Starting phenix.real_space_refine on Sun Sep 13 05:50:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6e2f_8961/09_2026/6e2f_8961.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e2f_8961/09_2026/6e2f_8961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e2f_8961/09_2026/6e2f_8961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e2f_8961/09_2026/6e2f_8961.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6e2f_8961/09_2026/6e2f_8961.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6e2f_8961/09_2026/6e2f_8961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e2f_8961/09_2026/6e2f_8961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e2f_8961/09_2026/6e2f_8961.map" } resolution = 3.9 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= 0.014 sd= 0.074 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 Ca 6 9.91 5 S 169 5.16 5 C 13637 2.51 5 N 3609 2.21 5 O 3783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21204 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4919 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 26, 'TRANS': 586} Chain: "B" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4978 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 26, 'TRANS': 592} Chain: "C" Number of atoms: 5217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5217 Classifications: {'peptide': 647} Link IDs: {'PTRANS': 26, 'TRANS': 620} Chain breaks: 1 Chain: "D" Number of atoms: 4919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4919 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 26, 'TRANS': 586} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.76, per 1000 atoms: 0.27 Number of scatterers: 21204 At special positions: 0 Unit cell: (135, 132.84, 135, 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) Ca 6 19.99 S 169 16.00 O 3783 8.00 N 3609 7.00 C 13637 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4984 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 4 sheets defined 63.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.712A pdb=" N SER A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.579A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.670A pdb=" N LYS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.686A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.087A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.764A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.550A pdb=" N PHE A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.563A pdb=" N PHE A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.584A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.650A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 205' Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.970A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.808A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.620A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.640A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.611A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 408 removed outlier: 3.824A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.577A pdb=" N ILE A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY A 422 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 446 removed outlier: 3.629A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 4.000A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.973A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 490 through 512 removed outlier: 3.825A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.952A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.849A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 567 removed outlier: 3.704A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 589 through 607 removed outlier: 3.970A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.564A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.726A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.515A pdb=" N ILE B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.654A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.774A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.679A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.830A pdb=" N PHE B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.503A pdb=" N ALA B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.586A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 205' Processing helix chain 'B' and resid 209 through 221 removed outlier: 4.357A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.688A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 302 through 309 removed outlier: 3.668A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.816A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.506A