Starting phenix.real_space_refine on Fri Mar 6 21:53:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x1l_66462/03_2026/9x1l_66462.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x1l_66462/03_2026/9x1l_66462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x1l_66462/03_2026/9x1l_66462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x1l_66462/03_2026/9x1l_66462.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x1l_66462/03_2026/9x1l_66462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x1l_66462/03_2026/9x1l_66462.map" } resolution = 2.8 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= 0.005 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 18 5.49 5 S 96 5.16 5 C 21460 2.51 5 N 5902 2.21 5 O 6470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s 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: 33946 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4556 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "B" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4556 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "C" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4556 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "D" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4556 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "E" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4556 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "F" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4556 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "G" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3212 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain breaks: 1 Chain: "H" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3212 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.71, per 1000 atoms: 0.23 Number of scatterers: 33946 At special positions: 0 Unit cell: (162.4, 156, 181.6, 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 96 16.00 P 18 15.00 O 6470 8.00 N 5902 7.00 C 21460 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: 3.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7764 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 21 sheets defined 46.3% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.877A pdb=" N ARG A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 removed outlier: 3.644A pdb=" N GLY A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.588A pdb=" N LEU A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.971A pdb=" N THR A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 260 through 277 Processing helix chain 'A' and resid 283 through 299 removed outlier: 4.065A pdb=" N VAL A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 340 removed outlier: 3.579A pdb=" N LYS A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.819A pdb=" N ILE A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 403 removed outlier: 3.702A pdb=" N TYR A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 428 removed outlier: 3.579A pdb=" N GLU A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.987A pdb=" N ALA A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 433' Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.195A pdb=" N PHE A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 465 removed outlier: 4.089A pdb=" N ARG A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.806A pdb=" N SER A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.779A pdb=" N ARG A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 96 through 99 removed outlier: 3.585A pdb=" N ILE B 99 " --> pdb=" O GLY B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 96 through 99' Processing helix chain 'B' and resid 141 through 149 removed outlier: 3.554A pdb=" N LEU B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 191 through 205 removed outlier: 3.588A pdb=" N GLU B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.758A pdb=" N ALA B 243 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 253 removed outlier: 3.665A pdb=" N ASP B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 278 Processing helix chain 'B' and resid 282 through 296 removed outlier: 4.010A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 341 removed outlier: 4.264A pdb=" N GLU B 324 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 367 through 403 removed outlier: 4.455A pdb=" N LYS B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 382 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.698A pdb=" N ALA B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 433' Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.168A pdb=" N PHE B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.567A pdb=" N LEU B 482 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 500 through 511 removed outlier: 4.077A pdb=" N GLN B 505 " --> pdb=" O PRO B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 523 removed outlier: 3.809A pdb=" N ASP B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 561 through 577 removed outlier: 4.377A pdb=" N ARG B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.555A pdb=" N TRP C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 95 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 141 through 149 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 191 through 205 Processing helix chain 'C' and resid 246 through 253 Processing helix chain 'C' and resid 259 through 277 removed outlier: 3.689A pdb=" N ARG C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 300 removed outlier: 4.291A pdb=" N VAL C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 299 " --> pdb=" O ARG C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 340 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.065A pdb=" N ILE C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 403 removed outlier: 3.725A pdb=" N LYS C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 393 " --> pdb=" O TYR C 389 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG C 395 " --> pdb=" O LYS C 391 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 428 Processing helix chain 'C' and resid 429 through 433 removed outlier: 4.122A pdb=" N ALA C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 433' Processing helix chain 'C' and resid 441 through 446 removed outlier: 4.289A pdb=" N PHE C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 469 removed outlier: 6.259A pdb=" N ARG C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS C 467 " --> pdb=" O ARG C 463 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'C' and resid 483 through 489 removed outlier: 3.535A pdb=" N LEU C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 515 through 523 removed outlier: 4.320A pdb=" N MET C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 552 Processing helix chain 'C' and resid 561 through 579 removed outlier: 4.195A pdb=" N ARG C 565 " --> pdb=" O GLY C 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 removed outlier: 3.569A pdb=" N ARG D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 49 through 54' Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.798A pdb=" N GLY D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.530A pdb=" N GLU D 101 " --> pdb=" O SER D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 149 removed outlier: 3.536A pdb=" N LEU D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 191 through 205 removed outlier: 3.656A pdb=" N VAL D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 259 through 277 removed outlier: 3.567A pdb=" N ARG D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 298 removed outlier: 3.978A pdb=" N SER D 298 " --> pdb=" O GLN D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 322 through 341 Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 348 through 353 removed outlier: 3.766A pdb=" N ALA D 351 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 403 removed outlier: 3.767A pdb=" N LEU D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR D 401 " --> pdb=" O ASP D 397 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 428 Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.318A pdb=" N PHE D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 469 removed outlier: 6.054A pdb=" N ARG D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS D 467 " --> pdb=" O ARG D 463 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.627A pdb=" N LEU D 482 " --> pdb=" O PRO D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 500 through 511 removed outlier: 3.756A pdb=" N GLN D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN D 505 " --> pdb=" O PRO D 501 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 