Starting phenix.real_space_refine on Wed Mar 4 11:52:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyg_21459/03_2026/6vyg_21459.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyg_21459/03_2026/6vyg_21459.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vyg_21459/03_2026/6vyg_21459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyg_21459/03_2026/6vyg_21459.map" model { file = "/net/cci-nas-00/data/ceres_data/6vyg_21459/03_2026/6vyg_21459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyg_21459/03_2026/6vyg_21459.cif" } 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8632 2.51 5 N 2320 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13616 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3404 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 14, 'TRANS': 418} Chain breaks: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 2.71, per 1000 atoms: 0.20 Number of scatterers: 13616 At special positions: 0 Unit cell: (117.791, 96.071, 116.121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2572 8.00 N 2320 7.00 C 8632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 236 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 236 " - pdb=" SG CYS D 237 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 598.6 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 51.3% alpha, 9.5% 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 28 through 40 removed outlier: 3.595A pdb=" N HIS A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 68 removed outlier: 3.876A pdb=" N GLU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 165 removed outlier: 3.809A pdb=" N GLY A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.530A pdb=" N LEU A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 223 " --> pdb=" O CYS A 219 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.831A pdb=" N ALA A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.334A pdb=" N LYS A 280 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.658A pdb=" N PHE A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.850A pdb=" N ILE A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.581A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.588A pdb=" N TRP A 351 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.644A pdb=" N GLY A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 384 removed outlier: 3.597A pdb=" N LYS A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 422 removed outlier: 3.666A pdb=" N ARG A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.568A pdb=" N CYS A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 447 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.016A pdb=" N GLY A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.676A pdb=" N VAL A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.595A pdb=" N HIS B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 68 removed outlier: 3.877A pdb=" N GLU B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 removed outlier: 3.808A pdb=" N GLY B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.529A pdb=" N LEU B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 223 " --> pdb=" O CYS B 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 removed outlier: 3.832A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.335A pdb=" N LYS B 280 " --> pdb=" O PRO B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.658A pdb=" N PHE B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.850A pdb=" N ILE B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.581A pdb=" N LEU B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.588A pdb=" N TRP B 351 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.643A pdb=" N GLY B 361 " --> pdb=" O ASN B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 384 removed outlier: 3.596A pdb=" N LYS B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 422 removed outlier: 3.665A pdb=" N ARG B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 441 through 456 removed outlier: 3.568A pdb=" N CYS B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 447 " --> pdb=" O TRP B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 471 through 479 removed outlier: 4.016A pdb=" N GLY B 475 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.675A pdb=" N VAL B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.595A pdb=" N HIS C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 68 removed outlier: 3.877A pdb=" N GLU C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 165 removed outlier: 3.808A pdb=" N GLY C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.528A pdb=" N LEU C 221 " --> pdb=" O ASP C 217 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 223 " --> pdb=" O CYS C 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.831A pdb=" N ALA C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 4.335A pdb=" N LYS C 280 " --> pdb=" O PRO C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.659A pdb=" N PHE C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.851A pdb=" N ILE C 325 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 3.581A pdb=" N LEU C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.589A pdb=" N TRP C 351 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 removed outlier: 3.643A pdb=" N GLY C 361 " --> pdb=" O ASN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 384 removed outlier: 3.596A pdb=" N LYS C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 422 removed outlier: 3.665A pdb=" N ARG