pdb=" N ILE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.508A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 420 removed outlier: 3.590A pdb=" N ILE B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 446 removed outlier: 3.542A pdb=" N ALA B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 4.089A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 4.044A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 removed outlier: 3.686A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 512 removed outlier: 4.065A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 3.781A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.888A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 567 removed outlier: 3.692A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.703A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 4.132A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 645 Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.536A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.537A pdb=" N LEU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.588A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.777A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.951A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.709A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.686A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.656A pdb=" N LEU C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.595A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 205' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.897A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.761A pdb=" N ALA C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.674A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 Processing helix chain 'C' and resid 302 through 309 removed outlier: 3.719A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.857A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.863A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 4.225A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.053A pdb=" N ILE C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 423 removed outlier: 4.741A pdb=" N LEU C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY C 422 " --> pdb=" O GLN C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 446 removed outlier: 3.589A pdb=" N ALA C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.796A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 458 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 4.020A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 4.094A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.812A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 567 removed outlier: 3.753A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 584 removed outlier: 3.677A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 581 " --> pdb=" O MET C 577 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.404A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 652 removed outlier: 4.286A pdb=" N ARG C 646 " --> pdb=" O GLN C 642 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 647 " --> pdb=" O ARG C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 703 removed outlier: 3.535A pdb=" N THR C 702 " --> pdb=" O LEU C 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.536A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.568A pdb=" N LEU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.688A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.534A pdb=" N ILE D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.696A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 4.144A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.556A pdb=" N PHE D 152 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D 153 " --> pdb=" O THR D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 149 through 153' Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.596A pdb=" N ALA D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.718A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.919A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 212 through 222 removed outlier: 4.123A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.671A pdb=" N ALA D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.601A pdb=" N MET D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.649A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 323 removed outlier: 3.606A pdb=" N SER D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 346 removed outlier: 3.529A pdb=" N ILE D 335 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 408 removed outlier: 3.625A pdb=" N ASP D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 399 " --> pdb=" O