523 removed outlier: 4.018A pdb=" N MET D 519 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 523 " --> pdb=" O MET D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 561 through 579 removed outlier: 3.690A pdb=" N ARG D 565 " --> pdb=" O GLY D 561 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU D 576 " --> pdb=" O ARG D 572 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.689A pdb=" N ARG E 53 " --> pdb=" O ASP E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 95 Processing helix chain 'E' and resid 141 through 149 removed outlier: 3.526A pdb=" N LEU E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.560A pdb=" N VAL E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 253 removed outlier: 3.556A pdb=" N LEU E 249 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 277 Processing helix chain 'E' and resid 283 through 297 removed outlier: 4.008A pdb=" N VAL E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 297 " --> pdb=" O LEU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 340 removed outlier: 3.758A pdb=" N GLU E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 367 through 403 removed outlier: 3.647A pdb=" N MET E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS E 377 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR E 385 " --> pdb=" O LYS E 381 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR E 403 " --> pdb=" O LEU E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 428 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.675A pdb=" N ALA E 432 " --> pdb=" O PRO E 429 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU E 433 " --> pdb=" O ALA E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 433' Processing helix chain 'E' and resid 441 through 446 removed outlier: 4.123A pdb=" N PHE E 445 " --> pdb=" O GLU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 465 Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 483 through 488 Processing helix chain 'E' and resid 500 through 509 removed outlier: 3.532A pdb=" N VAL E 508 " --> pdb=" O GLN E 504 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG E 509 " --> pdb=" O GLN E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 523 removed outlier: 4.335A pdb=" N SER E 520 " --> pdb=" O GLY E 516 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP E 521 " --> pdb=" O GLU E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 552 Processing helix chain 'E' and resid 561 through 581 removed outlier: 4.119A pdb=" N ARG E 565 " --> pdb=" O GLY E 561 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 576 " --> pdb=" O ARG E 572 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS E 577 " --> pdb=" O GLU E 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.760A pdb=" N GLY F 100 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU F 101 " --> pdb=" O SER F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 141 through 149 removed outlier: 3.506A pdb=" N LEU F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 179 Processing helix chain 'F' and resid 191 through 206 removed outlier: 3.637A pdb=" N LEU F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 253 removed outlier: 3.749A pdb=" N ASP F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 278 removed outlier: 3.842A pdb=" N ARG F 263 " --> pdb=" O ALA F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 298 removed outlier: 4.005A pdb=" N VAL F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER F 298 " --> pdb=" O GLN F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 340 Processing helix chain 'F' and resid 341 through 344 removed outlier: 3.651A pdb=" N LEU F 344 " --> pdb=" O GLY F 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 341 through 344' Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.619A pdb=" N ILE F 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 403 removed outlier: 4.146A pdb=" N LYS F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL F 382 " --> pdb=" O PHE F 378 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR F 401 " --> pdb=" O ASP F 397 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR F 403 " --> pdb=" O LEU F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 428 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.837A pdb=" N ALA F 432 " --> pdb=" O PRO F 429 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU F 433 " --> pdb=" O ALA F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 433' Processing helix chain 'F' and resid 441 through 446 removed outlier: 4.481A pdb=" N PHE F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 465 Processing helix chain 'F' and resid 478 through 482 Processing helix chain 'F' and resid 483 through 488 Processing helix chain 'F' and resid 500 through 511 Processing helix chain 'F' and resid 515 through 523 removed outlier: 4.031A pdb=" N ALA F 523 " --> pdb=" O MET F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 552 Processing helix chain 'F' and resid 561 through 581 removed outlier: 4.077A pdb=" N ARG F 565 " --> pdb=" O GLY F 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 26 removed outlier: 3.653A pdb=" N VAL G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 115 Processing helix chain 'G' and resid 124 through 131 removed outlier: 3.885A pdb=" N SER G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 148 removed outlier: 4.065A pdb=" N ALA G 148 " --> pdb=" O THR G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 179 removed outlier: 4.135A pdb=" N LYS G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU G 171 " --> pdb=" O GLU G 167 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU G 172 " --> pdb=" O HIS G 168 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G 179 " --> pdb=" O GLY G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 205 removed outlier: 4.096A pdb=" N PHE G 196 " --> pdb=" O LYS G 192 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA G 202 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N MET G 203 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 279 removed outlier: 3.748A pdb=" N LYS G 277 " --> pdb=" O TYR G 273 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU G 279 " --> pdb=" O LEU G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 removed outlier: 4.392A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 318 removed outlier: 3.951A pdb=" N TYR G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 344 Processing helix chain 'G' and resid 346 through 356 removed outlier: 3.690A pdb=" N GLU G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 388 removed outlier: 3.654A pdb=" N LEU G 384 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 405 Processing helix chain 'G' and resid 410 through 428 removed outlier: 4.303A pdb=" N GLU G 414 " --> pdb=" O LYS G 410 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA G 415 " --> pdb=" O LYS G 411 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU G 416 " --> pdb=" O ALA G 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 26 removed outlier: 3.635A pdb=" N VAL H 10 " --> pdb=" O ASP H 6 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 115 removed outlier: 3.920A pdb=" N ILE H 94 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU H 100 " --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 removed outlier: 3.720A pdb=" N SER H 128 " --> pdb=" O THR H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 148 removed outlier: 4.097A pdb=" N ALA H 148 " --> pdb=" O THR H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 179 removed outlier: 3.890A pdb=" N LYS H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS H 170 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU H 171 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 200 removed outlier: 4.043A pdb=" N PHE H 196 " --> pdb=" O LYS H 192 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 279 removed outlier: 3.807A pdb=" N ALA H 261 " --> pdb=" O ASP H 257 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL H 262 " --> pdb=" O ALA H 258 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR H 271 " --> pdb=" O GLY H 267 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU H 279 " --> pdb=" O LEU H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 300 removed outlier: 4.321A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 318 removed outlier: 3.878A pdb=" N TYR H 308 " --> pdb=" O VAL H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 344 removed outlier: 3.666A pdb=" N GLU H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 354 removed outlier: 3.738A pdb=" N GLU H 350 " --> pdb=" O PHE