C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 441 through 456 removed outlier: 3.568A pdb=" N CYS C 445 " --> pdb=" O ASN C 441 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 447 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 471 through 479 removed outlier: 4.017A pdb=" N GLY C 475 " --> pdb=" O GLY C 471 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 477 " --> pdb=" O GLY C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.676A pdb=" N VAL C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 removed outlier: 3.596A pdb=" N HIS D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 68 removed outlier: 3.877A pdb=" N GLU D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 165 removed outlier: 3.808A pdb=" N GLY D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.528A pdb=" N LEU D 221 " --> pdb=" O ASP D 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 252 removed outlier: 3.831A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 removed outlier: 4.335A pdb=" N LYS D 280 " --> pdb=" O PRO D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.659A pdb=" N PHE D 296 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.851A pdb=" N ILE D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 341 removed outlier: 3.582A pdb=" N LEU D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 352 removed outlier: 3.588A pdb=" N TRP D 351 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 removed outlier: 3.643A pdb=" N GLY D 361 " --> pdb=" O ASN D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 384 removed outlier: 3.595A pdb=" N LYS D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 422 removed outlier: 3.666A pdb=" N ARG D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 Processing helix chain 'D' and resid 441 through 456 removed outlier: 3.567A pdb=" N CYS D 445 " --> pdb=" O ASN D 441 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 447 " --> pdb=" O TRP D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 471 through 479 removed outlier: 4.016A pdb=" N GLY D 475 " --> pdb=" O GLY D 471 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D 477 " --> pdb=" O GLY D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 484 removed outlier: 3.676A pdb=" N VAL D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.657A pdb=" N SER A 84 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE A 288 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 272 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR A 261 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER A 430 " --> pdb=" O CYS A 260 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 262 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE A 429 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE A 466 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS A 431 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123 removed outlier: 9.105A pdb=" N GLY A 179 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR A 99 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR A 181 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 101 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 180 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187 Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.657A pdb=" N SER B 84 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 288 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 272 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR B 261 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER B 430 " --> pdb=" O CYS B 260 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 262 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE B 429 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE B 466 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 431 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 123 removed outlier: 9.105A pdb=" N GLY B 179 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR B 99 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR B 181 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 101 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 180 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.658A pdb=" N SER C 84 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE C 288 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 272 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR C 261 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER C 430 " --> pdb=" O CYS C 260 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 262 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE C 429 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE C 466 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS C 431 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123 removed outlier: 9.105A pdb=" N GLY C 179 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C 99 " --> pdb=" O GLY C 179 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR C 181 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 101 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE C 180 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB1, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.657A pdb=" N SER D 84 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE D 288 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 272 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR D 261 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER D 430 " --> pdb=" O CYS D 260 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 262 " --> pdb=" O SER D 430 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE D 429 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE D 466 " --> pdb=" O PHE D 429 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS D 431 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 121 through 123 removed outlier: 9.105A pdb=" N GLY D 179 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR D 99 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR D 181 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 101 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE D 180 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 187 560 hydrogen bonds defined for protein. 