MET cc_start: 0.6878 (mmm) cc_final: 0.6322 (mtt) REVERT: B 57 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6007 (tpt170) REVERT: B 67 MET cc_start: 0.7615 (tmm) cc_final: 0.7327 (tmm) REVERT: B 295 ASN cc_start: 0.7280 (t0) cc_final: 0.6935 (m-40) REVERT: C 47 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6951 (t80) REVERT: C 50 MET cc_start: 0.6975 (mmm) cc_final: 0.6293 (mtt) REVERT: C 57 ARG cc_start: 0.7256 (mtt180) cc_final: 0.5899 (mmt180) REVERT: C 295 ASN cc_start: 0.6885 (t0) cc_final: 0.6595 (m-40) REVERT: C 483 GLN cc_start: 0.7943 (mp10) cc_final: 0.7728 (mp10) REVERT: D 57 ARG cc_start: 0.7129 (mtt180) cc_final: 0.5961 (mmt180) REVERT: D 295 ASN cc_start: 0.6975 (t0) cc_final: 0.6679 (m-40) REVERT: D 334 MET cc_start: 0.2433 (mtm) cc_final: 0.1646 (ttm) outliers start: 51 outliers final: 22 residues processed: 193 average time/residue: 0.1041 time to fit residues: 31.9914 Evaluate side-chains 161 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 356 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 127 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 163 optimal weight: 0.9980 chunk 62 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.1531 > 50:) chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN B 327 GLN D 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.097401 restraints weight = 35552.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.100234 restraints weight = 19368.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.102130 restraints weight = 12946.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.103323 restraints weight = 9974.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103996 restraints weight = 8447.160| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15900 Z= 0.116 Angle : 0.583 7.632 21580 Z= 0.291 Chirality : 0.040 0.129 2468 Planarity : 0.004 0.044 2648 Dihedral : 7.074 44.644 2360 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.71 % Allowed : 10.22 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.19), residues: 1884 helix: -0.17 (0.17), residues: 964 sheet: -1.15 (0.37), residues: 212 loop : -2.60 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 486 TYR 0.010 0.001 TYR B 147 PHE 0.012 0.001 PHE A 493 TRP 0.007 0.001 TRP A 157 HIS 0.005 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (15888) covalent geometry : angle 0.58201 / 0.29 (21564) SS BOND : bond 0.00178 / 0.10 ( 8) SS BOND : angle 1.15146 / 0.59 ( 16) hydrogen bonds : bond 0.04759 / 3.00 ( 672) hydrogen bonds : angle 4.08540 / 2.80 ( 2112) Misc. bond : bond 0.00223 / 0.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.7029 (t80) REVERT: A 50 MET cc_start: 0.6926 (mmm) cc_final: 0.6161 (mtt) REVERT: A 57 ARG cc_start: 0.7187 (mtt180) cc_final: 0.5889 (tpt170) REVERT: A 67 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7041 (tmm) REVERT: A 68 LEU cc_start: 0.8870 (tp) cc_final: 0.8496 (tt) REVERT: A 350 PHE cc_start: 0.8465 (m-10) cc_final: 0.8146 (m-80) REVERT: A 459 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8100 (mtp) REVERT: B 47 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6821 (t80) REVERT: B 57 ARG cc_start: 0.7192 (mtt180) cc_final: 0.5864 (tpt170) REVERT: B 67 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7103 (tmm) REVERT: B 68 LEU cc_start: 0.8842 (tp) cc_final: 0.8469 (tt) REVERT: B 350 PHE cc_start: 0.8483 (m-10) cc_final: 0.8152 (m-80) REVERT: B 459 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: C 47 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6782 (t80) REVERT: C 57 ARG cc_start: 0.7212 (mtt180) cc_final: 0.5907 (tpt170) REVERT: C 67 