H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 389 removed outlier: 3.605A pdb=" N LEU H 384 " --> pdb=" O ASP H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 405 Processing helix chain 'H' and resid 409 through 428 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 125 removed outlier: 7.061A pdb=" N ALA A 104 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN A 73 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 106 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 71 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR A 108 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 65 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS A 114 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TRP A 63 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 41 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 39 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 40 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG A 42 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG A 136 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 12 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 13 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 23 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU A 105 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 172 removed outlier: 7.250A pdb=" N VAL A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 158 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 541 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 532 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 530 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 476 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 211 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLU A 440 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU A 213 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 210 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A 361 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL A 212 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 121 through 125 removed outlier: 7.099A pdb=" N ALA B 104 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASN B 73 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 106 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU B 71 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N THR B 108 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 65 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS B 114 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TRP B 63 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 41 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 39 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 40 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG B 42 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG B 136 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 12 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 23 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 25 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU B 105 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 172 removed outlier: 7.206A pdb=" N VAL B 169 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 158 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 476 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 211 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLU B 440 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU B 213 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 214 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 125 removed outlier: 3.514A pdb=" N LYS C 121 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 125 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 106 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU C 71 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR C 108 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE C 65 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS C 114 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TRP C 63 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 41 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 40 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG C 42 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ARG C 136 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 12 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN C 24 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 23 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 75 removed outlier: 3.532A pdb=" N ILE C 74 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 168 through 172 removed outlier: 7.156A pdb=" N VAL C 169 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 541 " --> pdb=" O ILE C 532 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 476 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 211 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU C 440 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU C 213 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 122 through 125 removed outlier: 7.006A pdb=" N ALA D 104 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN D 73 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 106 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU D 71 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N THR D 108 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE D 65 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS D 114 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TRP D 63 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 41 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 39 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 40 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ARG D 42 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG D 136 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 12 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR D 15 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR D 26 " --> pdb=" O THR D 15 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLU D 17 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN D 24 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER D 22 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE D 23 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU D 105 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 168 through 172 removed outlier: 7.310A pdb=" N VAL D 169 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 158 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 541 " --> pdb=" O ILE D 532 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 532 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 211 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLU D 440 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU D 213 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 305 through 306 removed outlier: 3.667A pdb=" N GLN D 311 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 121 through 125 removed outlier: 3.563A pdb=" N GLN E 116 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA E 104 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN E 73 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE E 106 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU E 71 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N THR E 108 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE E 65 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS E 114 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TRP E 63 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 41 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ARG E 42 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ARG E 136 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY E 12 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR E 15 " --> pdb=" O TYR E 26 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR E 26 " --> pdb=" O THR E 15 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU E 17 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLN E 24 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 22 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE E 23 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU E 105 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 168 through 172 removed outlier: 7.161A pdb=" N VAL E 169 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E 541 " --> pdb=" O ILE E 532 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE E 211 " --> pdb=" O ILE E 438 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLU E 440 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU E 213 