1620 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: 2.03 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4479 1.35 - 1.48: 3365 1.48 - 1.61: 5920 1.61 - 1.74: 0 1.74 - 1.87: 128 Bond restraints: 13892 Sorted by residual: bond pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.06e+00 bond pdb=" CB CYS C 237 " pdb=" SG CYS C 237 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.05e+00 bond pdb=" CB CYS D 237 " pdb=" SG CYS D 237 " ideal model delta sigma weight residual 1.808 1.865 -0.057 3.30e-02 9.18e+02 3.01e+00 bond pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " ideal model delta sigma weight residual 1.808 1.865 -0.057 3.30e-02 9.18e+02 3.01e+00 bond pdb=" CA ASN B 315 " pdb=" C ASN B 315 " ideal model delta sigma weight residual 1.531 1.517 0.014 1.12e-02 7.97e+03 1.53e+00 ... (remaining 13887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 18561 2.53 - 5.05: 163 5.05 - 7.58: 16 7.58 - 10.10: 4 10.10 - 12.63: 4 Bond angle restraints: 18748 Sorted by residual: angle pdb=" N CYS B 236 " pdb=" CA CYS B 236 " pdb=" C CYS B 236 " ideal model delta sigma weight residual 111.00 123.63 -12.63 2.80e+00 1.28e-01 2.03e+01 angle pdb=" N CYS A 236 " pdb=" CA CYS A 236 " pdb=" C CYS A 236 " ideal model delta sigma weight residual 111.00 123.62 -12.62 2.80e+00 1.28e-01 2.03e+01 angle pdb=" N CYS D 236 " pdb=" CA CYS D 236 " pdb=" C CYS D 236 " ideal model delta sigma weight residual 111.00 123.62 -12.62 2.80e+00 1.28e-01 2.03e+01 angle pdb=" N CYS C 236 " pdb=" CA CYS C 236 " pdb=" C CYS C 236 " ideal model delta sigma weight residual 111.00 123.58 -12.58 2.80e+00 1.28e-01 2.02e+01 angle pdb=" C CYS B 236 " pdb=" CA CYS B 236 " pdb=" CB CYS B 236 " ideal model delta sigma weight residual 110.10 102.91 7.19 1.90e+00 2.77e-01 1.43e+01 ... (remaining 18743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 7302 16.03 - 32.07: 850 32.07 - 48.10: 152 48.10 - 64.14: 28 64.14 - 80.17: 20 Dihedral angle restraints: 8352 sinusoidal: 3332 harmonic: 5020 Sorted by residual: dihedral pdb=" CA CYS C 236 " pdb=" C CYS C 236 " pdb=" N CYS C 237 " pdb=" CA CYS C 237 " ideal model delta harmonic sigma weight residual 180.00 123.07 56.93 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA CYS D 236 " pdb=" C CYS D 236 " pdb=" N CYS D 237 " pdb=" CA CYS D 237 " ideal model delta harmonic sigma weight residual 180.00 123.08 56.92 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA CYS A 236 " pdb=" C CYS A 236 " pdb=" N CYS A 237 " pdb=" CA CYS A 237 " ideal model delta harmonic sigma weight residual 180.00 123.09 56.91 0 5.00e+00 4.00e-02 1.30e+02 ... (remaining 8349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1819 0.064 - 0.127: 218 0.127 - 0.191: 15 0.191 - 0.254: 0 0.254 - 0.318: 4 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA CYS D 236 " pdb=" N CYS D 236 " pdb=" C CYS D 236 " pdb=" CB CYS D 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA CYS A 236 " pdb=" N CYS A 236 " pdb=" C CYS A 236 " pdb=" CB CYS A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA CYS B 236 " pdb=" N CYS B 236 " pdb=" C CYS B 236 " pdb=" CB CYS B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 2053 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 68 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO A 69 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 68 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 69 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 68 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO C 69 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " -0.022 5.00e-02 4.00e+02 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 152 2.66 - 3.22: 13210 3.22 - 3.78: 18997 3.78 - 4.34: 26786 4.34 - 4.90: 44694 Nonbonded interactions: 103839 Sorted by model distance: nonbonded pdb=" O CYS A 445 " pdb=" NE2 GLN A 449 " model vdw 2.094 3.120 nonbonded pdb=" O CYS B 445 " pdb=" NE2 GLN B 449 " model vdw 2.094 3.120 nonbonded pdb=" O CYS D 445 " pdb=" NE2 GLN D 449 " model vdw 2.095 3.120 nonbonded pdb=" O CYS C 445 " pdb=" NE2 GLN C 449 " model vdw 2.095 3.120 nonbonded pdb=" O GLU B 359 " pdb=" OG SER B 362 " model vdw 2.269 3.040 ... (remaining 103834 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: 0.03 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13896 Z= 0.180 Angle : 0.695 12.631 18756 Z= 0.406 Chirality : 0.044 0.318 2056 Planarity : 0.003 0.041 2404 Dihedral : 14.054 80.169 5100 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.54 % Allowed : 5.96 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.60 (0.17), residues: 1700 helix: -1.44 (0.18), residues: 688 sheet: -1.95 (0.34), residues: 212 loop : -3.44 (0.17), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 216 TYR 0.016 