Starting phenix.real_space_refine on Wed Aug 5 22:40:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s8p_19811/08_2026/8s8p_19811.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s8p_19811/08_2026/8s8p_19811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8s8p_19811/08_2026/8s8p_19811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s8p_19811/08_2026/8s8p_19811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s8p_19811/08_2026/8s8p_19811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s8p_19811/08_2026/8s8p_19811.map" } resolution = 3.11 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 43 5.16 5 C 7564 2.51 5 N 2057 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12134 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 414 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 441 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "K" Number of atoms: 4617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4617 Classifications: {'peptide': 557} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 535} Chain: "L" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4658 Classifications: {'peptide': 587} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 559} Chain: "R" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 2004 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 219} Time building chain proxies: 2.73, per 1000 atoms: 0.22 Number of scatterers: 12134 At special positions: 0 Unit cell: (103.806, 96.579, 159.651, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 40 15.00 O 2430 8.00 N 2057 7.00 C 7564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 459.7 milliseconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 37.9% alpha, 15.9% beta 19 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'K' and resid 39 through 44 Processing helix chain 'K' and resid 53 through 73 removed outlier: 3.966A pdb=" N ILE K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.689A pdb=" N GLY K 93 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE K 94 " --> pdb=" O LYS K 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 90 through 94' Processing helix chain 'K' and resid 104 through 120 removed outlier: 3.518A pdb=" N MET K 108 " --> pdb=" O ASN K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 130 Processing helix chain 'K' and resid 141 through 153 removed outlier: 3.652A pdb=" N PHE K 153 " --> pdb=" O MET K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 181 Processing helix chain 'K' and resid 183 through 199 Processing helix chain 'K' and resid 217 through 225 Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 396 through 409 removed outlier: 3.795A pdb=" N THR K 400 " --> pdb=" O GLY K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 488 removed outlier: 3.912A pdb=" N TYR K 487 " --> pdb=" O SER K 483 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE K 488 " --> pdb=" O ILE K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 499 Processing helix chain 'K' and resid 501 through 516 Processing helix chain 'K' and resid 527 through 539 Processing helix chain 'K' and resid 539 through 558 removed outlier: 3.636A pdb=" N ARG K 543 " --> pdb=" O ASP K 539 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS K 544 " --> pdb=" O ASP K 540 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU K 556 " --> pdb=" O ILE K 552 " (cutoff:3.500A) Processing helix chain 'K' and resid 564 through 584 removed outlier: 3.711A pdb=" N LYS K 568 " --> pdb=" O GLN K 564 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE K 580 " --> pdb=" O PHE K 576 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN K 581 " --> pdb=" O TYR K 577 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP K 582 " --> pdb=" O LYS K 578 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 19 Processing helix chain 'L' and resid 20 through 38 removed outlier: 3.580A pdb=" N LYS L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 94 Processing helix chain 'L' and resid 106 through 121 removed outlier: 3.557A pdb=" N LEU L 110 " --> pdb=" O MET L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 154 Processing helix chain 'L' and resid 175 through 183 removed outlier: 4.243A pdb=" N LEU L 179 " --> pdb=" O ASN L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 200 Processing helix chain 'L' and resid 327 through 334 removed outlier: 3.534A pdb=" N ASP L 332 " --> pdb=" O SER L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 358 removed outlier: 3.605A pdb=" N LEU L 358 " --> pdb=" O ARG L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 391 removed outlier: 3.632A pdb=" N LEU L 377 " --> pdb=" O CYS L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 467 through 481 removed outlier: 3.881A pdb=" N ASP L 471 " --> pdb=" O GLY L 467 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU L 472 " --> pdb=" O HIS L 468 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET L 481 " --> pdb=" O PHE L 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 501 Processing helix chain 'L' and resid 513 through 517 removed outlier: 3.775A pdb=" N GLN L 516 " --> pdb=" O ASN L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 547 Processing helix chain 'L' and resid 559 through 566 removed outlier: 4.183A pdb=" N LYS L 565 " --> pdb=" O SER L 561 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE L 566 " --> pdb=" O LEU L 562 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 584 Processing helix chain 'R' and resid 365 through 378 Processing helix chain 'R' and resid 379 through 382 removed outlier: 3.706A pdb=" N ARG R 382 " --> pdb=" O PRO R 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 379 through 382' Processing helix chain 'R' and resid 385 through 395 removed outlier: 3.530A pdb=" N ASP R 389 " --> pdb=" O HIS R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 410 Processing helix chain 'R' and resid 411 through 415 removed outlier: 3.891A pdb=" N LEU R 415 " --> pdb=" O SER R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 450 through 471 Processing helix chain 'R' and resid 521 through 534 removed outlier: 3.795A pdb=" N PHE R 525 " --> pdb=" O ILE R 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE R 526 " --> pdb=" O ALA R 522 " (cutoff:3.500A) Processing helix chain 'R' and resid 537 through 553 removed outlier: 3.618A pdb=" N TRP R 541 " --> pdb=" O THR R 537 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU R 550 " --> pdb=" O ARG R 546 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA R 551 " --> pdb=" O LYS R 547 " (cutoff:3.500A) Processing helix chain 'R' and resid 553 through 567 Processing sheet with id=AA1, first strand: chain 'K' and resid 95 through 102 removed outlier: 6.846A pdb=" N CYS K 80 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE K 78 " --> pdb=" O PRO K 99 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG K 101 " --> pdb=" O THR K 76 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR K 76 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU K 30 " --> pdb=" O ALA K 77 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLY K 79 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE K 32 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N TYR K 81 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE K 34 " --> pdb=" O TYR K 81 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N TYR K 83 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE K 36 " --> pdb=" O TYR K 83 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY K 31 " --> pdb=" O ARG K 167 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE K 169 " --> pdb=" O GLY K 31 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU K 33 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE K 171 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS K 35 " --> pdb=" O PHE K 171 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS K 166 " --> pdb=" O ASN K 202 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA K 204 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL K 168 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE K 206 " --> pdb=" O VAL K 168 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU K 170 " --> pdb=" O PHE K 206 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE K 208 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR K 172 " --> pdb=" O ILE K 208 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE K 248 " --> pdb=" O THR K 205 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE K 207 " --> pdb=" O ILE K 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 266 through 269 removed outlier: 6.606A pdb=" N GLY K 286 " --> pdb=" O MET K 267 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN K 269 " --> pdb=" O VAL K 284 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL K 284 " --> pdb=" O GLN K 269 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER K 385 " --> pdb=" O LEU K 446 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR K 447 " --> pdb=" O THR K 431 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU K 429 " --> pdb=" O VAL K 449 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LYS K 413 " --> pdb=" O PRO K 434 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP K 418 " --> pdb=" O ILE K 365 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE K 365 " --> pdb=" O TRP K 418 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LYS K 420 " --> pdb=" O LEU K 363 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU K 363 " --> pdb=" O LYS K 420 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP K 275 " --> pdb=" O ILE K 365 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N GLY K 367 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE K 280 " --> pdb=" O LEU K 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 308 through 311 removed outlier: 3.789A pdb=" N GLN K 310 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 313 through 319 removed outlier: 4.201A pdb=" N TYR L 282 " --> pdb=" O ILE L 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN L 286 " --> pdb=" O ILE L 304 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE L 304 " --> pdb=" O ASN L 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 341 through 342 