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7168 (tmm) REVERT: C 68 LEU cc_start: 0.8875 (tp) cc_final: 0.8404 (tt) REVERT: C 350 PHE cc_start: 0.8476 (m-10) cc_final: 0.8149 (m-80) REVERT: C 459 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: C 483 GLN cc_start: 0.7985 (mp10) cc_final: 0.7765 (mp10) REVERT: D 57 ARG cc_start: 0.7148 (mtt180) cc_final: 0.5880 (mmt180) REVERT: D 67 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7081 (tmm) REVERT: D 68 LEU cc_start: 0.8885 (tp) cc_final: 0.8481 (tt) REVERT: D 295 ASN cc_start: 0.6918 (t0) cc_final: 0.6623 (m-40) REVERT: D 334 MET cc_start: 0.2366 (mtm) cc_final: 0.0507 (ttt) REVERT: D 459 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8091 (mtp) outliers start: 29 outliers final: 11 residues processed: 191 average time/residue: 0.1064 time to fit residues: 31.2712 Evaluate side-chains 156 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN B 327 GLN C 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.121533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097358 restraints weight = 35565.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100159 restraints weight = 19334.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102024 restraints weight = 12912.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103220 restraints weight = 9937.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.103674 restraints weight = 8405.850| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15900 Z= 0.115 Angle : 0.559 8.066 21580 Z= 0.283 Chirality : 0.040 0.136 2468 Planarity : 0.003 0.043 2648 Dihedral : 6.695 43.930 2360 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.60 % Allowed : 10.93 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.19), residues: 1884 helix: 0.23 (0.17), residues: 960 sheet: -1.08 (0.37), residues: 212 loop : -2.52 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.011 0.001 TYR B 147 PHE 0.012 0.001 PHE A 235 TRP 0.006 0.001 TRP B 157 HIS 0.007 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (15888) covalent geometry : angle 0.55835 / 0.28 (21564) SS BOND : bond 0.00270 / 0.14 ( 8) SS BOND : angle 0.96937 / 0.51 ( 16) hydrogen bonds : bond 0.04481 / 2.81 ( 672) hydrogen bonds : angle 3.92138 / 2.70 ( 2112) Misc. bond : bond 0.00123 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.6877 (t80) REVERT: A 67 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7034 (tmm) REVERT: A 68 LEU cc_start: 0.8835 (tp) cc_final: 0.8528 (tt) REVERT: A 295 ASN cc_start: 0.6013 (t0) cc_final: 0.5430 (m-40) REVERT: A 350 PHE cc_start: 0.8403 (m-10) cc_final: 0.8123 (m-80) REVERT: A 483 GLN cc_start: 0.8154 (mp-120) cc_final: 0.7897 (mp10) REVERT: B 50 MET cc_start: 0.6753 (mmm) cc_final: 0.6453 (mtt) REVERT: B 67 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7042 (tmm) REVERT: B 68 LEU cc_start: 0.8842 (tp) cc_final: 0.8457 (tt) REVERT: B 295 ASN cc_start: 0.5876 (t0) cc_final: 0.5294 (m-40) REVERT: B 334 MET cc_start: 0.1869 (mtt) cc_final: 0.0240 (ttt) REVERT: B 350 PHE cc_start: 0.8390 (m-10) cc_final: 0.8113 (m-80) REVERT: C 47 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6733 (t80) REVERT: C 67 MET cc_start: 0.7352 (tmm) cc_final: 0.7007 (tmm) REVERT: C 68 LEU cc_start: 0.8854 (tp) cc_final: 0.8545 (tt) REVERT: C 295 ASN cc_start: 0.6017 (t0) cc_final: 0.5424 (m-40) REVERT: C 334 MET cc_start: 0.2127 (mtt) cc_final: 0.1759 (mtt) REVERT: C 350 PHE cc_start: 0.8426 (m-10) cc_final: 0.8108 (m-80) REVERT: D 57 ARG cc_start: 0.7191 (mtt180) cc_final: 0.5830 (mmt180) REVERT: D 67 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6956 (tmm) REVERT: D 68 LEU cc_start: 0.8838 (tp) cc_final: 0.8503 (tt) REVERT: D 295 ASN cc_start: 0.6952 (t0) cc_final: 0.6636 (m-40) REVERT: D 334 MET cc_start: 0.1891 (mtm) cc_final: 0.0247 (ttt) outliers start: 44 outliers final: 26 residues processed: 188 average time/residue: 0.0974 time to fit residues: 30.2620 Evaluate side-chains 167 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.116171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.092130 restraints weight = 35765.