0.001 TYR B 284 PHE 0.014 0.002 PHE B 54 TRP 0.006 0.001 TRP B 199 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00383 (13892) covalent geometry : angle 0.69089 (18748) SS BOND : bond 0.01150 ( 4) SS BOND : angle 3.55014 ( 8) hydrogen bonds : bond 0.19505 ( 560) hydrogen bonds : angle 6.55002 ( 1620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5303 (mtp) cc_final: 0.4798 (mmm) REVERT: A 299 ASP cc_start: 0.7097 (p0) cc_final: 0.6838 (p0) REVERT: B 164 MET cc_start: 0.5353 (mtp) cc_final: 0.4793 (mmm) REVERT: B 299 ASP cc_start: 0.7147 (p0) cc_final: 0.6926 (p0) REVERT: C 112 ARG cc_start: 0.6056 (mtp180) cc_final: 0.5076 (mtp180) REVERT: C 164 MET cc_start: 0.5376 (mtp) cc_final: 0.4940 (mmm) REVERT: C 203 PHE cc_start: 0.6420 (m-80) cc_final: 0.6180 (m-80) REVERT: C 299 ASP cc_start: 0.7132 (p0) cc_final: 0.6864 (p0) REVERT: D 164 MET cc_start: 0.5106 (mtp) cc_final: 0.4621 (mmm) REVERT: D 299 ASP cc_start: 0.7038 (p0) cc_final: 0.6808 (p0) outliers start: 8 outliers final: 4 residues processed: 227 average time/residue: 0.1404 time to fit residues: 43.4586 Evaluate side-chains 142 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain D residue 236 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 295 ASN A 391 GLN A 426 HIS B 36 HIS B 295 ASN B 391 GLN B 426 HIS C 36 HIS C 295 ASN C 391 GLN C 426 HIS D 36 HIS D 391 GLN D 426 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110770 restraints weight = 22090.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112682 restraints weight = 14776.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113835 restraints weight = 11642.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114301 restraints weight = 10160.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114962 restraints weight = 9488.336| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 13896 Z= 0.240 Angle : 0.676 7.976 18756 Z= 0.360 Chirality : 0.046 0.150 2056 Planarity : 0.004 0.045 2404 Dihedral : 5.714 35.458 1860 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 2.44 % Allowed : 12.47 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.62 (0.19), residues: 1700 helix: -0.40 (0.19), residues: 708 sheet: -1.75 (0.36), residues: 212 loop : -3.09 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 216 TYR 0.021 0.002 TYR D 284 PHE 0.017 0.002 PHE C 108 TRP 0.008 0.002 TRP D 72 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00574 (13892) covalent geometry : angle 0.66885 (18748) SS BOND : bond 0.01069 ( 4) SS BOND : angle 4.88958 ( 8) hydrogen bonds : bond 0.06378 ( 560) hydrogen bonds : angle 5.31276 ( 1620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.515 Fit side-chains REVERT: A 164 MET cc_start: 0.5390 (mtp) cc_final: 0.4781 (mmm) REVERT: A 246 LEU cc_start: 0.8754 (tp) cc_final: 0.8322 (tt) REVERT: A 299 ASP cc_start: 0.7377 (p0) cc_final: 0.7049 (p0) REVERT: B 164 MET cc_start: 0.5396 (mtp) cc_final: 0.4735 (mmm) REVERT: B 221 LEU cc_start: 0.7192 (tt) cc_final: 0.6752 (tt) REVERT: B 246 LEU cc_start: 0.8773 (tp) cc_final: 0.8329 (tt) REVERT: C 164 MET cc_start: 0.5320 (mtp) cc_final: 0.4763 (mmm) REVERT: C 246 LEU cc_start: 0.8725 (tp) cc_final: 0.8287 (tt) REVERT: C 299 ASP cc_start: 0.7380 (p0) cc_final: 0.7048 (p0) REVERT: D 153 PHE cc_start: 0.4800 (m-10) cc_final: 0.4561 (m-10) REVERT: D 164 MET cc_start: 0.5264 (mtp) cc_final: 0.4680 (mmm) REVERT: D 221 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6774 (tt) REVERT: D 299 ASP cc_start: 0.7376 (p0) cc_final: 0.7090 (p0) outliers start: 36 outliers final: 23 residues processed: 207 average time/residue: 0.1119 time to fit residues: 34.2899 Evaluate side-chains 183 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 63 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 171 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111913 restraints weight = 22142.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113843 restraints weight = 14536.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115104 restraints weight = 11366.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115797 restraints weight = 9818.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116005 restraints weight = 9031.266| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 13896 Z= 0.223 Angle : 0.743 17.681 18756 Z= 0.372 Chirality : 0.051 0.507 2056 Planarity : 0.004 0.045 2404 Dihedral : 6.160 62.254 1856 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 2.85 % Allowed : 14.70 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.29 (0.19), residues: 1700 helix: -0.10 (0.19), residues: 712 sheet: -1.38 (0.38), residues: 192 loop : -2.98 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 216 TYR 0.018 0.002 TYR D 284 PHE 0.017 0.002 PHE C 108 TRP 0.008 0.002 TRP C 72 HIS 0.004 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00545 (13892) covalent geometry : angle 0.73246 (18748) SS BOND : bond 0.02744 ( 4) SS BOND : angle 6.05508 ( 8) hydrogen bonds : bond 0.06039 ( 560) hydrogen bonds : angle 5.15967 ( 1620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.509 Fit side-chains REVERT: A 112 ARG cc_start: 0.6136 (mtp180) cc_final: 0.5825 (ttt180) REVERT: A 164 MET cc_start: 0.5291 (mtp) cc_final: 0.4700 (mmm) REVERT: B 112 ARG cc_start: 0.6150 (mtp180) cc_final: 0.5831 (ttt180) REVERT: B 164 MET cc_start: 0.5325 (mtp) cc_final: 0.4696 (mmm) REVERT: B 221 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7038 (tt) REVERT: C 112 ARG cc_start: 0.6136 (mtp180) cc_final: 0.5841 (ttt180) REVERT: C 164 MET cc_start: 0.5293 (mtp) cc_final: 0.4744 (mmm) REVERT: D 153 PHE cc_start: 0.4561 (m-80) cc_final: 0.4338 (m-10) REVERT: D 164 MET cc_start: 0.5211 (mtp) cc_final: 0.4636 (mmm) REVERT: D 221 LEU cc_start: 0.7287 (tt) cc_final: 0.6820 (tt) REVERT: D 299 ASP cc_start: 0.7409 (p0) cc_final: 0.7068 (p0) outliers start: 42 outliers final: 28 residues processed: 186 average time/residue: 0.1066 time to fit residues: 29.9793 Evaluate side-chains 178 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 26 optimal weight: 0.0040 chunk 47 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117202 restraints weight = 21899.