removed outlier: 3.750A pdb=" N VAL L 274 " --> pdb=" O VAL L 262 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG L 272 " --> pdb=" O VAL L 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 394 through 395 Processing sheet with id=AA7, first strand: chain 'L' and resid 65 through 72 removed outlier: 6.635A pdb=" N CYS L 48 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER L 70 " --> pdb=" O ILE L 46 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE L 46 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU L 72 " --> pdb=" O ASP L 44 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASP L 44 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU L 4 " --> pdb=" O TRP L 45 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N SER L 47 " --> pdb=" O GLU L 4 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR L 6 " --> pdb=" O SER L 47 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N TYR L 49 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE L 8 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA L 51 " --> pdb=" O PHE L 8 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL L 10 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER L 5 " --> pdb=" O GLN L 129 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL L 131 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR L 7 " --> pdb=" O VAL L 131 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N PHE L 133 " --> pdb=" O THR L 7 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE L 9 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS L 128 " --> pdb=" O ARG L 157 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE L 159 " --> pdb=" O LYS L 128 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE L 130 " --> pdb=" O ILE L 159 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE L 161 " --> pdb=" O ILE L 130 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL L 132 " --> pdb=" O ILE L 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 248 through 250 removed outlier: 6.389A pdb=" N SER L 362 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA L 367 " --> pdb=" O LYS L 429 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N LYS L 429 " --> pdb=" O ALA L 367 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET L 408 " --> pdb=" O LEU L 436 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LYS L 392 " --> pdb=" O PRO L 413 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY L 346 " --> pdb=" O VAL L 395 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ARG L 397 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU L 344 " --> pdb=" O ARG L 397 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL L 399 " --> pdb=" O LEU L 342 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU L 342 " --> pdb=" O VAL L 399 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU L 342 " --> pdb=" O SER L 213 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU L 215 " --> pdb=" O LEU L 342 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU L 344 " --> pdb=" O GLU L 215 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ARG L 217 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY L 346 " --> pdb=" O ARG L 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 317 through 319 Processing sheet with id=AB1, first strand: chain 'R' and resid 418 through 419 Processing sheet with id=AB2, first strand: chain 'R' and resid 478 through 479 removed outlier: 3.585A pdb=" N THR R 496 " --> pdb=" O ARG R 478 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3489 1.34 - 1.45: 2062 1.45 - 1.57: 6763 1.57 - 1.69: 80 1.69 - 1.81: 71 Bond restraints: 12465 Sorted by residual: bond pdb=" C3' DG D 6 " pdb=" C2' DG D 6 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC C 8 " pdb=" C2' DC C 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA C 17 " pdb=" C2' DA C 17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.44e+00 bond pdb=" C3' DC C 16 " pdb=" C2' DC C 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.28e+00 bond pdb=" C3' DT D 21 " pdb=" C2' DT D 21 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.56e+00 ... (remaining 12460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 16665 1.89 - 3.78: 323 3.78 - 5.67: 24 5.67 - 7.55: 5 7.55 - 9.44: 1 Bond angle restraints: 17018 Sorted by residual: angle pdb=" N3 DT D 19 " pdb=" C4 DT D 19 " pdb=" O4 DT D 19 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT D 9 " pdb=" C4 DT D 9 " pdb=" O4 DT D 9 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT D 7 " pdb=" C4 DT D 7 " pdb=" O4 DT D 7 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" C GLU L 464 " pdb=" CA GLU L 464 " pdb=" CB GLU L 464 " ideal model delta sigma weight residual 116.34 110.54 5.80 1.40e+00 5.10e-01 1.72e+01 ... (remaining 17013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 7085 34.87 - 69.75: 423 69.75 - 104.62: 24 104.62 - 139.49: 0 139.49 - 174.37: 1 Dihedral angle restraints: 7533 sinusoidal: 3417 harmonic: 4116 Sorted by residual: dihedral pdb=" CA PHE R 363 " pdb=" C PHE R 363 " pdb=" N THR R 364 " pdb=" CA THR R 364 