GLY D 395 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.686A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 removed outlier: 3.636A pdb=" N PHE D 416 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY D 422 " --> pdb=" O GLN D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 445 removed outlier: 3.574A pdb=" N VAL D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.742A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 471 removed outlier: 4.151A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 4.188A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.057A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.857A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 removed outlier: 4.204A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 584 removed outlier: 3.628A pdb=" N THR D 581 " --> pdb=" O MET D 577 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 4.072A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU D 592 " --> pdb=" O GLU D 588 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 20 Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.540A pdb=" N THR E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 39 " --> pdb=" O VAL E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.662A pdb=" N GLU E 54 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.532A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.691A pdb=" N GLU E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.520A pdb=" N VAL E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.903A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.590A pdb=" N THR B 274 " --> pdb=" O ASP B 635 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 635 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 633 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.562A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 633 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 removed outlier: 3.579A pdb=" N THR D 274 " --> pdb=" O ASP D 635 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 633 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2439 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: 3.39 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5472 1.33 - 1.45: 4148 1.45 - 1.57: 11756 1.57 - 1.69: 0 1.69 - 1.81: 290 Bond restraints: 21666 Sorted by residual: bond pdb=" C ASP A 550 " pdb=" N LEU A 551 " ideal model delta sigma weight residual 1.330 1.208 0.122 1.37e-02 5.33e+03 7.98e+01 bond pdb=" C ASP D 550 " pdb=" N LEU D 551 " ideal model delta sigma weight residual 1.330 1.246 0.084 1.47e-02 4.63e+03 3.25e+01 bond pdb=" C ASP B 550 " pdb=" N LEU B 551 " ideal model delta sigma weight residual 1.330 1.261 0.069 1.47e-02 4.63e+03 2.21e+01 bond pdb=" C VAL A 404 " pdb=" N PRO A 405 " ideal model delta sigma weight residual 1.337 1.385 -0.048 1.11e-02 8.12e+03 1.87e+01 bond pdb=" C VAL B 404 " pdb=" N PRO B 405 " ideal model delta sigma weight residual 1.337 1.382 -0.045 1.11e-02 8.12e+03 1.66e+01 ... (remaining 21661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 28680 3.74 - 7.47: 557 7.47 - 11.21: 124 11.21 - 14.94: 4 14.94 - 18.68: 5 Bond angle restraints: 29370 Sorted by residual: angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" C VAL A 427 " ideal model delta sigma weight residual 113.71 102.60 11.11 9.50e-01 1.11e+00 1.37e+02 angle pdb=" N VAL D 427 " pdb=" CA VAL D 427 " pdb=" C VAL D 427 " ideal model delta sigma weight residual 113.71 102.80 10.91 9.50e-01 1.11e+00 1.32e+02 angle pdb=" N VAL C 427 " pdb=" CA VAL C 427 " pdb=" C VAL C 427 " ideal model delta sigma weight residual 113.71 103.56 10.15 9.50e-01 1.11e+00 1.14e+02 angle pdb=" C ASP B 550 " pdb=" N LEU B 551 " pdb=" CA LEU B 551 " ideal model delta sigma weight residual 120.68 132.28 -11.60 1.52e+00 4.33e-01 5.83e+01 angle pdb=" C GLN A 369 " pdb=" N GLN A 370 " pdb=" CA GLN A 370 " ideal model delta sigma weight residual 122.17 112.00 10.17 1.54e+00 4.22e-01 4.36e+01 ... (remaining 29365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 11911 15.43 - 30.85: 825 30.85 - 46.28: 245 46.28 - 61.71: 3 61.71 - 77.13: 17 Dihedral angle restraints: 13001 sinusoidal: 5288 harmonic: 7713 Sorted by residual: dihedral pdb=" CA LYS B 371 " pdb=" C LYS B 371 " pdb=" N LEU B 372 " pdb=" CA LEU B 372 " ideal model delta harmonic sigma weight residual 180.00 134.17 45.83 0 5.00e+00 4.00e-02 8.40e+01 dihedral pdb=" CA LYS D 371 " pdb=" C LYS D 371 " pdb=" N LEU D 372 " pdb=" CA LEU D 372 " ideal model delta harmonic sigma weight residual 180.00 134.55 45.45 0 5.00e+00 4.00e-02 8.26e+01 dihedral pdb=" CA GLN A 290 " pdb=" C GLN A 290 " pdb=" N SER A 291 " pdb=" CA SER A 291 " ideal model delta harmonic sigma weight