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119707 restraints weight = 12980.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121333 restraints weight = 9524.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122158 restraints weight = 7907.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122862 restraints weight = 7153.717| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 13896 Z= 0.106 Angle : 0.596 12.650 18756 Z= 0.302 Chirality : 0.043 0.272 2056 Planarity : 0.003 0.036 2404 Dihedral : 5.522 53.840 1856 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.03 % Allowed : 16.33 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.68 (0.20), residues: 1700 helix: 0.48 (0.20), residues: 712 sheet: -1.25 (0.38), residues: 192 loop : -2.67 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 216 TYR 0.010 0.001 TYR C 251 PHE 0.015 0.001 PHE C 108 TRP 0.004 0.001 TRP D 383 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00223 (13892) covalent geometry : angle 0.58760 (18748) SS BOND : bond 0.01789 ( 4) SS BOND : angle 4.74501 ( 8) hydrogen bonds : bond 0.04075 ( 560) hydrogen bonds : angle 4.69198 ( 1620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.525 Fit side-chains REVERT: A 112 ARG cc_start: 0.5968 (mtp180) cc_final: 0.5706 (ttt180) REVERT: A 164 MET cc_start: 0.5226 (mtp) cc_final: 0.4682 (mmm) REVERT: A 221 LEU cc_start: 0.7126 (tt) cc_final: 0.6841 (tt) REVERT: A 299 ASP cc_start: 0.7377 (p0) cc_final: 0.7053 (p0) REVERT: B 112 ARG cc_start: 0.6002 (mtp180) cc_final: 0.5736 (ttt180) REVERT: B 164 MET cc_start: 0.5198 (mtp) cc_final: 0.4633 (mmm) REVERT: B 221 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6861 (tt) REVERT: B 299 ASP cc_start: 0.7424 (p0) cc_final: 0.7108 (p0) REVERT: C 112 ARG cc_start: 0.6040 (mtp180) cc_final: 0.5709 (ttt180) REVERT: C 164 MET cc_start: 0.5358 (mtp) cc_final: 0.4844 (mmm) REVERT: C 221 LEU cc_start: 0.7426 (tt) cc_final: 0.7196 (tt) REVERT: D 112 ARG cc_start: 0.6239 (mtp180) cc_final: 0.5892 (ttt180) REVERT: D 164 MET cc_start: 0.4835 (mtp) cc_final: 0.4469 (mmm) REVERT: D 221 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6684 (tt) REVERT: D 299 ASP cc_start: 0.7383 (p0) cc_final: 0.7072 (p0) outliers start: 30 outliers final: 12 residues processed: 210 average time/residue: 0.1170 time to fit residues: 35.9458 Evaluate side-chains 177 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 96 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 165 optimal weight: 0.1980 chunk 125 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.139991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113699 restraints weight = 22140.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115916 restraints weight = 13654.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117380 restraints weight = 10298.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118075 restraints weight = 8712.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118685 restraints weight = 7958.984| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 13896 Z= 0.179 Angle : 0.730 22.465 18756 Z= 0.358 Chirality : 0.052 0.638 2056 Planarity : 0.003 0.041 2404 Dihedral : 5.833 64.122 1856 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.51 % Allowed : 17.75 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.67 (0.20), residues: 1700 helix: 0.48 (0.20), residues: 712 sheet: -1.30 (0.38), residues: 192 loop : -2.64 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 123 TYR 0.022 0.002 TYR B 284 PHE 0.014 0.001 PHE C 108 TRP 0.007 0.001 TRP D 199 HIS 0.009 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00441 (13892) covalent geometry : angle 0.71426 (18748) SS BOND : bond 0.02384 ( 4) SS BOND : angle 7.29877 ( 8) hydrogen bonds : bond 0.05071 ( 560) hydrogen bonds : angle 4.84410 ( 1620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.549 Fit side-chains REVERT: A 112 ARG cc_start: 0.6108 (mtp180) cc_final: 0.5829 (ttt180) REVERT: A 164 MET cc_start: 0.5302 (mtp) cc_final: 0.4663 (mmm) REVERT: A 221 LEU cc_start: 0.7239 (tt) cc_final: 0.6907 (tt) REVERT: B 112 ARG cc_start: 0.6113 (mtp180) cc_final: 0.5870 (ttt180) REVERT: B 164 MET cc_start: 0.5326 (mtp) cc_final: 0.4617 (mmm) REVERT: B 221 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6816 (tt) REVERT: C 112 ARG cc_start: 0.6110 (mtp180) cc_final: 0.5772 (ttt180) REVERT: C 164 MET cc_start: 0.5395 (mtp) cc_final: 0.4900 (mmm) REVERT: C 221 LEU cc_start: 0.7589 (tt) cc_final: 0.7322 (tt) REVERT: D 112 ARG cc_start: 0.6424 (mtp180) cc_final: 0.6122 (ttt180) REVERT: D 164 MET cc_start: 0.5011 (mtp) cc_final: 0.4536 (mmm) REVERT: D 221 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6976 (tt) outliers start: 37 outliers final: 31 residues processed: 185 average time/residue: 0.1109 time to fit residues: 30.5224 Evaluate side-chains 186 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 131 optimal weight: 0.3980 chunk 14 optimal weight: 0.0050 chunk 136 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN C 70 ASN D 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119261 restraints weight = 21877.