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA THR R 364 " pdb=" C THR R 364 " pdb=" N ASP R 365 " pdb=" CA ASP R 365 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C4' DC C 16 " pdb=" C3' DC C 16 " pdb=" O3' DC C 16 " pdb=" P DA C 17 " ideal model delta sinusoidal sigma weight residual 220.00 45.63 174.37 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1103 0.028 - 0.057: 491 0.057 - 0.085: 169 0.085 - 0.113: 96 0.113 - 0.142: 25 Chirality restraints: 1884 Sorted by residual: chirality pdb=" CA PHE R 363 " pdb=" N PHE R 363 " pdb=" C PHE R 363 " pdb=" CB PHE R 363 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" C3' DC C 16 " pdb=" C4' DC C 16 " pdb=" O3' DC C 16 " pdb=" C2' DC C 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE L 188 " pdb=" N ILE L 188 " pdb=" C ILE L 188 " pdb=" CB ILE L 188 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1881 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 558 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO L 559 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO L 559 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 559 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL K 388 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO K 389 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO K 389 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 389 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE L 489 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO L 490 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO L 490 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 490 " 0.022 5.00e-02 4.00e+02 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 419 2.71 - 3.26: 11661 3.26 - 3.80: 19419 3.80 - 4.35: 25064 4.35 - 4.90: 41126 Nonbonded interactions: 97689 Sorted by model distance: nonbonded pdb=" OE1 GLU K 37 " pdb=" OG1 THR K 172 " model vdw 2.162 3.040 nonbonded pdb=" O ARG R 382 " pdb=" OH TYR R 388 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR K 494 " pdb=" O PRO L 437 " model vdw 2.207 3.040 nonbonded pdb=" O PRO R 487 " pdb=" OG1 THR R 488 " model vdw 2.253 3.040 nonbonded pdb=" O ILE L 68 " pdb=" NH1 ARG L 86 " model vdw 2.267 3.120 ... (remaining 97684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.150 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.340 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.003 0.053 12465 Z= 0.233 Angle : 0.602 9.443 17018 Z= 0.396 Chirality : 0.041 0.142 1884 Planarity : 0.004 0.052 2055 Dihedral : 19.608 174.366 4865 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 0.31 % Allowed : 21.52 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.64 (0.22), residues: 1380 helix: 1.26 (0.24), residues: 465 sheet: -1.16 (0.38), residues: 170 loop : -1.38 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 543 TYR 0.014 0.001 TYR K 394 PHE 0.009 0.001 PHE K 98 TRP 0.014 0.001 TRP K 418 HIS 0.003 0.001 HIS L 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.23 (12465) covalent geometry : angle 0.60161 / 0.40 (17018) hydrogen bonds : bond 0.16772 / 19.19 ( 479) hydrogen bonds : angle 6.50329 / 8.52 ( 1300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: K 213 LYS cc_start: 0.7622 (tttm) cc_final: 0.7082 (tmtt) REVERT: R 412 SER cc_start: 0.7887 (p) cc_final: 0.7584 (p) outliers start: 4 outliers final: 3 residues processed: 132 average time/residue: 0.1112 time to fit residues: 21.1539 Evaluate side-chains 120 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 225 GLN L 390 ASN ** R 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.215056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.170294 restraints weight = 13734.998| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.75 r_work: 0.3700 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12465 Z= 0.182 Angle : 0.622 8.701 17018 Z= 0.335 Chirality : 0.044 0.254 1884 Planarity : 0.005 0.050 2055 Dihedral : 16.821 176.594 1978 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 3.29 % Allowed : 20.19 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.73 (0.22), residues: 1380 helix: 1.25 (0.24), residues: 472 sheet: -1.20 (0.39), residues: 169 loop : -1.51 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 543 TYR 0.019 0.002 TYR L 532 PHE 0.015 0.002 PHE K 98 TRP 0.011 0.002 TRP K 418 HIS 0.005 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (12465) covalent geometry : angle 0.62183 / 0.33 (17018) hydrogen bonds : bond 0.04426 / 4.96 ( 479) hydrogen bonds : angle 5.32766 / 7.12 ( 1300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: K 216 ASP cc_start: 0.7230 (m-30) cc_final: 0.6965 (t0) REVERT: L 142 ILE cc_start: 0.4098 (OUTLIER) cc_final: 0.3720 (mt) REVERT: L 181 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: R 543 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6263 (t0) outliers start: 42 outliers final: 25 residues processed: 150 average time/residue: 0.0953 time to fit residues: 21.1309 Evaluate side-chains 140 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 449 VAL Chi-restraints excluded: chain K residue 485 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 