residual 180.00 134.74 45.26 0 5.00e+00 4.00e-02 8.19e+01 ... (remaining 12998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2392 0.063 - 0.125: 800 0.125 - 0.188: 102 0.188 - 0.250: 16 0.250 - 0.313: 13 Chirality restraints: 3323 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3320 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 372 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C LEU C 372 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU C 372 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 373 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 629 " 0.013 2.00e-02 2.50e+03 1.68e-02 7.09e+00 pdb=" CG TRP C 629 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 629 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 629 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP C 629 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 629 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 629 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 629 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 629 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP C 629 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 629 " -0.004 2.00e-02 2.50e+03 1.57e-02 6.16e+00 pdb=" CG TRP A 629 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 629 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 629 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP A 629 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 629 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 629 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 629 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 629 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 629 " 0.002 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5766 2.79 - 3.32: 20333 3.32 - 3.85: 32661 3.85 - 4.37: 37379 4.37 - 4.90: 60903 Nonbonded interactions: 157042 Sorted by model distance: nonbonded pdb=" O ASP C 284 " pdb=" OG SER C 291 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP B 279 " pdb=" OG1 THR B 281 " model vdw 2.274 3.040 nonbonded pdb=" ND2 ASN B 174 " pdb=" O PHE B 211 " model vdw 2.292 3.120 nonbonded pdb=" O ASP D 284 " pdb=" OG SER D 291 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASP B 193 " pdb=" N ASN B 197 " model vdw 2.306 3.120 ... (remaining 157037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 28 through 640) selection = (chain 'B' and resid 28 through 640) selection = (chain 'C' and resid 28 through 640) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.220 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.010 0.122 21666 Z= 0.469 Angle : 1.364 18.678 29370 Z= 0.764 Chirality : 0.062 0.313 3323 Planarity : 0.007 0.052 3736 Dihedral : 11.827 77.133 8017 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.62 % Favored : 89.00 % Rotamer: Outliers : 1.40 % Allowed : 5.50 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.19 (0.12), residues: 2628 helix: -3.56 (0.08), residues: 1336 sheet: -4.76 (0.30), residues: 82 loop : -3.11 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 492 TYR 0.026 0.003 TYR B 524 PHE 0.034 0.003 PHE B 211 TRP 0.038 0.004 TRP D 629 HIS 0.012 0.003 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00971 / 0.47 (21666) covalent geometry : angle 1.36385 / 0.76 (29370) hydrogen bonds : bond 0.31610 / 20.41 ( 848) hydrogen bonds : angle 9.20345 / 6.47 ( 2439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 461 time to evaluate : 0.890 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: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.8343 (t60) cc_final: 0.8042 (t60) REVERT: A 61 LEU cc_start: 0.9648 (mt) cc_final: 0.9211 (pp) REVERT: A 105 LEU cc_start: 0.9650 (mt) cc_final: 0.9264 (tt) REVERT: A 209 LYS cc_start: 0.9313 (mttp) cc_final: 0.8988 (mmmm) REVERT: A 331 MET cc_start: 0.9259 (tmm) cc_final: 0.8739 (tmm) REVERT: A 332 LEU cc_start: 0.9377 (tp) cc_final: 0.9043 (tt) REVERT: A 410 MET cc_start: 0.9243 (mmm) cc_final: 0.9015 (mpp) REVERT: A 414 ARG cc_start: 0.9088 (tpp80) cc_final: 0.8635 (tpt90) REVERT: A 437 LEU cc_start: 0.9557 (mp) cc_final: 0.9198 (mm) REVERT: A 474 MET cc_start: 0.9153 (pp-130) cc_final: 0.8846 (ppp) REVERT: A 528 MET cc_start: 0.9362 (tpt) cc_final: 0.8950 (tpp) REVERT: A 554 MET cc_start: 0.9430 (tpt) cc_final: 0.8961 (tpp) REVERT: A 557 ILE cc_start: 0.9725 (mt) cc_final: 0.9425 (tp) REVERT: A 603 MET cc_start: 0.9408 (ttp) cc_final: 0.8794 (tmm) REVERT: B 57 ASP cc_start: 0.9301 (m-30) cc_final: 0.8883 (m-30) REVERT: B 168 SER cc_start: 0.9786 (m) cc_final: 0.9500 (p) REVERT: B 183 ILE cc_start: 0.9721 (OUTLIER) cc_final: 0.9485 (mt) REVERT: B 255 MET cc_start: 0.9413 (tpp) cc_final: 0.9206 (tpp) REVERT: B 305 