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094680 restraints weight = 19788.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096444 restraints weight = 13424.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097490 restraints weight = 10415.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098349 restraints weight = 8900.318| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15900 Z= 0.281 Angle : 0.713 8.717 21580 Z= 0.363 Chirality : 0.045 0.316 2468 Planarity : 0.004 0.046 2648 Dihedral : 7.288 43.130 2360 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.96 % Allowed : 10.58 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.19), residues: 1884 helix: 0.06 (0.17), residues: 960 sheet: -1.26 (0.36), residues: 212 loop : -2.39 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 419 TYR 0.015 0.002 TYR D 169 PHE 0.015 0.002 PHE A 235 TRP 0.008 0.001 TRP D 354 HIS 0.011 0.002 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 (15888) covalent geometry : angle 0.71264 / 0.36 (21564) SS BOND : bond 0.00437 / 0.24 ( 8) SS BOND : angle 1.30725 / 0.69 ( 16) hydrogen bonds : bond 0.05469 / 3.45 ( 672) hydrogen bonds : angle 4.38312 / 3.01 ( 2112) Misc. bond : bond 0.00144 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 123 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 57 ARG cc_start: 0.7459 (mtt180) cc_final: 0.5871 (mmt180) REVERT: A 67 MET cc_start: 0.7632 (tmm) cc_final: 0.7205 (tmm) REVERT: A 325 LEU cc_start: 0.7248 (tt) cc_final: 0.6993 (pp) REVERT: A 350 PHE cc_start: 0.8454 (m-10) cc_final: 0.8191 (m-80) REVERT: A 483 GLN cc_start: 0.8246 (mp-120) cc_final: 0.7934 (mp10) REVERT: B 67 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7228 (tmm) REVERT: B 325 LEU cc_start: 0.7190 (tt) cc_final: 0.6980 (pp) REVERT: B 350 PHE cc_start: 0.8456 (m-10) cc_final: 0.8179 (m-80) REVERT: C 47 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.6940 (t80) REVERT: C 67 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7260 (tmm) REVERT: C 350 PHE cc_start: 0.8447 (m-10) cc_final: 0.8148 (m-80) REVERT: D 57 ARG cc_start: 0.7427 (mtt180) cc_final: 0.5976 (mmt180) REVERT: D 67 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7218 (tmm) REVERT: D 295 ASN cc_start: 0.6866 (t0) cc_final: 0.6538 (m-40) REVERT: D 334 MET cc_start: 0.2143 (mtm) cc_final: 0.0512 (ttt) outliers start: 67 outliers final: 46 residues processed: 178 average time/residue: 0.0997 time to fit residues: 29.0546 Evaluate side-chains 173 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.119560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.095558 restraints weight = 35460.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098301 restraints weight = 19390.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100138 restraints weight = 12955.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101068 restraints weight = 9965.