543 ASP Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 333 GLN L 513 ASN ** R 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.216583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.171687 restraints weight = 13784.349| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.56 r_work: 0.3732 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12465 Z= 0.135 Angle : 0.566 7.797 17018 Z= 0.305 Chirality : 0.042 0.252 1884 Planarity : 0.004 0.047 2055 Dihedral : 16.800 176.748 1976 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.68 % Allowed : 20.50 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.68 (0.22), residues: 1380 helix: 1.27 (0.24), residues: 474 sheet: -1.21 (0.38), residues: 176 loop : -1.47 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 543 TYR 0.013 0.001 TYR R 388 PHE 0.012 0.001 PHE K 98 TRP 0.007 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (12465) covalent geometry : angle 0.56561 / 0.30 (17018) hydrogen bonds : bond 0.03978 / 4.44 ( 479) hydrogen bonds : angle 5.08552 / 6.82 ( 1300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 213 LYS cc_start: 0.7665 (tttm) cc_final: 0.7108 (tmtt) REVERT: K 216 ASP cc_start: 0.7221 (m-30) cc_final: 0.6996 (t0) REVERT: L 142 ILE cc_start: 0.4041 (OUTLIER) cc_final: 0.3662 (mt) REVERT: L 181 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: L 324 VAL cc_start: 0.7363 (OUTLIER) cc_final: 0.7102 (m) REVERT: R 543 ASP cc_start: 0.6505 (OUTLIER) cc_final: 0.6266 (t0) outliers start: 47 outliers final: 25 residues processed: 164 average time/residue: 0.0871 time to fit residues: 21.5462 Evaluate side-chains 150 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 485 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 333 GLN Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 543 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 74 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.0170 chunk 120 optimal weight: 0.5980 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 405 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.218919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174506 restraints weight = 13738.489| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.40 r_work: 0.3792 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12465 Z= 0.109 Angle : 0.536 7.404 17018 Z= 0.292 Chirality : 0.041 0.259 1884 Planarity : 0.004 0.045 2055 Dihedral : 16.738 177.388 1974 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.35 % Allowed : 22.14 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.55 (0.22), residues: 1380 helix: 1.42 (0.24), residues: 472 sheet: -1.19 (0.38), residues: 175 loop : -1.40 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 272 TYR 0.016 0.001 TYR K 83 PHE 0.014 0.001 PHE K 240 TRP 0.007 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (12465) covalent geometry : angle 0.53574 / 0.29 (17018) hydrogen bonds : bond 0.03504 / 3.87 ( 479) hydrogen bonds : angle 4.89076 / 6.60 ( 1300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: K 213 LYS cc_start: 0.7669 (tttm) cc_final: 0.7134 (tmtt) REVERT: K 218 GLU cc_start: 0.7645 (pm20) cc_final: 0.7170 (pm20) REVERT: L 142 ILE cc_start: 0.3911 (OUTLIER) cc_final: 0.3596 (mt) REVERT: L 181 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: L 324 VAL cc_start: 0.7222 (OUTLIER) cc_final: 0.6970 (m) outliers start: 30 outliers final: 19 residues processed: 156 average time/residue: 0.1088 time to fit residues: 25.2398 Evaluate side-chains 140 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 485 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 70 optimal weight: 6.9990 chunk 123 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 125 optimal weight: 0.0010 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 225 GLN L 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.219339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.174729 restraints weight = 13786.117| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.51 r_work: 0.3758 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12465 Z= 0.119 Angle : 0.535 7.259 17018 Z= 0.290 Chirality : 0.041 0.269 1884 Planarity : 0.004 0.044 2055 Dihedral : 16.738 176.522 1974 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.05 % Allowed : 21.67 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.49 (0.22), residues: 1380 helix: 1.49 (0.24), residues: 473 sheet: -1.13 (0.38), residues: 175 loop : -1.38 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 272 TYR 0.018 0.001 TYR L 532 PHE 0.014 0.001 PHE L 133 TRP 0.006 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (12465) covalent geometry : angle 0.53483 / 0.29 (17018) hydrogen bonds : bond 0.03432 / 3.80 ( 479) hydrogen bonds : angle 4.80998 / 6.52 ( 1300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7891 (t80) cc_final: 0.7585 (m-80) REVERT: K 213 LYS cc_start: 0.7684 (tttm) cc_final: 0.7168 (tmtt) REVERT: L 142 ILE cc_start: 0.3891 (OUTLIER) cc_final: 0.3577 (mt) REVERT: L 324 VAL cc_start: 0.7294 (OUTLIER) cc_final: 0.7028 (m) outliers start: 39 outliers final: 29 