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 122 through 125 removed outlier: 7.171A pdb=" N ALA F 104 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN F 73 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE F 106 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU F 71 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR F 108 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE F 65 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS F 114 " --> pdb=" O TRP F 63 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TRP F 63 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA F 41 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 40 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG F 42 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ARG F 136 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY F 12 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN F 24 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU F 17 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER F 22 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE F 23 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE F 25 " --> pdb=" O VAL F 107 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU F 105 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 168 through 172 removed outlier: 7.268A pdb=" N VAL F 169 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 541 " --> pdb=" O ILE F 532 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE F 211 " --> pdb=" O ILE F 438 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLU F 440 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU F 213 " --> pdb=" O GLU F 440 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL F 210 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE F 361 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 212 " --> pdb=" O ILE F 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 46 through 56 removed outlier: 3.701A pdb=" N SER G 51 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 61 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR G 63 " --> pdb=" O ASN G 82 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN G 82 " --> pdb=" O TYR G 63 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 78 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE G 182 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 119 through 122 removed outlier: 7.078A pdb=" N MET G 359 " --> pdb=" O ILE G 327 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 391 through 392 Processing sheet with id=AC1, first strand: chain 'H' and resid 46 through 56 removed outlier: 3.622A pdb=" N SER H 51 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 61 " --> pdb=" O MET H 84 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR H 63 " --> pdb=" O ASN H 82 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN H 82 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU H 78 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 69 " --> pdb=" O TYR H 76 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR H 76 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE H 182 " --> pdb=" O ARG H 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 119 through 122 removed outlier: 7.094A pdb=" N MET H 359 " --> pdb=" O ILE H 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 391 through 392 1513 hydrogen bonds defined for protein. 4377 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: 7.40 Time building geometry restraints manager: 4.12 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: 11400 1.34 - 1.46: 4644 1.46 - 1.57: 18279 1.57 - 1.69: 29 1.69 - 1.81: 186 Bond restraints: 34538 Sorted by residual: bond pdb=" O3A ANP F 601 " pdb=" PB ANP F 601 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP C 601 " pdb=" PB ANP C 601 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" O3A ANP E 601 " pdb=" PB ANP E 601 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" O3A ANP D 601 " pdb=" PB ANP D 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 34533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 46563 3.67 - 7.34: 88 7.34 - 11.00: 20 11.00 - 14.67: 1 14.67 - 18.34: 6 Bond angle restraints: 46678 Sorted by residual: angle pdb=" PB ANP C 601 " pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 126.95 108.61 18.34 3.00e+00 1.11e-01 3.74e+01 angle pdb=" PB ANP D 601 " pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 126.95 108.89 18.06 3.00e+00 1.11e-01 3.62e+01 angle pdb=" PB ANP A 601 " pdb=" N3B ANP A 601 " pdb=" PG ANP A 601 " ideal model delta sigma weight residual 126.95 108.91 18.04 3.00e+00 1.11e-01 3.62e+01 angle pdb=" PB ANP F 601 " pdb=" N3B ANP F 601 " pdb=" PG ANP F 601 " ideal model delta sigma weight residual 126.95 109.17 17.78 3.00e+00 1.11e-01 3.51e+01 angle pdb=" PB ANP B 601 " pdb=" N3B ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sigma weight residual 126.95 109.46 17.49 3.00e+00 1.11e-01 3.40e+01 ... (remaining 46673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.28: 20658 32.28 - 64.56: 262 64.56 - 96.84: 37 96.84 - 129.11: 3 129.11 - 161.39: 2 Dihedral angle restraints: 20962 sinusoidal: 8750 harmonic: 12212 Sorted by residual: dihedral pdb=" O1A ANP E 601 " pdb=" O3A ANP E 601 " pdb=" PA ANP E 601 " pdb=" PB ANP E 601 " ideal model delta sinusoidal sigma weight residual 83.11 -78.28 161.39 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O1B ANP F 601 " pdb=" N3B ANP F 601 " pdb=" PB ANP F 601 " pdb=" PG ANP F 601 " ideal model delta sinusoidal sigma weight residual 35.15 -115.45 150.60 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" O1A ANP A 601 " pdb=" O3A ANP A 601 " pdb=" PA ANP A 601 " pdb=" PB ANP A 601 " ideal model delta sinusoidal sigma weight residual 83.11 -160.31 -116.58 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 20959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4365 0.056 - 0.112: 696 0.112 - 0.167: 111 0.167 - 0.223: 0 0.223 - 0.279: 6 Chirality restraints: 5178 Sorted by residual: chirality pdb=" C3' ANP F 601 " pdb=" C2' ANP F 601 " pdb=" C4' ANP F 601 " pdb=" O3' ANP F 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ANP A 601 " pdb=" C2' ANP A 601 " pdb=" C4' ANP A 601 " pdb=" O3' ANP A 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP C 601 " pdb=" C2' ANP C 601 " pdb=" C4' ANP C 601 " pdb=" O3' ANP C 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 5175 not shown) Planarity restraints: 6014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 321 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO G 322 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO G 322 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 322 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 129 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO E 130 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 130 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 130 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 321 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO H 322 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 322 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 322 " -0.023 5.00e-02 4.00e+02 ... (remaining 6011 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5810 2.77 - 3.30: 28620 3.30 - 3.84: 48478 3.84 - 4.37: 52539 4.37 - 4.90: 101283 Nonbonded interactions: 236730 Sorted by model distance: nonbonded pdb=" O2A ANP A 601 " pdb=" O2B ANP A 601 " model vdw 2.238 3.040 nonbonded pdb=" OG SER A 480 " pdb=" OD1 ASP A 503 " model vdw 2.238 3.040 nonbonded pdb=" O1B ANP B 601 " pdb=" O2G ANP B 601 " model vdw 2.257 3.040 nonbonded pdb=" O1B ANP A 601 " pdb=" O3G ANP A 601 " model vdw 2.261 3.040 nonbonded pdb=" OG SER F 480 " pdb=" OD1 ASP F 503 " model vdw 2.281 3.040 ... (remaining 236725 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.490 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: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 32.180 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 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:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 0.146 34538 Z= 0.210 Angle : 0.580 18.341 46678 Z= 0.282 Chirality : 0.043 0.279 5178 Planarity : 0.004 0.047 6014 Dihedral : 11.361 161.393 13198 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.22 % Allowed : 4.50 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.22 (0.13), residues: 4258 helix: 2.13 (0.14), residues: 1626 sheet: -0.42 (0.20), residues: 778 loop : -2.24 (0.11), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 44 TYR 0.012 0.001 TYR A 150 PHE 0.017 0.002 PHE F 23 TRP 0.010 0.001 TRP G 389 HIS 