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121532 restraints weight = 13652.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122991 restraints weight = 10262.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123918 restraints weight = 8672.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124348 restraints weight = 7831.112| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 13896 Z= 0.108 Angle : 0.583 13.910 18756 Z= 0.294 Chirality : 0.044 0.379 2056 Planarity : 0.003 0.033 2404 Dihedral : 5.396 60.130 1856 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.05 % Allowed : 18.36 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.22 (0.20), residues: 1700 helix: 0.92 (0.20), residues: 712 sheet: -1.24 (0.38), residues: 192 loop : -2.41 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 123 TYR 0.005 0.001 TYR D 282 PHE 0.012 0.001 PHE A 108 TRP 0.004 0.001 TRP C 383 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00239 (13892) covalent geometry : angle 0.57608 (18748) SS BOND : bond 0.02176 ( 4) SS BOND : angle 4.36522 ( 8) hydrogen bonds : bond 0.03571 ( 560) hydrogen bonds : angle 4.51417 ( 1620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6019 (mtp180) cc_final: 0.5763 (ttt180) REVERT: A 164 MET cc_start: 0.5012 (mtp) cc_final: 0.4701 (mmm) REVERT: A 221 LEU cc_start: 0.7294 (tt) cc_final: 0.6939 (tt) REVERT: A 299 ASP cc_start: 0.7319 (p0) cc_final: 0.6985 (p0) REVERT: B 112 ARG cc_start: 0.6036 (mtp180) cc_final: 0.5782 (ttt180) REVERT: B 164 MET cc_start: 0.5057 (mtp) cc_final: 0.4695 (mmm) REVERT: B 221 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6972 (tt) REVERT: B 299 ASP cc_start: 0.7287 (p0) cc_final: 0.7024 (p0) REVERT: B 449 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7305 (mp-120) REVERT: C 112 ARG cc_start: 0.6016 (mtp180) cc_final: 0.5698 (ttt180) REVERT: C 164 MET cc_start: 0.5063 (mtp) cc_final: 0.4727 (mmm) REVERT: C 221 LEU cc_start: 0.7514 (tt) cc_final: 0.7211 (tt) REVERT: C 449 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7349 (mp-120) REVERT: D 66 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7785 (ttm170) REVERT: D 112 ARG cc_start: 0.6267 (mtp180) cc_final: 0.5956 (ttt180) REVERT: D 221 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6982 (tt) REVERT: D 299 ASP cc_start: 0.7293 (p0) cc_final: 0.6997 (p0) REVERT: D 449 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7294 (mp-120) outliers start: 45 outliers final: 27 residues processed: 214 average time/residue: 0.1065 time to fit residues: 34.3199 Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 111 optimal weight: 0.2980 chunk 25 optimal weight: 0.1980 chunk 166 optimal weight: 6.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120801 restraints weight = 21783.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123152 restraints weight = 13624.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124600 restraints weight = 10200.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125552 restraints weight = 8621.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125901 restraints weight = 7776.639| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 13896 Z= 0.123 Angle : 0.714 25.291 18756 Z= 0.340 Chirality : 0.051 0.704 2056 Planarity : 0.003 0.030 2404 Dihedral : 5.362 66.294 1856 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.98 % Allowed : 18.70 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.21), residues: 1700 helix: 1.17 (0.20), residues: 716 sheet: -1.43 (0.36), residues: 192 loop : -2.25 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 123 TYR 0.007 0.001 TYR B 284 PHE 0.011 0.001 PHE D 108 TRP 0.006 0.001 TRP A 199 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00317 (13892) covalent geometry : angle 0.68361 (18748) SS BOND : bond 0.02293 ( 4) SS BOND : angle 9.91896 ( 8) hydrogen bonds : bond 0.03307 ( 560) hydrogen bonds : angle 4.37424 ( 1620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.547 Fit side-chains REVERT: A 112 ARG cc_start: 0.6023 (mtp180) cc_final: 0.5699 (ttt180) REVERT: A 164 MET cc_start: 0.5021 (mtp) cc_final: 0.4721 (mmm) REVERT: A 203 PHE cc_start: 0.6587 (m-80) cc_final: 0.6331 (m-80) REVERT: A 221 LEU cc_start: 0.7274 (tt) cc_final: 0.6969 (tt) REVERT: A 299 ASP cc_start: 0.7249 (p0) cc_final: 0.6913 (p0) REVERT: A 449 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: B 112 ARG cc_start: 0.6116 (mtp180) cc_final: 0.5781 (ttt180) REVERT: B 153 PHE cc_start: 0.4520 (m-10) cc_final: 0.4307 (m-10) REVERT: B 164 MET cc_start: 0.5032 (mtp) cc_final: 0.4723 (mmm) REVERT: B 203 PHE cc_start: 0.6593 (m-80) cc_final: 0.6347 (m-80) REVERT: B 221 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6840 (tt) REVERT: B 299 ASP cc_start: 0.7206 (p0) cc_final: 0.6921 (p0) REVERT: B 449 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: C 112 ARG cc_start: 0.6121 (mtp180) cc_final: 0.5736 (ttt180) REVERT: C 164 MET cc_start: 0.5134 (mtp) cc_final: 0.4827 (mmm) REVERT: C 203 PHE cc_start: 0.6499 (m-80) cc_final: 0.6294 (m-80) REVERT: C 221 LEU cc_start: 0.7492 (tt) cc_final: 0.7152 (tt) REVERT: C 449 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: D 66 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7737 (ttm170) REVERT: D 112 ARG cc_start: 0.6279 (mtp180) cc_final: 0.5941 (ttt180) REVERT: D 153 PHE cc_start: 0.4400 (m-10) cc_final: 0.4160 (m-10) REVERT: D 203 PHE cc_start: 0.6635 (m-80) cc_final: 0.6367 (m-80) REVERT: D 221 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6945 (tt) REVERT: D 299 ASP cc_start: 0.7213 (p0) cc_final: 0.6911 (p0) REVERT: D 449 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: D 456 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7158 (pp) outliers start: 44 outliers final: 26 residues processed: 215 average time/residue: 0.1282 time to fit residues: 39.4852 Evaluate side-chains 204 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 456 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 110 optimal weight: 0.2980 chunk 106 optimal weight: 8.9990 chunk 154 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 169 optimal weight: 0.0470 chunk 38 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118134 restraints weight = 22086.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120629 restraints weight = 13312.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122243 restraints weight = 9855.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.123233 restraints weight = 8207.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123640 restraints weight = 7358.405| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 13896 Z= 0.132 Angle : 0.658 20.707 18756 Z= 0.321 Chirality : 0.049 0.587 2056 Planarity : 0.003 0.031 2404 Dihedral : 5.318 63.784 1856 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.57 % Allowed : 19.85 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.21), residues: 1700 helix: 1.19 (0.20), residues: 716 sheet: -1.45 (0.36), residues: 192 loop : -2.26 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 123 TYR 0.012 0.001 TYR B 284 PHE 0.012 0.001 PHE B 108 TRP 0.005 0.001 TRP C 443 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00336 (13892) covalent geometry : angle 0.64186 (18748) SS BOND : bond 0.02251 ( 4) SS BOND : angle 7.00386 ( 8) hydrogen bonds : bond 0.03800 ( 560) hydrogen bonds : angle 4.44137 ( 1620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6026 (mtp180) cc_final: 0.5783 (ttt180) REVERT: A 153 PHE cc_start: 0.4704 (m-10) cc_final: 0.4441 (m-10) REVERT: A 164 MET cc_start: 0.5039 (mtp) cc_final: 0.4720 (mmm) REVERT: A 221 LEU cc_start: 0.7311 (tt) cc_final: 0.6894 (tt) REVERT: A 299 ASP cc_start: 0.7227 (p0) cc_final: 0.6945 (p0) REVERT: A 449 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7320 (mp-120) REVERT: B 112 ARG cc_start: 0.6138 (mtp180) cc_final: 0.5804 (ttt180) REVERT: B 153 PHE cc_start: 0.4499 (m-10) cc_final: 0.4261 (m-10) REVERT: B 164 MET cc_start: 0.5067 (mtp) cc_final: 0.4714 (mmm) REVERT: B 221 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6950 (tt) REVERT: B 299 ASP cc_start: 0.7220 (p0) cc_final: 0.6964 (p0) REVERT: B 449 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7308 (mp-120) REVERT: C 112 ARG cc_start: 0.6116 (mtp180) cc_final: 0.5743 (ttt180) REVERT: C 164 MET cc_start: 0.5138 (mtp) cc_final: 0.4813 (mmm) REVERT: C 221 LEU cc_start: 0.7601 (tt) cc_final: 0.7369 (tt) REVERT: D 66 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7853 (ttm170) REVERT: D 112 ARG cc_start: 0.6256 (mtp180) cc_final: 0.5950 (ttt180) REVERT: D 153 PHE cc_start: 0.4440 (m-10) cc_final: 0.4208 (m-10) REVERT: D 221 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6962 (tt) REVERT: D 299 ASP cc_start: 0.7202 (p0) cc_final: 0.6925 (p0) REVERT: D 456 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7111 (pp) outliers start: 38 outliers final: 27 residues processed: 202 average time/residue: 0.1083 time to fit residues: 32.4250 Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 456 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 30 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 0.0030 chunk 48 optimal weight: 0.0020 chunk 18 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.141938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115968 restraints weight = 22006.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118294 restraints weight = 13607.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119789 restraints weight = 10185.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120667 restraints weight = 8575.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121124 restraints weight = 7748.276| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13896 Z= 0.162 Angle : 0.665 18.575 18756 Z= 0.330 Chirality : 0.049 0.523 2056 Planarity : 0.003 0.034 2404 Dihedral : 5.466 62.100 1856 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.71 % Allowed : 20.05 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.09 (0.20), residues: 1700 helix: 1.04 (0.20), residues: 716 sheet: -1.39 (0.37), residues: 192 loop : -2.31 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 123 TYR 0.019 0.001 TYR B 284 PHE 0.013 0.001 PHE C 108 TRP 0.007 0.001 TRP D 383 HIS 0.005 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00398 (13892) covalent geometry : angle 0.65534 (18748) SS BOND : bond 0.02349 ( 4) SS BOND : angle 5.63500 ( 8) hydrogen bonds : bond 0.04566 ( 560) hydrogen bonds : angle 4.59022 ( 1620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.514 Fit side-chains REVERT: A 112 ARG cc_start: 0.6067 (mtp180) cc_final: 0.5829 (ttt180) REVERT: A 153 PHE cc_start: 