residues processed: 156 average time/residue: 0.1170 time to fit residues: 26.5514 Evaluate side-chains 149 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 466 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 333 GLN Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 72 optimal weight: 0.0050 chunk 101 optimal weight: 0.0970 chunk 120 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 333 GLN L 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.218480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.174867 restraints weight = 13651.041| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.59 r_work: 0.3761 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12465 Z= 0.113 Angle : 0.529 8.244 17018 Z= 0.286 Chirality : 0.041 0.263 1884 Planarity : 0.004 0.043 2055 Dihedral : 16.749 177.406 1974 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.13 % Allowed : 21.60 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.46 (0.22), residues: 1380 helix: 1.49 (0.24), residues: 475 sheet: -1.08 (0.38), residues: 176 loop : -1.36 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 543 TYR 0.018 0.001 TYR K 83 PHE 0.010 0.001 PHE K 98 TRP 0.005 0.001 TRP K 573 HIS 0.004 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (12465) covalent geometry : angle 0.52932 / 0.29 (17018) hydrogen bonds : bond 0.03334 / 3.70 ( 479) hydrogen bonds : angle 4.71202 / 6.40 ( 1300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7897 (t80) cc_final: 0.7582 (m-80) REVERT: K 213 LYS cc_start: 0.7681 (tttm) cc_final: 0.7113 (tmtt) REVERT: K 300 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8322 (mtpt) REVERT: L 142 ILE cc_start: 0.3796 (OUTLIER) cc_final: 0.3500 (mt) REVERT: L 181 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7865 (pt0) REVERT: L 324 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.7020 (m) outliers start: 40 outliers final: 30 residues processed: 155 average time/residue: 0.1113 time to fit residues: 25.5258 Evaluate side-chains 152 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 466 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 109 optimal weight: 0.0010 chunk 66 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 333 GLN L 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.217238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.173077 restraints weight = 13724.967| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.59 r_work: 0.3729 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12465 Z= 0.130 Angle : 0.537 7.253 17018 Z= 0.288 Chirality : 0.041 0.261 1884 Planarity : 0.004 0.041 2055 Dihedral : 16.826 177.920 1974 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.36 % Allowed : 21.75 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.45 (0.22), residues: 1380 helix: 1.48 (0.24), residues: 481 sheet: -1.02 (0.39), residues: 169 loop : -1.38 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 543 TYR 0.016 0.001 TYR K 394 PHE 0.013 0.001 PHE K 98 TRP 0.006 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (12465) covalent geometry : angle 0.53706 / 0.29 (17018) hydrogen bonds : bond 0.03399 / 3.74 ( 479) hydrogen bonds : angle 4.66202 / 6.34 ( 1300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7885 (t80) cc_final: 0.7553 (m-80) REVERT: K 213 LYS cc_start: 0.7667 (tttm) cc_final: 0.7083 (tmtt) REVERT: K 300 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8303 (mtpt) REVERT: L 142 ILE cc_start: 0.3805 (OUTLIER) cc_final: 0.3507 (mt) REVERT: L 181 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7887 (pt0) outliers start: 43 outliers final: 35 residues processed: 164 average time/residue: 0.1046 time to fit residues: 25.3042 Evaluate side-chains 155 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 466 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 104 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.217243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.173091 restraints weight = 13728.621| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.58 r_work: 0.3729 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12465 Z= 0.131 Angle : 0.548 9.367 17018 Z= 0.293 Chirality : 0.042 0.261 1884 Planarity : 0.004 0.040 2055 Dihedral : 16.851 178.418 1974 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.60 % Allowed : 21.75 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.45 (0.22), residues: 1380 helix: 1.44 (0.24), residues: 481 sheet: -0.99 (0.39), residues: 169 loop : -1.37 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 543 TYR 0.017 0.001 TYR K 83 PHE 0.013 0.001 PHE K 98 TRP 0.006 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (12465) covalent geometry : angle 0.54814 / 0.29 (17018) hydrogen bonds : bond 0.03381 / 3.73 ( 479) hydrogen bonds : angle 4.69164 / 6.33 ( 1300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7908 (t80) cc_final: 0.7603 (m-80) REVERT: K 213 LYS cc_start: 0.7687 (tttm) cc_final: 0.7121 (tmtt) REVERT: K 300 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8335 (mtpt) REVERT: L 17 MET cc_start: 0.6627 (mmt) cc_final: 0.6333 (mmm) REVERT: L 142 ILE