0.005 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00446 (34538) covalent geometry : angle 0.57985 (46678) hydrogen bonds : bond 0.22042 ( 1513) hydrogen bonds : angle 5.72562 ( 4377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 378 time to evaluate : 1.377 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: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8168 (mmm) cc_final: 0.7765 (mtp) REVERT: C 305 TRP cc_start: 0.8248 (t-100) cc_final: 0.7502 (t-100) REVERT: C 307 PRO cc_start: 0.8135 (Cg_endo) cc_final: 0.7505 (Cg_exo) REVERT: D 247 GLU cc_start: 0.7468 (pp20) cc_final: 0.6864 (mm-30) REVERT: E 304 TYR cc_start: 0.6254 (t80) cc_final: 0.5843 (t80) REVERT: F 146 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7751 (mtp180) REVERT: F 318 ILE cc_start: 0.6403 (OUTLIER) cc_final: 0.6141 (tp) outliers start: 44 outliers final: 18 residues processed: 416 average time/residue: 1.0583 time to fit residues: 494.3492 Evaluate side-chains 219 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 256 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 382 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 ASN G 400 GLN H 82 ASN H 400 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066208 restraints weight = 76651.885| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.57 r_work: 0.2811 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34538 Z= 0.129 Angle : 0.547 8.567 46678 Z= 0.295 Chirality : 0.042 0.145 5178 Planarity : 0.004 0.050 6014 Dihedral : 8.422 164.582 4954 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.53 % Allowed : 9.77 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.13), residues: 4258 helix: 2.20 (0.14), residues: 1666 sheet: 0.09 (0.22), residues: 648 loop : -1.98 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 571 TYR 0.012 0.001 TYR A 150 PHE 0.019 0.001 PHE F 23 TRP 0.008 0.001 TRP B 305 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00272 (34538) covalent geometry : angle 0.54684 (46678) hydrogen bonds : bond 0.06390 ( 1513) hydrogen bonds : angle 4.49989 ( 4377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8001 (mmm) cc_final: 0.7234 (mtp) REVERT: A 292 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7054 (tm) REVERT: B 484 GLU cc_start: 0.8315 (pm20) cc_final: 0.8102 (pm20) REVERT: C 305 TRP cc_start: 0.7148 (t-100) cc_final: 0.6741 (t-100) REVERT: C 307 PRO cc_start: 0.7128 (Cg_endo) cc_final: 0.6653 (Cg_exo) REVERT: C 327 MET cc_start: 0.8137 (mmp) cc_final: 0.7908 (tpp) REVERT: C 331 MET cc_start: 0.9250 (mtp) cc_final: 0.8922 (mtm) REVERT: C 496 MET cc_start: 0.8872 (mtt) cc_final: 0.8520 (mtp) REVERT: D 247 GLU cc_start: 0.7615 (pp20) cc_final: 0.7058 (mm-30) REVERT: D 327 MET cc_start: 0.8046 (mmp) cc_final: 0.7392 (tpp) REVERT: D 331 MET cc_start: 0.8887 (mmm) cc_final: 0.8485 (mmm) REVERT: E 304 TYR cc_start: 0.5617 (t80) cc_final: 0.5084 (t80) REVERT: E 484 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7172 (tp30) REVERT: F 146 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7634 (mtp180) REVERT: F 318 ILE cc_start: 0.5726 (OUTLIER) cc_final: 0.5501 (tp) REVERT: G 18 GLU cc_start: 0.9015 (tt0) cc_final: 0.8517 (tm-30) REVERT: H 90 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7675 (pp) outliers start: 55 outliers final: 16 residues processed: 244 average time/residue: 0.8256 time to fit residues: 234.8100 Evaluate side-chains 201 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 324 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 422 optimal weight: 0.0270 chunk 162 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.099297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.064725 restraints weight = 76549.365| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.58 r_work: 0.2779 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 34538 Z= 0.161 Angle : 0.530 7.858 46678 Z= 0.290 Chirality : 0.043 0.145 5178 Planarity : 0.004 0.059 6014 Dihedral : 7.592 163.865 4932 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.75 % Allowed : 10.66 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.17 (0.13), residues: 4258 helix: 2.20 (0.13), residues: 1662 sheet: 0.52 (0.22), residues: 650 loop : -2.04 (0.12), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 400 TYR 0.013 0.001 TYR A 150 PHE 0.019 0.002 PHE F 23 TRP 0.010 0.001 TRP G 389 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00371 (34538) covalent geometry : angle 0.53041 (46678) hydrogen bonds : bond 0.06855 ( 1513) hydrogen bonds : angle 4.38470 ( 4377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: A 244 MET cc_start: 0.7958 (mmm) cc_final: 0.7149 (mtp) REVERT: A 327 MET cc_start: 0.8028 (tpp) cc_final: 0.7567 (tpp) REVERT: A 331 MET cc_start: 0.8817 (mmp) cc_final: 0.8478 (mmm) REVERT: A 521 ASP cc_start: 0.9091 (m-30) cc_final: 0.8827 (m-30) REVERT: C 305 TRP cc_start: 0.7188 (t-100) cc_final: 0.6766 (t-100) REVERT: C 307 PRO cc_start: 0.7158 (Cg_endo) cc_final: 0.6701 (Cg_exo) REVERT: C 331 MET cc_start: 0.9226 (mtp) cc_final: 0.8944 (mtm) REVERT: D 247 GLU cc_start: 0.7541 (pp20) cc_final: 0.6891 (mm-30) REVERT: D 275 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7330 (m-70) REVERT: D 327 MET cc_start: 0.8085 (mmp) cc_final: 0.7312 (tpp) REVERT: D 331 MET cc_start: 0.8961 (mmm) cc_final: 0.8537 (mmm) REVERT: D 433 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: D 496 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8368 (mtt) REVERT: E 304 TYR cc_start: 0.5570 (t80) cc_final: 0.5004 (t80) REVERT: E 484 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7368 (tp30) REVERT: E 512 GLU cc_start: 0.9037 (pt0) cc_final: 0.8700 (pm20) REVERT: E 574 LEU cc_start: 0.9155 (mm) cc_final: 0.8812 (pp) REVERT: F 146 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7642 (mtp180) REVERT: F 318 ILE cc_start: 0.5679 (OUTLIER) cc_final: 0.5437 (tp) REVERT: G 18 GLU cc_start: 0.9026 (tt0) cc_final: 0.8539 (tm-30) REVERT: G 149 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8778 (tt) REVERT: H 90 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7693 (pp) REVERT: H 191 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8491 (tm-30) REVERT: H 297 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8859 (tp40) outliers start: 63 outliers final: 28 residues processed: 233 average time/residue: 0.7835 time to fit residues: 214.0918 Evaluate side-chains 202 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 199 PHE Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 330 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 384 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 276 optimal weight: 8.9990 chunk 323 optimal weight: 7.9990 chunk 421 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.096608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.062247 restraints weight = 76653.830| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.57 r_work: 0.2703 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 34538 Z= 0.298 Angle : 0.662 8.893 46678 Z= 0.364 Chirality : 0.047 0.158 5178 Planarity : 0.005 0.053 6014 Dihedral : 7.651 166.321 4932 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.17 % Allowed : 11.72 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.14 (0.13), residues: 4258 helix: 1.93 (0.13), residues: 1664 sheet: 0.32 (0.22), residues: 650 loop : -2.19 (0.11), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 456 TYR 0.017 0.002 TYR A 150 PHE 0.023 0.002 PHE F 23 TRP 0.015 0.002 TRP G 389 HIS 0.008 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00732 (34538) covalent geometry : angle 0.66170 (46678) hydrogen bonds : bond 0.09230 ( 1513) hydrogen bonds : angle 4.65300 ( 4377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 175 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: A 244 MET cc_start: 0.7941 (mmm) cc_final: 0.7177 (mtp) REVERT: A 521 ASP cc_start: 0.9158 (m-30) cc_final: 0.8912 (m-30) REVERT: B 436 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8717 (ttm) REVERT: C 305 TRP cc_start: 0.7145 (t-100) cc_final: 0.6733 (t-100) REVERT: C 307 PRO cc_start: 0.7114 (Cg_endo) cc_final: 0.6646 (Cg_exo) REVERT: C 327 MET cc_start: 0.8317 (mmp) cc_final: 0.7920 (tpp) REVERT: C 331 MET cc_start: 0.9237 (mtp) cc_final: 0.8922 (mtm) REVERT: D 247 GLU cc_start: 0.7626 (pp20) cc_final: 0.6762 (mm-30) REVERT: D 275 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7444 (m-70) REVERT: D 327 MET cc_start: 0.8089 (mmp) cc_final: 0.7343 (tpp) REVERT: D 331 MET cc_start: 0.8983 (mmm) cc_final: 0.8589 (mmm) REVERT: D 433 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: D 496 