ARG cc_start: 0.8294 (mpt-90) cc_final: 0.7912 (mpt180) REVERT: B 345 MET cc_start: 0.9117 (mmm) cc_final: 0.8552 (tmm) REVERT: B 554 MET cc_start: 0.8882 (tpt) cc_final: 0.8463 (tpp) REVERT: B 570 MET cc_start: 0.9621 (tpt) cc_final: 0.9325 (mmm) REVERT: B 577 MET cc_start: 0.9318 (tmt) cc_final: 0.8131 (tmt) REVERT: B 591 GLU cc_start: 0.9157 (pt0) cc_final: 0.8745 (pm20) REVERT: B 637 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8456 (tm-30) REVERT: B 641 ARG cc_start: 0.9050 (mtt180) cc_final: 0.8737 (mmp80) REVERT: C 35 GLU cc_start: 0.9312 (tt0) cc_final: 0.9021 (pp20) REVERT: C 67 TYR cc_start: 0.8457 (t80) cc_final: 0.8196 (t80) REVERT: C 96 MET cc_start: 0.9417 (mmm) cc_final: 0.9180 (mmm) REVERT: C 99 MET cc_start: 0.9512 (mmt) cc_final: 0.9168 (mmm) REVERT: C 110 MET cc_start: 0.8154 (mtp) cc_final: 0.7942 (mmm) REVERT: C 330 CYS cc_start: 0.9487 (t) cc_final: 0.9229 (t) REVERT: C 345 MET cc_start: 0.9325 (mmm) cc_final: 0.9078 (mmm) REVERT: C 432 TYR cc_start: 0.9404 (t80) cc_final: 0.9153 (t80) REVERT: C 491 MET cc_start: 0.9227 (tpt) cc_final: 0.8882 (tpp) REVERT: C 532 SER cc_start: 0.9840 (t) cc_final: 0.9462 (p) REVERT: C 603 MET cc_start: 0.9255 (ttp) cc_final: 0.8763 (tmm) REVERT: D 35 GLU cc_start: 0.9495 (tt0) cc_final: 0.9256 (mt-10) REVERT: D 38 LEU cc_start: 0.9750 (mt) cc_final: 0.9535 (tp) REVERT: D 61 LEU cc_start: 0.9633 (mt) cc_final: 0.9404 (mt) REVERT: D 331 MET cc_start: 0.9017 (tmm) cc_final: 0.8642 (tmm) REVERT: D 345 MET cc_start: 0.9289 (mmm) cc_final: 0.9061 (mmp) REVERT: D 363 ARG cc_start: 0.9001 (mtt180) cc_final: 0.8776 (mmp80) REVERT: D 364 ASP cc_start: 0.9431 (m-30) cc_final: 0.9200 (m-30) REVERT: D 367 LEU cc_start: 0.9137 (tt) cc_final: 0.8752 (tt) REVERT: D 483 GLN cc_start: 0.9107 (tt0) cc_final: 0.8670 (tm-30) REVERT: D 484 LYS cc_start: 0.9143 (tptt) cc_final: 0.8886 (tppp) REVERT: D 491 MET cc_start: 0.8958 (tpt) cc_final: 0.8587 (tmm) REVERT: D 492 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7899 (ptt90) REVERT: D 535 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8873 (mm-30) REVERT: D 569 LEU cc_start: 0.9471 (tp) cc_final: 0.9208 (tt) REVERT: D 603 MET cc_start: 0.9173 (ttp) cc_final: 0.8463 (tmm) REVERT: D 625 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9349 (tm) REVERT: E 8 GLN cc_start: 0.8816 (mt0) cc_final: 0.8558 (mt0) REVERT: E 13 LYS cc_start: 0.9473 (ttpp) cc_final: 0.9131 (tptm) REVERT: E 14 GLU cc_start: 0.9616 (mm-30) cc_final: 0.9151 (tm-30) REVERT: E 18 LEU cc_start: 0.9239 (tt) cc_final: 0.8980 (pp) REVERT: E 30 LYS cc_start: 0.9496 (ttmp) cc_final: 0.9290 (tttt) REVERT: E 71 MET cc_start: 0.9583 (ttt) cc_final: 0.9184 (ttt) REVERT: E 72 MET cc_start: 0.8966 (mmp) cc_final: 0.8510 (mmm) REVERT: E 116 LEU cc_start: 0.9124 (mt) cc_final: 0.8673 (tp) REVERT: E 124 MET cc_start: 0.6819 (mtp) cc_final: 0.6502 (mtp) REVERT: E 143 GLN cc_start: 0.6794 (mt0) cc_final: 0.6414 (tm-30) REVERT: E 148 LYS cc_start: 0.6684 (pmtt) cc_final: 0.6033 (mmtm) outliers start: 32 outliers final: 7 residues processed: 489 average time/residue: 0.1566 time to fit residues: 119.5309 Evaluate side-chains 305 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 295 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 91 ASN A 365 ASN A 370 GLN A 374 GLN A 582 HIS A 587 HIS A 596 GLN B 158 ASN B 165 HIS B 206 GLN B 217 ASN B 258 HIS B 267 GLN B 306 GLN B 365 ASN B 370 GLN ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN C 73 HIS C 365 ASN C 370 GLN C 374 GLN C 464 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 91 ASN D 165 HIS ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 ASN D 370 GLN D 374 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.066511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.049853 restraints weight = 83877.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.051691 restraints weight = 45563.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.052955 restraints weight = 30418.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.053827 restraints weight = 22894.