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102041 restraints weight = 8542.836| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15900 Z= 0.112 Angle : 0.568 8.705 21580 Z= 0.287 Chirality : 0.040 0.165 2468 Planarity : 0.003 0.045 2648 Dihedral : 6.777 44.535 2360 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.83 % Allowed : 12.41 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.20), residues: 1884 helix: 0.46 (0.17), residues: 960 sheet: -1.01 (0.37), residues: 208 loop : -2.30 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.010 0.001 TYR B 497 PHE 0.012 0.001 PHE B 225 TRP 0.007 0.001 TRP D 398 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (15888) covalent geometry : angle 0.56754 / 0.29 (21564) SS BOND : bond 0.00146 / 0.08 ( 8) SS BOND : angle 0.75234 / 0.40 ( 16) hydrogen bonds : bond 0.04511 / 2.83 ( 672) hydrogen bonds : angle 3.97420 / 2.72 ( 2112) Misc. bond : bond 0.00065 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 67 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7052 (tmm) REVERT: A 334 MET cc_start: 0.1946 (mtt) cc_final: 0.0428 (ttt) REVERT: A 350 PHE cc_start: 0.8366 (m-10) cc_final: 0.8093 (m-80) REVERT: B 50 MET cc_start: 0.6761 (mmm) cc_final: 0.6430 (mtm) REVERT: B 67 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7056 (tmm) REVERT: B 334 MET cc_start: 0.1962 (mtt) cc_final: 0.0334 (ttt) REVERT: B 350 PHE cc_start: 0.8351 (m-10) cc_final: 0.8087 (m-80) REVERT: C 47 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.7157 (t80) REVERT: C 50 MET cc_start: 0.7184 (mmm) cc_final: 0.6489 (mtt) REVERT: C 67 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7063 (tmm) REVERT: C 350 PHE cc_start: 0.8355 (m-10) cc_final: 0.8086 (m-80) REVERT: D 57 ARG cc_start: 0.7314 (mtt180) cc_final: 0.5917 (mmt180) REVERT: D 67 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7019 (tmm) REVERT: D 334 MET cc_start: 0.1759 (mtm) cc_final: 0.0188 (ttt) outliers start: 31 outliers final: 19 residues processed: 174 average time/residue: 0.1042 time to fit residues: 29.0125 Evaluate side-chains 155 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 140 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.120165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096256 restraints weight = 35540.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098918 restraints weight = 19397.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100785 restraints weight = 12925.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102014 restraints weight = 9901.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102732 restraints weight = 8305.671| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15900 Z= 0.111 Angle : 0.588 9.103 21580 Z= 0.292 Chirality : 0.040 0.137 2468 Planarity : 0.003 0.043 2648 Dihedral : 7.066 48.871 2360 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.84 % Allowed : 12.06 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1884 helix: 0.54 (0.17), residues: 984 sheet: -0.86 (0.37), residues: 212 loop : -2.43 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.010 0.001 TYR B 497 PHE 0.012 0.001 PHE A 235 TRP 0.006 0.001 TRP D 398 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15888) covalent geometry : angle 0.58677 / 0.29 (21564) SS BOND : bond 0.00186 / 0.09 ( 8) SS BOND : angle 1.22971 / 0.64 ( 16) hydrogen bonds : bond 0.04343 / 2.74 ( 672) hydrogen bonds : angle 3.91246 / 2.67 ( 2112) Misc. bond : bond 0.00282 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6878 (t80) REVERT: A 57 ARG cc_start: 0.7271 (mtt180) cc_final: 0.5904 (tpt170) REVERT: A 334 MET cc_start: 0.1883 (mtt) cc_final: 0.0333 (ttt) REVERT: A 350 PHE cc_start: 0.8371 (m-10) cc_final: 0.8109 (m-80) REVERT: B 50 MET cc_start: 0.6767 (mmm) cc_final: 0.6352 (mtm) REVERT: B 57 ARG cc_start: 0.7172 (mtt180) cc_final: 0.5493 (mmt180) REVERT: B 334 MET cc_start: 0.1884 (mtt) cc_final: 0.0323 (ttt) REVERT: B 350 PHE cc_start: 0.8329 (m-10) cc_final: 0.8062 (m-80) REVERT: C 