0.4661 (m-10) cc_final: 0.4382 (m-10) REVERT: A 164 MET cc_start: 0.5061 (mtp) cc_final: 0.4525 (mmt) REVERT: A 221 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6961 (tt) REVERT: A 299 ASP cc_start: 0.7311 (p0) cc_final: 0.7050 (p0) REVERT: A 449 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7343 (mp-120) REVERT: B 112 ARG cc_start: 0.6213 (mtp180) cc_final: 0.5905 (ttt180) REVERT: B 164 MET cc_start: 0.5116 (mtp) cc_final: 0.4557 (mmt) REVERT: B 221 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7086 (tt) REVERT: B 299 ASP cc_start: 0.7299 (p0) cc_final: 0.7068 (p0) REVERT: B 449 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7333 (mp-120) REVERT: C 112 ARG cc_start: 0.6105 (mtp180) cc_final: 0.5829 (ttt180) REVERT: C 153 PHE cc_start: 0.4929 (m-10) cc_final: 0.4692 (m-10) REVERT: C 164 MET cc_start: 0.5115 (mtp) cc_final: 0.4833 (mmm) REVERT: C 221 LEU cc_start: 0.7720 (tt) cc_final: 0.7383 (tt) REVERT: C 449 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7385 (mp-120) REVERT: D 112 ARG cc_start: 0.6319 (mtp180) cc_final: 0.5986 (ttt180) REVERT: D 221 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7077 (tt) REVERT: D 299 ASP cc_start: 0.7296 (p0) cc_final: 0.7070 (p0) REVERT: D 449 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7348 (mp-120) outliers start: 40 outliers final: 28 residues processed: 201 average time/residue: 0.1135 time to fit residues: 33.9765 Evaluate side-chains 199 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 2 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 41 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 161 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118278 restraints weight = 21805.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120608 restraints weight = 13540.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122094 restraints weight = 10125.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122944 restraints weight = 8530.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123544 restraints weight = 7708.726| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13896 Z= 0.116 Angle : 0.617 17.551 18756 Z= 0.306 Chirality : 0.046 0.481 2056 Planarity : 0.003 0.032 2404 Dihedral : 5.309 61.763 1856 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.44 % Allowed : 20.53 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.96 (0.21), residues: 1700 helix: 1.18 (0.20), residues: 716 sheet: -1.42 (0.36), residues: 192 loop : -2.24 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 123 TYR 0.007 0.001 TYR B 284 PHE 0.012 0.001 PHE D 108 TRP 0.004 0.001 TRP C 443 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00276 (13892) covalent geometry : angle 0.60843 (18748) SS BOND : bond 0.02303 ( 4) SS BOND : angle 5.00510 ( 8) hydrogen bonds : bond 0.03823 ( 560) hydrogen bonds : angle 4.45619 ( 1620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6081 (mtp180) cc_final: 0.5776 (ttt180) REVERT: A 153 PHE cc_start: 0.4547 (m-10) cc_final: 0.4270 (m-10) REVERT: A 164 MET cc_start: 0.4900 (mtp) cc_final: 0.4666 (mmm) REVERT: A 221 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6993 (tt) REVERT: A 299 ASP cc_start: 0.7242 (p0) cc_final: 0.6983 (p0) REVERT: B 112 ARG cc_start: 0.6211 (mtp180) cc_final: 0.5894 (ttt180) REVERT: B 164 MET cc_start: 0.5020 (mtp) cc_final: 0.4451 (mmt) REVERT: B 221 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7174 (tt) REVERT: B 299 ASP cc_start: 0.7260 (p0) cc_final: 0.6992 (p0) REVERT: C 112 ARG cc_start: 0.6083 (mtp180) cc_final: 0.5794 (ttt180) REVERT: C 153 PHE cc_start: 0.4861 (m-10) cc_final: 0.4627 (m-10) REVERT: C 221 LEU cc_start: 0.7687 (tt) cc_final: 0.7326 (tt) REVERT: D 112 ARG cc_start: 0.6300 (mtp180) cc_final: 0.5994 (ttt180) REVERT: D 221 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7163 (tt) REVERT: D 299 ASP cc_start: 0.7235 (p0) cc_final: 0.7001 (p0) outliers start: 36 outliers final: 31 residues processed: 199 average time/residue: 0.1090 time to fit residues: 32.4257 Evaluate side-chains 204 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 72 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113616 restraints weight = 22333.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115912 restraints weight = 13901.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117357 restraints weight = 10485.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118128 restraints weight = 8902.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118615 restraints weight = 8133.463| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 13896 Z= 0.196 Angle : 0.681 16.985 18756 Z= 0.342 Chirality : 0.049 0.459 2056 Planarity : 0.003 0.035 2404 Dihedral : 5.570 59.537 1856 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 2.78 % Allowed : 20.05 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.26 (0.20), residues: 1700 helix: 0.87 (0.20), residues: 716 sheet: -1.41 (0.37), residues: 192 loop : -2.38 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 123 TYR 0.025 0.002 TYR B 284 PHE 0.015 0.002 PHE D 108 TRP 0.008 0.002 TRP D 383 HIS 0.006 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00475 (13892) covalent geometry : angle 0.67378 (18748) SS BOND : bond 0.02168 ( 4) SS BOND : angle 4.87488 ( 8) hydrogen bonds : bond 0.05103 ( 560) hydrogen bonds : angle 4.72377 ( 1620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1939.59 seconds wall clock time: 34 minutes 23.89 seconds (2063.89 seconds total)