cc_start: 0.3805 (OUTLIER) cc_final: 0.3512 (mt) REVERT: L 181 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7935 (pt0) outliers start: 46 outliers final: 34 residues processed: 161 average time/residue: 0.1071 time to fit residues: 25.1878 Evaluate side-chains 151 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 466 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 120 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.216783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.172566 restraints weight = 13635.866| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.60 r_work: 0.3723 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12465 Z= 0.134 Angle : 0.550 8.369 17018 Z= 0.293 Chirality : 0.042 0.264 1884 Planarity : 0.004 0.040 2055 Dihedral : 16.889 179.026 1974 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.29 % Allowed : 21.99 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.44 (0.22), residues: 1380 helix: 1.48 (0.24), residues: 478 sheet: -1.02 (0.39), residues: 169 loop : -1.37 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 543 TYR 0.016 0.001 TYR K 394 PHE 0.013 0.001 PHE K 98 TRP 0.008 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (12465) covalent geometry : angle 0.54969 / 0.29 (17018) hydrogen bonds : bond 0.03375 / 3.71 ( 479) hydrogen bonds : angle 4.64384 / 6.27 ( 1300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7921 (t80) cc_final: 0.7611 (m-80) REVERT: K 213 LYS cc_start: 0.7688 (tttm) cc_final: 0.7079 (tmtt) REVERT: K 300 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8251 (mtpt) REVERT: L 142 ILE cc_start: 0.3782 (OUTLIER) cc_final: 0.3477 (mt) REVERT: L 181 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7939 (pt0) outliers start: 42 outliers final: 35 residues processed: 155 average time/residue: 0.1009 time to fit residues: 23.4793 Evaluate side-chains 153 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 42 MET Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 466 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 86 optimal weight: 0.0070 chunk 98 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 0.0060 chunk 132 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 333 GLN L 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.218291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.174812 restraints weight = 13704.849| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.54 r_work: 0.3750 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12465 Z= 0.110 Angle : 0.535 8.622 17018 Z= 0.284 Chirality : 0.041 0.267 1884 Planarity : 0.004 0.040 2055 Dihedral : 16.870 179.837 1974 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.90 % Allowed : 22.69 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.33 (0.22), residues: 1380 helix: 1.54 (0.24), residues: 478 sheet: -0.93 (0.39), residues: 167 loop : -1.28 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 272 TYR 0.020 0.001 TYR K 394 PHE 0.009 0.001 PHE K 98 TRP 0.007 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (12465) covalent geometry : angle 0.53505 / 0.28 (17018) hydrogen bonds : bond 0.03225 / 3.55 ( 479) hydrogen bonds : angle 4.56091 / 6.14 ( 1300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7945 (t80) cc_final: 0.7622 (m-80) REVERT: K 213 LYS cc_start: 0.7717 (tttm) cc_final: 0.7129 (tmtt) REVERT: K 300 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8221 (mtpt) REVERT: L 17 MET cc_start: 0.6516 (mmt) cc_final: 0.6239 (mmm) REVERT: L 142 ILE cc_start: 0.3789 (OUTLIER) cc_final: 0.3498 (mt) REVERT: L 181 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: R 412 SER cc_start: 0.7944 (p) cc_final: 0.7635 (p) outliers start: 37 outliers final: 32 residues processed: 150 average time/residue: 0.0900 time to fit residues: 19.9938 Evaluate side-chains 150 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 466 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 0.0370 chunk 136 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 482 GLN L 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.217092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.173444 restraints weight = 13702.819| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.64 r_work: 0.3724 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12465 Z= 0.131 Angle : 0.557 8.117 17018 Z= 0.295 Chirality : 0.042 0.267 1884 Planarity : 0.004 0.041 2055 Dihedral : 16.909 179.736 1974 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.97 % Allowed : 22.54 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.35 (0.22), residues: 1380 helix: 1.51 (0.24), residues: 478 sheet: -0.97 (0.39), residues: 168 loop : -1.27 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 543 TYR 0.019 0.001 TYR K 83 PHE 0.012 0.001 PHE K 129 TRP 0.006 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (12465) covalent geometry : angle 0.55667 / 0.29 (17018) hydrogen bonds : bond 0.03303 / 3.62 ( 479) hydrogen bonds : angle 4.61836 / 6.18 ( 1300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3137.61 seconds wall clock time: 54 minutes 33.81 seconds (3273.81 seconds total)