47 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6994 (t80) REVERT: C 68 LEU cc_start: 0.8888 (tp) cc_final: 0.8518 (tt) REVERT: C 334 MET cc_start: 0.2013 (mtt) cc_final: 0.0481 (ttt) REVERT: C 350 PHE cc_start: 0.8352 (m-10) cc_final: 0.8092 (m-80) REVERT: D 57 ARG cc_start: 0.7392 (mtt180) cc_final: 0.5881 (mmt180) REVERT: D 68 LEU cc_start: 0.8873 (tp) cc_final: 0.8536 (tt) REVERT: D 334 MET cc_start: 0.1703 (mtm) cc_final: 0.0118 (ttt) outliers start: 48 outliers final: 36 residues processed: 183 average time/residue: 0.1053 time to fit residues: 31.1548 Evaluate side-chains 174 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 161 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN ** A 483 GLN ** 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 = 0.3742 r_free = 0.3742 target = 0.120567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096704 restraints weight = 35219.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.099482 restraints weight = 19137.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101360 restraints weight = 12769.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102480 restraints weight = 9761.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.103398 restraints weight = 8244.772| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15900 Z= 0.127 Angle : 0.651 16.059 21580 Z= 0.325 Chirality : 0.041 0.235 2468 Planarity : 0.003 0.043 2648 Dihedral : 6.843 48.430 2360 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.60 % Allowed : 12.35 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1884 helix: 0.61 (0.17), residues: 988 sheet: -0.98 (0.39), residues: 192 loop : -2.40 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 168 TYR 0.009 0.001 TYR B 497 PHE 0.013 0.001 PHE A 235 TRP 0.006 0.001 TRP B 398 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (15888) covalent geometry : angle 0.64169 / 0.32 (21564) SS BOND : bond 0.01145 / 0.68 ( 8) SS BOND : angle 4.00309 / 2.02 ( 16) hydrogen bonds : bond 0.04256 / 2.67 ( 672) hydrogen bonds : angle 3.86509 / 2.64 ( 2112) Misc. bond : bond 0.00275 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6934 (t80) REVERT: A 57 ARG cc_start: 0.7143 (mtt180) cc_final: 0.5503 (mmt180) REVERT: A 68 LEU cc_start: 0.8893 (tp) cc_final: 0.8563 (tt) REVERT: A 334 MET cc_start: 0.1947 (mtt) cc_final: 0.0413 (ttt) REVERT: A 350 PHE cc_start: 0.8362 (m-10) cc_final: 0.8098 (m-80) REVERT: B 350 PHE cc_start: 0.8330 (m-10) cc_final: 0.8076 (m-80) REVERT: C 50 MET cc_start: 0.7211 (mmm) cc_final: 0.6707 (mtt) REVERT: C 68 LEU cc_start: 0.8839 (tp) cc_final: 0.8502 (tt) REVERT: C 334 MET cc_start: 0.2034 (mtt) cc_final: 0.0405 (ttt) REVERT: C 350 PHE cc_start: 0.8337 (m-10) cc_final: 0.8069 (m-80) REVERT: D 57 ARG cc_start: 0.7280 (mtt180) cc_final: 0.5805 (mmt180) REVERT: D 68 LEU cc_start: 0.8883 (tp) cc_final: 0.8549 (tt) REVERT: D 334 MET cc_start: 0.1791 (mtm) cc_final: 0.0145 (ttt) outliers start: 44 outliers final: 38 residues processed: 183 average time/residue: 0.0998 time to fit residues: 29.9181 Evaluate side-chains 176 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 153 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.097193 restraints weight = 35508.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099983 restraints weight = 19365.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101867 restraints weight = 12890.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102991 restraints weight = 9884.