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8478 (mtt) REVERT: E 101 GLU cc_start: 0.8374 (tp30) cc_final: 0.8146 (tp30) REVERT: E 103 GLU cc_start: 0.8932 (pt0) cc_final: 0.8428 (pm20) REVERT: E 436 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8724 (ttm) REVERT: E 484 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7469 (tp30) REVERT: E 509 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8578 (ttp-110) REVERT: E 512 GLU cc_start: 0.9055 (pt0) cc_final: 0.8709 (pm20) REVERT: E 574 LEU cc_start: 0.9215 (mm) cc_final: 0.8856 (pp) REVERT: F 146 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7692 (mtp180) REVERT: F 318 ILE cc_start: 0.5720 (OUTLIER) cc_final: 0.5459 (tp) REVERT: F 481 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8277 (mtt180) REVERT: G 18 GLU cc_start: 0.9024 (tt0) cc_final: 0.8546 (tm-30) REVERT: G 30 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: G 149 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8692 (tt) REVERT: H 90 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8049 (pp) REVERT: H 191 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8425 (tm-30) REVERT: H 297 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8851 (tp40) outliers start: 78 outliers final: 29 residues processed: 233 average time/residue: 0.7894 time to fit residues: 215.4826 Evaluate side-chains 204 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 387 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 481 ARG Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 199 PHE Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 227 optimal weight: 0.9990 chunk 371 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 318 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 361 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.064885 restraints weight = 76451.457| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.56 r_work: 0.2784 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34538 Z= 0.134 Angle : 0.514 8.377 46678 Z= 0.278 Chirality : 0.042 0.141 5178 Planarity : 0.004 0.041 6014 Dihedral : 7.341 168.268 4930 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.86 % Allowed : 12.63 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.03 (0.13), residues: 4258 helix: 2.15 (0.13), residues: 1662 sheet: 0.25 (0.23), residues: 602 loop : -2.05 (0.11), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 456 TYR 0.013 0.001 TYR A 150 PHE 0.021 0.001 PHE F 23 TRP 0.009 0.001 TRP G 33 HIS 0.004 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00294 (34538) covalent geometry : angle 0.51426 (46678) hydrogen bonds : bond 0.06271 ( 1513) hydrogen bonds : angle 4.29489 ( 4377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: A 244 MET cc_start: 0.8007 (mmm) cc_final: 0.7200 (mtp) REVERT: A 327 MET cc_start: 0.8029 (tpp) cc_final: 0.7505 (tpp) REVERT: A 331 MET cc_start: 0.8781 (mmp) cc_final: 0.8417 (mmm) REVERT: A 521 ASP cc_start: 0.9097 (m-30) cc_final: 0.8796 (m-30) REVERT: B 244 MET cc_start: 0.7382 (tpt) cc_final: 0.7000 (tpt) REVERT: C 305 TRP cc_start: 0.7234 (t-100) cc_final: 0.6764 (t-100) REVERT: C 307 PRO cc_start: 0.7100 (Cg_endo) cc_final: 0.6654 (Cg_exo) REVERT: C 327 MET cc_start: 0.8319 (mmp) cc_final: 0.7908 (tpp) REVERT: C 331 MET cc_start: 0.9245 (mtp) cc_final: 0.8946 (mtm) REVERT: D 44 CYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7346 (p) REVERT: D 247 GLU cc_start: 0.7598 (pp20) cc_final: 0.6787 (mm-30) REVERT: D 275 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7351 (m-70) REVERT: D 327 MET cc_start: 0.8109 (mmp) cc_final: 0.7354 (tpp) REVERT: D 331 MET cc_start: 0.9023 (mmm) cc_final: 0.8636 (mmm) REVERT: D 433 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: D 496 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8366 (mtt) REVERT: E 101 GLU cc_start: 0.8369 (tp30) cc_final: 0.8147 (tp30) REVERT: E 481 ARG cc_start: 0.8823 (mtm180) cc_final: 0.8580 (mtm180) REVERT: E 484 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7353 (tp30) REVERT: E 512 GLU cc_start: 0.9037 (pt0) cc_final: 0.8715 (pm20) REVERT: E 574 LEU cc_start: 0.9163 (mm) cc_final: 0.8838 (pp) REVERT: F 44 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7141 (p) REVERT: F 146 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7630 (mtp180) REVERT: F 318 ILE cc_start: 0.5697 (OUTLIER) cc_final: 0.5441 (tp) REVERT: F 436 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8899 (ttm) REVERT: F 481 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8001 (mtt180) REVERT: G 18 GLU cc_start: 0.8995 (tt0) cc_final: 0.8518 (tm-30) REVERT: G 19 ARG cc_start: 0.9209 (tmm-80) cc_final: 0.8916 (ttp80) REVERT: G 149 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8846 (tt) REVERT: H 90 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7878 (pp) REVERT: H 191 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8453 (tm-30) outliers start: 67 outliers final: 23 residues processed: 223 average time/residue: 0.7710 time to fit residues: 202.3464 Evaluate side-chains 199 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 481 ARG Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 199 PHE Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 102 optimal weight: 4.9990 chunk 416 optimal weight: 1.9990 chunk 396 optimal weight: 0.9990 chunk 296 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 chunk 376 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.098041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.063835 restraints weight = 76310.438| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.54 r_work: 0.2736 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 34538 Z= 0.199 Angle : 0.558 8.996 46678 Z= 0.306 Chirality : 0.043 0.148 5178 Planarity : 0.004 0.045 6014 Dihedral : 7.378 169.672 4930 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.86 % Allowed : 12.94 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.03 (0.13), residues: 4258 helix: 2.13 (0.13), residues: 1664 sheet: 0.40 (0.22), residues: 652 loop : -2.15 (0.11), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 456 TYR 0.014 0.001 TYR A 150 PHE 0.018 0.002 PHE F 25 TRP 0.012 0.001 TRP G 389 HIS 0.007 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00474 (34538) covalent geometry : angle 0.55833 (46678) hydrogen bonds : bond 0.07457 ( 1513) hydrogen bonds : angle 4.38013 ( 4377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 164 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: A 244 MET cc_start: 0.7943 (mmm) cc_final: 0.7170 (mtp) REVERT: A 327 MET cc_start: 0.8113 (tpp) cc_final: 0.7632 (tpp) REVERT: A 331 MET cc_start: 0.8791 (mmp) cc_final: 0.8425 (mmm) REVERT: A 521 ASP cc_start: 0.9131 (m-30) cc_final: 0.8810 (m-30) REVERT: B 244 MET cc_start: 0.7287 (tpt) cc_final: 0.6974 (tpt) REVERT: B 436 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8713 (ttm) REVERT: C 305 TRP cc_start: 0.7129 (t-100) cc_final: 0.6719 (t-100) REVERT: C 307 PRO cc_start: 0.7088 (Cg_endo) cc_final: 0.6637 (Cg_exo) REVERT: C 331 MET cc_start: 0.9218 (mtp) cc_final: 0.8944 (mtm) REVERT: D 44 CYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7480 (p) REVERT: D 275 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.7382 (m-70) REVERT: D 327 MET cc_start: 0.8129 (mmp) cc_final: 0.7336 (tpp) REVERT: D 331 MET cc_start: 0.9055 (mmm) cc_final: 0.8679 (mmm) REVERT: D 433 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: D 496 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8379 (mtt) REVERT: E 101 GLU cc_start: 0.8396 (tp30) cc_final: 0.8111 (tp30) REVERT: E 484 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7438 (tp30) REVERT: E 509 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8432 (ttp-110) REVERT: E 512 GLU cc_start: 0.9051 (pt0) cc_final: 0.8712 (pm20) REVERT: E 574 LEU cc_start: 0.9168 (mm) cc_final: 0.8820 (pp) REVERT: F 44 CYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7310 (p) REVERT: F 146 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7635 (mtp180) REVERT: F 318 ILE cc_start: 0.5681 (OUTLIER) cc_final: 0.5426 (tp) REVERT: F 436 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8902 (ttm) REVERT: F 460 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8133 (ttp-170) REVERT: G 18 GLU cc_start: 0.9013 (tt0) cc_final: 0.8542 (tm-30) REVERT: G 19 ARG cc_start: 0.9210 (tmm-80) cc_final: 0.8924 (ttp80) REVERT: G 30 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: G 149 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8707 (tt) REVERT: H 90 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7960 (pp) REVERT: H 191 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8382 (tm-30) REVERT: H 297 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8813 (tp40) outliers start: 67 outliers final: 31 residues processed: 213 average time/residue: 0.7787 time to fit residues: 195.2614 Evaluate side-chains 209 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 460 ARG Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 199 PHE Chi-restraints excluded: chain G residue 203 MET Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 129 optimal weight: 0.7980 chunk 312 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 389 optimal weight: 0.0070 chunk 77 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 177 optimal weight: 0.1980 chunk 280 optimal weight: 5.9990 chunk 293 optimal weight: 0.0670 chunk 60 optimal weight: 0.7980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN F 443 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.102321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.068601 restraints weight = 76254.212| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.57 r_work: 0.2847 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34538 Z= 0.094 Angle : 0.469 9.366 46678 Z= 0.248 Chirality : 0.041 0.134 5178 Planarity : 0.003 0.047 6014 Dihedral : 7.061 171.014 4930 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.28 % Allowed : 13.83 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.17 (0.13), residues: 4258 helix: 2.18 (0.13), residues: 1700 sheet: 0.21 (0.22), residues: 638 loop : -1.96 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 456 TYR 0.011 0.001 TYR A 150 PHE 0.020 0.001 PHE H 199 TRP 0.009 0.001 TRP A 270 HIS 0.002 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00185 (34538) covalent geometry : angle 0.46914 (46678) hydrogen bonds : bond 0.04492 ( 1513) hydrogen bonds : angle 4.03822 ( 4377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 244 MET cc_start: 0.8027 (mmm) cc_final: 0.7213 (mtp) REVERT: A 327 MET cc_start: 0.8094 (tpp) cc_final: 0.7644 (tpp) REVERT: A 331 MET cc_start: 0.8847 (mmp) cc_final: 0.8495 (mmm) REVERT: A 521 ASP cc_start: 0.9040 (m-30) cc_final: 0.8703 (m-30) REVERT: A 559 ASP cc_start: 0.7295 (t70) cc_final: 0.7060 (t0) REVERT: B 244 MET cc_start: 0.7303 (tpt) cc_final: 0.6968 (tpt) REVERT: C 305 TRP cc_start: 0.7104 (t-100) cc_final: 0.6711 (t-100) REVERT: C 307 PRO cc_start: 0.7106 (Cg_endo) cc_final: 0.6644 (Cg_exo) REVERT: C 327 MET cc_start: 0.8237 (mmp) cc_final: 0.7686 (tpp) REVERT: C 331 MET cc_start: 0.9244 (mtp) cc_final: 0.8944 (mtm) REVERT: D 44 CYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7104 (p) REVERT: D 327 MET cc_start: 0.8151 (mmp) cc_final: 0.7360 (tpp) REVERT: D 331 MET cc_start: 0.9085 (mmm) cc_final: 0.8753 (mmm) REVERT: D 496 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8293 (mtt) REVERT: E 101 GLU cc_start: 0.8377 (tp30) cc_final: 0.8116 (tp30) REVERT: E 484 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7274 (tp30) REVERT: E 512 GLU cc_start: 0.9033 (pt0) cc_final: 0.8690 (pm20) REVERT: E 574 LEU cc_start: 0.9148 (mm) cc_final: 0.8846 (pp) REVERT: F 44 CYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6794 (p) REVERT: F 146 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7576 (mtp180) REVERT: F 318 ILE cc_start: 0.5671 (OUTLIER) cc_final: 0.5431 (tp) REVERT: F 331 MET cc_start: 0.9257 (mtp) cc_final: 0.8967 (mtm) REVERT: F 575 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7897 (tm-30) REVERT: G 18 GLU cc_start: 0.8975 (tt0) cc_final: 0.8499 (tm-30) REVERT: G 19 ARG cc_start: 0.9194 (tmm-80) cc_final: 0.8888 (ttp80) REVERT: G 131 ARG cc_start: 0.8435 (mmm160) cc_final: 0.8163 (tpm170) REVERT: G 439 ARG cc_start: 0.8814 (mtm110) cc_final: 0.8333 (mtm-85) REVERT: H 90 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7582 (pp) REVERT: H 191 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8500 (tm-30) outliers start: 46 outliers final: 19 residues processed: 229 average time/residue: 0.7453 time to fit residues: 200.7690 Evaluate side-chains 203 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain G residue 199 PHE Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 215 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 350 optimal weight: 10.0000 chunk 179 optimal weight: 0.0040 chunk 308 optimal weight: 2.9990 chunk 341 optimal weight: 8.9990 chunk 419 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.063989 restraints weight = 76233.981| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.55 r_work: 0.2740 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 34538 Z= 0.199 Angle : 0.561 9.499 46678 Z= 0.306 Chirality : 0.044 0.184 5178 Planarity : 0.004 0.051 6014 Dihedral : 7.243 174.337 4930 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.55 % Allowed : 14.05 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.18 (0.13), residues: 4258 helix: 2.27 (0.13), residues: 1664 sheet: 0.48 (0.22), residues: 652 loop : -2.08 (0.11), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 456 TYR 0.014 0.001 TYR A 150 PHE 0.019 0.002 PHE H 199 TRP 0.012 0.001 TRP G 389 HIS 0.007 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00478 (34538) covalent geometry : angle 0.56133 (46678) hydrogen bonds : bond 0.07314 ( 1513) hydrogen bonds : angle 4.33832 ( 4377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: A 244 MET cc_start: 0.7944 (mmm) cc_final: 0.7192 (mtp) REVERT: A 327 MET cc_start: 0.8129 (tpp) cc_final: 0.7726 (tpp) REVERT: A 331 MET cc_start: 0.8828 (mmp) cc_final: 0.8482 (mmm) REVERT: A 521 ASP cc_start: 0.9101 (m-30) cc_final: 0.8763 (m-30) REVERT: A 559 ASP cc_start: 0.7410 (t70) cc_final: 0.7179 (t0) REVERT: B 244 MET cc_start: 0.7352 (tpt) cc_final: 0.7077 (tpt) REVERT: C 305 TRP cc_start: 0.7095 (t-100) cc_final: 0.6737 (t-100) REVERT: C 307 PRO cc_start: 0.7208 (Cg_endo) cc_final: 0.6707 (Cg_exo) REVERT: C 327 MET cc_start: 0.8298 (mmp) cc_final: 0.7886 (tpp) REVERT: C 331 MET cc_start: 0.9226 (mtp) cc_final: 0.8939 (mtm) REVERT: D 44 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7458 (p) REVERT: D 275 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.7318 (m-70) REVERT: D 327 MET cc_start: 0.8152 (mmp) cc_final: 0.7913 (mmp) REVERT: D 331 MET cc_start: 0.9087 (mmm) cc_final: 0.8870 (mmm) REVERT: D 484 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8130 (mm-30) REVERT: D 496 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: E 101 GLU cc_start: 0.8422 (tp30) cc_final: 0.8076 (tp30) REVERT: E 103 GLU cc_start: 0.8889 (pt0) cc_final: 0.8427 (pm20) REVERT: E 484 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7518 (tp30) REVERT: E 509 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8405 (ttp-110) REVERT: E 512 GLU cc_start: 0.9053 (pt0) cc_final: 0.8718 (pm20) REVERT: E 574 LEU cc_start: 0.9141 (mm) cc_final: 0.8798 (pp) REVERT: F 44 CYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7292 (p) REVERT: F 146 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7621 (mtp180) REVERT: F 318 ILE cc_start: 0.5644 (OUTLIER) cc_final: 0.5362 (OUTLIER) REVERT: G 18 GLU cc_start: 0.9012 (tt0) cc_final: 0.8540 (tm-30) REVERT: G 19 ARG cc_start: 0.9213 (tmm-80) cc_final: 0.8917 (ttp80) REVERT: G 131 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8276 (mmm160) REVERT: G 203 MET cc_start: 0.8564 (mpp) cc_final: 0.8315 (pmm) REVERT: G 297 GLN cc_start: 0.9195 (tp-100) cc_final: 0.8886 (tp-100) REVERT: G 439 ARG cc_start: 0.8829 (mtm110) cc_final: 0.8348 (mtm-85) REVERT: H 90 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7878 (pp) REVERT: H 138 SER cc_start: 0.8011 (t) cc_final: 0.7697 (p) REVERT: H 191 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8369 (tm-30) outliers start: 56 outliers final: 21 residues processed: 220 average time/residue: 0.7519 time to fit residues: 194.5771 Evaluate side-chains 196 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain G residue 199 PHE Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 259 optimal weight: 4.9990 chunk 234 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 396 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 168 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.100774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.066812 restraints weight = 76337.955| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.56 r_work: 0.2809 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34538 Z= 0.107 Angle : 0.487 9.834 46678 Z= 0.258 Chirality : 0.041 0.139 5178 Planarity : 0.004 0.056 6014 Dihedral : 7.083 175.849 4930 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.89 % Allowed : 14.71 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.18 (0.13), residues: 4258 helix: 2.19 (0.13), residues: 1706 sheet: 0.18 (0.22), residues: 638 loop : -1.95 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 456 TYR 0.012 0.001 TYR A 150 PHE 0.017 0.001 PHE H 199 TRP 0.008 0.001 TRP E 296 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00224 (34538) covalent geometry : angle 0.48689 (46678) hydrogen bonds : bond 0.05276 ( 1513) hydrogen bonds : angle 4.10424 ( 4377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: A 244 MET cc_start: 0.7986 (mmm) cc_final: 0.7194 (mtp) REVERT: A 327 MET cc_start: 0.8107 (tpp) cc_final: 0.7693 (tpp) REVERT: A 331 MET cc_start: 0.8852 (mmp) cc_final: 0.8515 (mmm) REVERT: A 521 ASP cc_start: 0.9048 (m-30) cc_final: 0.8696 (m-30) REVERT: A 559 ASP cc_start: 0.7325 (t70) cc_final: 0.7097 (t0) REVERT: B 244 MET cc_start: 0.7378 (tpt) cc_final: 0.7111 (tpt) REVERT: C 307 PRO cc_start: 0.7122 (Cg_endo) cc_final: 0.6871 (Cg_exo) REVERT: C 327 MET cc_start: 0.8297 (mmp) cc_final: 0.7870 (tpp) REVERT: C 331 MET cc_start: 0.9253 (mtp) cc_final: 0.8969 (mtm) REVERT: D 44 CYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7246 (p) REVERT: D 244 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7745 (ptm) REVERT: D 275 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7187 (m-70) REVERT: D 295 ARG cc_start: 0.7922 (tmm-80) cc_final: 0.7698 (tmm-80) REVERT: D 327 MET cc_start: 0.8149 (mmp) cc_final: 0.7912 (mmp) REVERT: D 331 MET cc_start: 0.9096 (mmm) cc_final: 0.8878 (mmm) REVERT: D 484 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8077 (mm-30) REVERT: D 496 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8347 (mtt) REVERT: E 101 GLU cc_start: 0.8416 (tp30) cc_final: 0.8129 (tp30) REVERT: E 327 MET cc_start: 0.7443 (mmp) cc_final: 0.7105 (mmm) REVERT: E 484 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7394 (tp30) REVERT: E 512 GLU cc_start: 0.9033 (pt0) cc_final: 0.8700 (pm20) REVERT: E 574 LEU cc_start: 0.9144 (mm) cc_final: 0.8825 (pp) REVERT: F 44 CYS cc_start: 0.7314 (OUTLIER) cc_final: 0.7042 (p) REVERT: F 146 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7594 (mtp180) REVERT: F 318 ILE cc_start: 0.5602 (OUTLIER) cc_final: 0.5331 (OUTLIER) REVERT: F 331 MET cc_start: 0.9209 (mtp) cc_final: 0.8900 (mtm) REVERT: F 575 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7893 (tm-30) REVERT: G 18 GLU cc_start: 0.8998 (tt0) cc_final: 0.8523 (tm-30) REVERT: G 19 ARG cc_start: 0.9202 (tmm-80) cc_final: 0.8909 (ttp80) REVERT: G 297 GLN cc_start: 0.9197 (tp-100) cc_final: 0.8892 (tp-100) REVERT: G 439 ARG cc_start: 0.8824 (mtm110) cc_final: 0.8369 (mtm-85) REVERT: H 90 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7710 (pp) REVERT: H 138 SER cc_start: 0.8049 (t) cc_final: 0.7754 (p) REVERT: H 191 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8494 (tm-30) outliers start: 32 outliers final: 21 residues processed: 204 average time/residue: 0.8153 time to fit residues: 195.0098 Evaluate side-chains 201 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain G residue 199 PHE Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 167 optimal weight: 0.0030 chunk 127 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 425 optimal weight: 1.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.100100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.066017 restraints weight = 76497.428| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.56 r_work: 0.2784 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34538 Z= 0.133 Angle : 0.504 9.676 46678 Z= 0.270 Chirality : 0.042 0.258 5178 Planarity : 0.004 0.061 6014 Dihedral : 7.082 178.325 4930 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.05 % Allowed : 14.58 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.13), residues: 4258 helix: 2.19 (0.13), residues: 1706 sheet: 0.33 (0.23), residues: 602 loop : -1.94 (0.12), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 456 TYR 0.012 0.001 TYR A 150 PHE 0.021 0.001 PHE H 199 TRP 0.027 0.001 TRP C 305 HIS 0.005 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00303 (34538) covalent geometry : angle 0.50428 (46678) hydrogen bonds : bond 0.05849 ( 1513) hydrogen bonds : angle 4.14472 ( 4377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8516 Ramachandran restraints generated. 4258 Oldfield, 0 Emsley, 4258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: A 123 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: A 244 MET cc_start: 0.7954 (mmm) cc_final: 0.7172 (mtp) REVERT: A 327 MET cc_start: 0.8089 (tpp) cc_final: 0.7737 (tpp) REVERT: A 331 MET cc_start: 0.8850 (mmp) cc_final: 0.8548 (mmm) REVERT: A 521 ASP cc_start: 0.9068 (m-30) cc_final: 0.8712 (m-30) REVERT: A 559 ASP cc_start: 0.7422 (t70) cc_final: 0.7197 (t0) REVERT: B 72 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8505 (ttpp) REVERT: B 244 MET cc_start: 0.7379 (tpt) cc_final: 0.7078 (tpt) REVERT: C 305 TRP cc_start: 0.6892 (t-100) cc_final: 0.6624 (t-100) REVERT: C 331 MET cc_start: 0.9249 (mtp) cc_final: 0.8982 (mtm) REVERT: C 484 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8104 (mm-30) REVERT: D 44 CYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7303 (p) REVERT: D 244 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7767 (ptm) REVERT: D 275 HIS cc_start: 0.7537 (OUTLIER) cc_final: 0.7163 (m-70) REVERT: D 295 ARG cc_start: 0.7913 (tmm-80) cc_final: 0.7689 (tmm-80) REVERT: D 327 MET cc_start: 0.8142 (mmp) cc_final: 0.7905 (mmp) REVERT: D 331 MET cc_start: 0.9092 (mmm) cc_final: 0.8873 (mmm) REVERT: D 484 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8104 (mm-30) REVERT: D 496 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8345 (mtt) REVERT: E 101 GLU cc_start: 0.8422 (tp30) cc_final: 0.8085 (tp30) REVERT: E 103 GLU cc_start: 0.8897 (pt0) cc_final: 0.8405 (pm20) REVERT: E 484 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7466 (tp30) REVERT: E 509 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8387 (ttp-110) REVERT: E 512 GLU cc_start: 0.9057 (pt0) cc_final: 0.8713 (pm20) REVERT: E 574 LEU cc_start: 0.9138 (mm) cc_final: 0.8811 (pp) REVERT: F 44 CYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7085 (p) REVERT: F 146 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7614 (mtp180) REVERT: F 318 ILE cc_start: 0.5553 (OUTLIER) cc_final: 0.5291 (OUTLIER) REVERT: F 331 MET cc_start: 0.9203 (mtp) cc_final: 0.8893 (mtm) REVERT: F 575 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7879 (tm-30) REVERT: G 18 GLU cc_start: 0.8989 (tt0) cc_final: 0.8525 (tm-30) REVERT: G 19 ARG cc_start: 0.9211 (tmm-80) cc_final: 0.8915 (ttp80) REVERT: G 297 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8857 (tp-100) REVERT: G 439 ARG cc_start: 0.8806 (mtm110) cc_final: 0.8353 (mtm-85) REVERT: H 90 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7731 (pp) REVERT: H 131 ARG cc_start: 0.8413 (mmm160) cc_final: 0.8154 (tpm170) REVERT: H 138 SER cc_start: 0.8024 (t) cc_final: 0.7702 (p) REVERT: H 191 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8482 (tm-30) outliers start: 38 outliers final: 23 residues processed: 205 average time/residue: 0.7721 time to fit residues: 185.9010 Evaluate side-chains 206 residues out of total 3602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain G residue 199 PHE Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain H residue 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 349 optimal weight: 0.9980 chunk 371 optimal weight: 3.9990 chunk 338 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 418 optimal weight: 0.7980 chunk 359 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.066144 restraints weight = 75876.267| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.54 r_work: 0.2788 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34538 Z= 0.131 Angle : 0.507 11.779 46678 Z= 0.270 Chirality : 0.042 0.230 5178 Planarity : 0.004 0.060 6014 Dihedral : 7.072 179.342 4930 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.08 % Allowed : 14.52 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.21 (0.13), residues: 4258 helix: 2.20 (0.13), residues: 1706 sheet: 0.34 (0.23), residues: 602 loop : -1.94 (0.12), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 456 TYR 0.012 0.001 TYR A 150 PHE 0.017 0.001 PHE H 199 TRP 0.021 0.001 TRP C 305 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00296 (34538) covalent geometry : angle 0.50717 (46678) hydrogen bonds : bond 0.05791 ( 1513) hydrogen bonds : angle 4.14001 ( 4377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11451.36 seconds wall clock time: 194 minutes 56.07 seconds (11696.07 seconds total)