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.103454 restraints weight = 8374.897| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15900 Z= 0.113 Angle : 0.616 12.284 21580 Z= 0.307 Chirality : 0.041 0.245 2468 Planarity : 0.003 0.043 2648 Dihedral : 6.577 49.928 2360 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.36 % Allowed : 12.41 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1884 helix: 0.68 (0.17), residues: 996 sheet: -0.94 (0.37), residues: 204 loop : -2.29 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 168 TYR 0.010 0.001 TYR D 497 PHE 0.012 0.001 PHE A 235 TRP 0.007 0.001 TRP B 398 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15888) covalent geometry : angle 0.60643 / 0.30 (21564) SS BOND : bond 0.01422 / 0.75 ( 8) SS BOND : angle 3.97222 / 2.12 ( 16) hydrogen bonds : bond 0.04074 / 2.56 ( 672) hydrogen bonds : angle 3.81766 / 2.61 ( 2112) Misc. bond : bond 0.00247 / 0.12 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7071 (mmm) cc_final: 0.6600 (mtt) REVERT: A 57 ARG cc_start: 0.7107 (mtt180) cc_final: 0.5400 (mmt180) REVERT: A 68 LEU cc_start: 0.8885 (tp) cc_final: 0.8578 (tt) REVERT: A 334 MET cc_start: 0.1925 (mtt) cc_final: 0.0415 (ttt) REVERT: A 350 PHE cc_start: 0.8376 (m-10) cc_final: 0.8099 (m-80) REVERT: B 68 LEU cc_start: 0.8872 (tp) cc_final: 0.8569 (tt) REVERT: B 350 PHE cc_start: 0.8313 (m-10) cc_final: 0.8032 (m-80) REVERT: C 50 MET cc_start: 0.6986 (mmm) cc_final: 0.6722 (mtp) REVERT: C 57 ARG cc_start: 0.7116 (mtt180) cc_final: 0.5401 (mmt180) REVERT: C 68 LEU cc_start: 0.8838 (tp) cc_final: 0.8485 (tt) REVERT: C 334 MET cc_start: 0.1829 (mtt) cc_final: 0.0308 (ttt) REVERT: C 350 PHE cc_start: 0.8372 (m-10) cc_final: 0.8095 (m-80) REVERT: D 57 ARG cc_start: 0.7283 (mtt180) cc_final: 0.5809 (mmt180) REVERT: D 68 LEU cc_start: 0.8872 (tp) cc_final: 0.8590 (tt) REVERT: D 334 MET cc_start: 0.1843 (mtm) cc_final: 0.0281 (ttt) outliers start: 40 outliers final: 39 residues processed: 179 average time/residue: 0.1074 time to fit residues: 31.0320 Evaluate side-chains 184 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 104 optimal weight: 0.0030 chunk 110 optimal weight: 0.0770 chunk 112 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 overall best weight: 0.5148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN ** B 481 GLN ** 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 = 0.3763 r_free = 0.3763 target = 0.122045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098104 restraints weight = 35136.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100798 restraints weight = 19224.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102690 restraints weight = 12872.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103790 restraints weight = 9861.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104699 restraints weight = 8368.846| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15900 Z= 0.104 Angle : 0.601 10.100 21580 Z= 0.301 Chirality : 0.041 0.241 2468 Planarity : 0.003 0.042 2648 Dihedral : 6.533 51.094 2360 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.42 % Allowed : 12.77 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1884 helix: 0.80 (0.17), residues: 996 sheet: -0.82 (0.37), residues: 204 loop : -2.25 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.010 0.001 TYR B 497 PHE 0.012 0.001 PHE B 407 TRP 0.006 0.001 TRP B 398 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (15888) covalent geometry : angle 0.59522 / 0.30 (21564) SS BOND : bond 0.01052 / 0.62 ( 8) SS BOND : angle 3.19841 / 1.75 ( 16) hydrogen bonds : bond 0.03894 / 2.45 ( 672) hydrogen bonds : angle 3.81127 / 2.61 ( 2112) Misc. bond : bond 0.00163 / 0.08 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.23 seconds wall clock time: 41 minutes 26.09 seconds (2486.09 seconds total)