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.054446 restraints weight = 18733.646| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21666 Z= 0.188 Angle : 0.851 13.079 29370 Z= 0.433 Chirality : 0.044 0.203 3323 Planarity : 0.004 0.037 3736 Dihedral : 7.060 59.656 2918 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.70 % Favored : 90.14 % Rotamer: Outliers : 4.02 % Allowed : 11.44 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.15), residues: 2628 helix: -1.16 (0.12), residues: 1427 sheet: -4.23 (0.35), residues: 82 loop : -2.87 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 643 TYR 0.019 0.001 TYR C 324 PHE 0.028 0.002 PHE A 493 TRP 0.017 0.002 TRP D 495 HIS 0.007 0.001 HIS C 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (21666) covalent geometry : angle 0.85051 / 0.43 (29370) hydrogen bonds : bond 0.05718 / 3.66 ( 848) hydrogen bonds : angle 5.02978 / 3.50 ( 2439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 362 time to evaluate : 0.841 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: symmetry clash REVERT: A 61 LEU cc_start: 0.9633 (mt) cc_final: 0.9310 (pp) REVERT: A 209 LYS cc_start: 0.9271 (mttp) cc_final: 0.8984 (mmtt) REVERT: A 315 GLU cc_start: 0.8812 (mp0) cc_final: 0.8456 (mp0) REVERT: A 414 ARG cc_start: 0.9115 (tpp80) cc_final: 0.8749 (tpt170) REVERT: A 437 LEU cc_start: 0.9460 (mp) cc_final: 0.8845 (mm) REVERT: A 440 MET cc_start: 0.9024 (tmm) cc_final: 0.8685 (ppp) REVERT: A 474 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.9018 (ppp) REVERT: A 485 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8992 (ttm) REVERT: A 528 MET cc_start: 0.9355 (tpt) cc_final: 0.8811 (tpp) REVERT: A 535 GLU cc_start: 0.9351 (mt-10) cc_final: 0.8836 (tt0) REVERT: A 557 ILE cc_start: 0.9683 (mt) cc_final: 0.9375 (tp) REVERT: A 603 MET cc_start: 0.9463 (ttp) cc_final: 0.8841 (tmm) REVERT: B 38 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9455 (tp) REVERT: B 57 ASP cc_start: 0.9187 (m-30) cc_final: 0.8681 (m-30) REVERT: B 110 MET cc_start: 0.8781 (mtm) cc_final: 0.8513 (mtm) REVERT: B 168 SER cc_start: 0.9803 (m) cc_final: 0.9534 (p) REVERT: B 215 MET cc_start: 0.8950 (ttm) cc_final: 0.8739 (ttt) REVERT: B 301 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8928 (mtpt) REVERT: B 345 MET cc_start: 0.8937 (mmm) cc_final: 0.8568 (tmm) REVERT: B 464 ASN cc_start: 0.9398 (OUTLIER) cc_final: 0.8759 (t0) REVERT: B 570 MET cc_start: 0.9652 (tpt) cc_final: 0.9218 (mmm) REVERT: B 591 GLU cc_start: 0.9264 (pt0) cc_final: 0.8723 (pm20) REVERT: B 637 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8339 (tm-30) REVERT: B 641 ARG cc_start: 0.9146 (mtt180) cc_final: 0.8826 (mmp80) REVERT: C 38 LEU cc_start: 0.9662 (mt) cc_final: 0.9241 (tt) REVERT: C 96 MET cc_start: 0.9360 (mmm) cc_final: 0.9119 (mmm) REVERT: C 99 MET cc_start: 0.9559 (mmt) cc_final: 0.9111 (mmm) REVERT: C 110 MET cc_start: 0.7991 (mtp) cc_final: 0.7725 (mtm) REVERT: C 130 MET cc_start: 0.8355 (mmt) cc_final: 0.8000 (mmm) REVERT: C 284 ASP cc_start: 0.8844 (t70) cc_final: 0.8491 (t0) REVERT: C 315 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.8881 (mp0) REVERT: C 410 MET cc_start: 0.7920 (mtp) cc_final: 0.7326 (ttp) REVERT: C 434 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.9140 (t80) REVERT: C 491 MET cc_start: 0.9120 (tpt) cc_final: 0.8802 (tpp) REVERT: C 515 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8653 (tp30) REVERT: C 528 MET cc_start: 0.9305 (ttm) cc_final: 0.9023 (tpp) REVERT: C 532 SER cc_start: 0.9794 (t) cc_final: 0.9352 (p) REVERT: C 535 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8906 (mp0) REVERT: C 577 MET cc_start: 0.9225 (tmt) cc_final: 0.8881 (tmm) REVERT: C 591 GLU cc_start: 0.8976 (pt0) cc_final: 0.8630 (pm20) REVERT: C 603 MET cc_start: 0.9308 (ttp) cc_final: 0.8892 (tmm) REVERT: D 35 GLU cc_start: 0.9544 (tt0) cc_final: 0.9108 (mt-10) REVERT: D 38 LEU cc_start: 0.9716 (mt) cc_final: 0.9509 (tp) REVERT: D 61 LEU cc_start: 0.9605 (mt) cc_final: 0.9372 (mt) REVERT: D 85 ILE cc_start: 0.9819 (mm) cc_final: 0.9557 (tp) REVERT: D 99 MET cc_start: 0.9479 (mmt) cc_final: 0.8859 (mmm) REVERT: D 184 GLU cc_start: 0.8792 (mp0) cc_final: 0.8539 (mp0) REVERT: D 282 GLU cc_start: 0.8260 (mp0) cc_final: 0.8006 (mp0) REVERT: D 289 GLU cc_start: 0.8204 (mp0) cc_final: 0.7939 (pm20) REVERT: D 331 MET cc_start: 0.9045 (tmm) cc_final: 0.8762 (mmt) REVERT: D 364 ASP cc_start: 0.9453 (m-30) cc_final: 0.8369 (m-30) REVERT: D 483 GLN cc_start: 0.8932 (tt0) cc_final: 0.8580 (tm-30) REVERT: D 491 MET cc_start: 0.8993 (tpt) cc_final: 0.8499 (tmm) REVERT: D 492 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7985 (ptt180) REVERT: D 577 MET cc_start: 0.9225 (tmt) cc_final: 0.9004 (tmm) REVERT: D 588 GLU cc_start: 0.9326 (tt0) cc_final: 0.9102 (tt0) REVERT: D 603 MET cc_start: 0.9253 (ttp) cc_final: 0.8812 (tmm) REVERT: D 625 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9323 (tm) REVERT: E 8 GLN cc_start: 0.8904 (mt0) cc_final: 0.8667 (mt0) REVERT: E 14 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9325 (tm-30) REVERT: E 18 LEU cc_start: 0.9288 (tt) cc_final: 0.9074 (pp) REVERT: E 30 LYS cc_start: 0.9361 (ttmp) cc_final: 0.9142 (tttt) REVERT: E 49 GLN cc_start: 0.9097 (pt0) cc_final: 0.8768 (pm20) REVERT: E 71 MET cc_start: 0.9562 (ttt) cc_final: 0.9147 (ttt) REVERT: E 72 MET cc_start: 0.8873 (mmp) cc_final: 0.8312 (mmm) REVERT: E 116 LEU cc_start: 0.8980 (mt) cc_final: 0.8522 (tp) REVERT: E 143 GLN cc_start: 0.6782 (mt0) cc_final: 0.6294 (tm-30) REVERT: E 144 MET cc_start: 0.7867 (mmp) cc_final: 0.7204 (mtt) REVERT: E 148 LYS cc_start: 0.6816 (pmtt) cc_final: 0.5964 (mmtm) outliers start: 92 outliers final: 31 residues processed: 429 average time/residue: 0.1459 time to fit residues: 100.4456 Evaluate side-chains 319 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 280 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 434 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 613 TRP Chi-restraints excluded: chain D residue 615 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 109 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 241 optimal weight: 0.0470 chunk 33 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 208 ASN A 572 ASN B 217 ASN B 582 HIS C 165 HIS C 230 GLN C 587 HIS D 91 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.050769 restraints weight = 83934.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.052660 restraints weight = 45046.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.053965 restraints weight = 29923.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.054864 restraints weight = 22454.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.055515 restraints weight = 18309.313| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21666 Z= 0.145 Angle : 0.794 14.251 29370 Z= 0.390 Chirality : 0.042 0.212 3323 Planarity : 0.004 0.042 3736 Dihedral : 6.271 53.119 2908 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.44 % Favored : 90.41 % Rotamer: Outliers : 3.71 % Allowed : 14.37 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.16), residues: 2628 helix: 0.06 (0.13), residues: 1448 sheet: -3.64 (0.41), residues: 84 loop : -2.72 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 302 TYR 0.025 0.001 TYR A 324 PHE 0.026 0.001 PHE E 68 TRP 0.017 0.002 TRP A 613 HIS 0.008 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (21666) covalent geometry : angle 0.79355 / 0.39 (29370) hydrogen bonds : bond 0.04081 / 2.64 ( 848) hydrogen bonds : angle 4.31516 / 3.00 ( 2439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 323 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9620 (mt) cc_final: 0.9305 (pp) REVERT: A 128 GLN cc_start: 0.9119 (tt0) cc_final: 0.7798 (tm-30) REVERT: A 209 LYS cc_start: 0.9184 (mttp) cc_final: 0.8907 (mmtt) REVERT: A 311 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 315 GLU cc_start: 0.8994 (mp0) cc_final: 0.8651 (mp0) REVERT: A 372 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8915 (pp) REVERT: A 410 MET cc_start: 0.8179 (mpp) cc_final: 0.7738 (mpp) REVERT: A 414 ARG cc_start: 0.9092 (tpp80) cc_final: 0.8606 (tpt90) REVERT: A 437 LEU cc_start: 0.9513 (mp) cc_final: 0.8929 (mm) REVERT: A 440 MET cc_start: 0.9108 (tmm) cc_final: 0.8738 (ppp) REVERT: A 450 GLU cc_start: 0.9133 (pt0) cc_final: 0.8651 (tm-30) REVERT: A 454 MET cc_start: 0.9574 (mmm) cc_final: 0.9339 (mmm) REVERT: A 474 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8974 (ppp) REVERT: A 485 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.9021 (ttm) REVERT: A 515 GLU cc_start: 0.8902 (mm-30) cc_final: 0.7919 (mp0) REVERT: A 528 MET cc_start: 0.9250 (tpt) cc_final: 0.8802 (tpp) REVERT: A 557 ILE cc_start: 0.9668 (mt) cc_final: 0.9411 (tp) REVERT: A 577 MET cc_start: 0.9283 (tmt) cc_final: 0.8957 (tmm) REVERT: A 603 MET cc_start: 0.9466 (ttp) cc_final: 0.8837 (tmm) REVERT: A 635 ASP cc_start: 0.8369 (t70) cc_final: 0.7877 (p0) REVERT: B 57 ASP cc_start: 0.9167 (m-30) cc_final: 0.8675 (m-30) REVERT: B 110 MET cc_start: 0.8550 (mtm) cc_final: 0.8308 (mtm) REVERT: B 130 MET cc_start: 0.8530 (mmm) cc_final: 0.8061 (mmm) REVERT: B 168 SER cc_start: 0.9812 (m) cc_final: 0.9556 (p) REVERT: B 255 MET cc_start: 0.9755 (tpp) cc_final: 0.9546 (tpp) REVERT: B 260 MET cc_start: 0.9626 (tpp) cc_final: 0.9281 (tpp) REVERT: B 301 LYS cc_start: 0.9145 (mtpp) cc_final: 0.8935 (mtpt) REVERT: B 345 MET cc_start: 0.9007 (mmm) cc_final: 0.8628 (tmm) REVERT: B 489 ASP cc_start: 0.8617 (t0) cc_final: 0.7529 (t0) REVERT: B 528 MET cc_start: 0.9108 (tpp) cc_final: 0.8721 (tpp) REVERT: B 577 MET cc_start: 0.9083 (tmt) cc_final: 0.8661 (tmt) REVERT: B 591 GLU cc_start: 0.9164 (pt0) cc_final: 0.8766 (pm20) REVERT: B 637 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8315 (tm-30) REVERT: B 641 ARG cc_start: 0.9177 (mtt180) cc_final: 0.8857 (mmp80) REVERT: C 96 MET cc_start: 0.9349 (mmm) cc_final: 0.9093 (mmm) REVERT: C 99 MET cc_start: 0.9567 (mmt) cc_final: 0.9160 (mmm) REVERT: C 284 ASP cc_start: 0.8830 (t70) cc_final: 0.8510 (t70) REVERT: C 410 MET cc_start: 0.8281 (mtp) cc_final: 0.7637 (ttp) REVERT: C 432 TYR cc_start: 0.8670 (t80) cc_final: 0.8307 (t80) REVERT: C 491 MET cc_start: 0.9078 (tpt) cc_final: 0.8279 (tpp) REVERT: C 515 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8358 (tp30) REVERT: C 528 MET cc_start: 0.9309 (ttm) cc_final: 0.8974 (tpp) REVERT: C 532 SER cc_start: 0.9774 (t) cc_final: 0.9362 (p) REVERT: C 535 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8859 (mp0) REVERT: C 591 GLU cc_start: 0.8881 (pt0) cc_final: 0.8651 (pm20) REVERT: C 603 MET cc_start: 0.9299 (ttp) cc_final: 0.8871 (tmm) REVERT: D 35 GLU cc_start: 0.9528 (tt0) cc_final: 0.9091 (mt-10) REVERT: D 61 LEU cc_start: 0.9558 (mt) cc_final: 0.9343 (mt) REVERT: D 85 ILE cc_start: 0.9832 (mm) cc_final: 0.9583 (tp) REVERT: D 184 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8637 (mm-30) REVERT: D 345 MET cc_start: 0.9110 (mmp) cc_final: 0.8447 (tmm) REVERT: D 378 MET cc_start: 0.8796 (pmm) cc_final: 0.8542 (pmm) REVERT: D 483 GLN cc_start: 0.8934 (tt0) cc_final: 0.8593 (tm-30) REVERT: D 491 MET cc_start: 0.8975 (tpt) cc_final: 0.8438 (tmm) REVERT: D 492 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8325 (ptt180) REVERT: D 535 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8649 (mt-10) REVERT: D 570 MET cc_start: 0.9275 (tpp) cc_final: 0.9067 (mmm) REVERT: D 577 MET cc_start: 0.9116 (tmt) cc_final: 0.8895 (tmm) REVERT: D 603 MET cc_start: 0.9269 (ttp) cc_final: 0.8879 (tmm) REVERT: D 625 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9343 (tm) REVERT: E 8 GLN cc_start: 0.8960 (mt0) cc_final: 0.8733 (mt0) REVERT: E 14 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9291 (tm-30) REVERT: E 18 LEU cc_start: 0.9282 (tt) cc_final: 0.9040 (pp) REVERT: E 30 LYS cc_start: 0.9377 (ttmp) cc_final: 0.9119 (tttt) REVERT: E 36 MET cc_start: 0.9274 (ttt) cc_final: 0.8853 (tpp) REVERT: E 68 PHE cc_start: 0.9179 (t80) cc_final: 0.8858 (t80) REVERT: E 69 LEU cc_start: 0.9689 (mt) cc_final: 0.9479 (mt) REVERT: E 71 MET cc_start: 0.9557 (ttt) cc_final: 0.9112 (ttt) REVERT: E 72 MET cc_start: 0.8802 (mmp) cc_final: 0.8133 (mmm) REVERT: E 99 TYR cc_start: 0.6688 (m-10) cc_final: 0.6418 (m-80) REVERT: E 143 GLN cc_start: 0.6178 (mt0) cc_final: 0.5756 (tm-30) REVERT: E 144 MET cc_start: 0.7730 (mmp) cc_final: 0.7517 (tpp) REVERT: E 145 MET cc_start: 0.8250 (mmm) cc_final: 0.8008 (mmm) REVERT: E 148 LYS cc_start: 0.6726 (pmtt) cc_final: 0.5853 (mmtm) outliers start: 85 outliers final: 33 residues processed: 380 average time/residue: 0.1372 time to fit residues: 83.7821 Evaluate side-chains 319 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 109 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 219 optimal weight: 0.0040 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 73 HIS A 464 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.052892 restraints weight = 83751.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.054746 restraints weight = 45854.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.056050 restraints weight = 30684.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.056947 restraints weight = 23061.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.057564 restraints weight = 18860.957| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21666 Z= 0.129 Angle : 0.771 14.757 29370 Z= 0.372 Chirality : 0.042 0.282 3323 Planarity : 0.004 0.039 3736 Dihedral : 5.889 48.994 2904 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.36 % Favored : 90.49 % Rotamer: Outliers : 3.76 % Allowed : 15.46 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.17), residues: 2628 helix: 0.62 (0.14), residues: 1437 sheet: -3.75 (0.44), residues: 76 loop : -2.56 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 106 TYR 0.013 0.001 TYR C 623 PHE 0.023 0.001 PHE E 68 TRP 0.014 0.001 TRP A 613 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (21666) covalent geometry : angle 0.77122 / 0.37 (29370) hydrogen bonds : bond 0.03542 / 2.28 ( 848) hydrogen bonds : angle 4.01069 / 2.79 ( 2439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 296 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9604 (mt) cc_final: 0.9279 (pp) REVERT: A 99 MET cc_start: 0.9346 (mmm) cc_final: 0.8974 (mmm) REVERT: A 128 GLN cc_start: 0.9140 (tt0) cc_final: 0.7802 (tm-30) REVERT: A 209 LYS cc_start: 0.9116 (mttp) cc_final: 0.8850 (mmtt) REVERT: A 215 MET cc_start: 0.9033 (ttm) cc_final: 0.8732 (ttm) REVERT: A 311 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8162 (p) REVERT: A 315 GLU cc_start: 0.9019 (mp0) cc_final: 0.8660 (mp0) REVERT: A 410 MET cc_start: 0.8366 (mpp) cc_final: 0.8035 (mpp) REVERT: A 414 ARG cc_start: 0.9035 (tpp80) cc_final: 0.8598 (tpt90) REVERT: A 437 LEU cc_start: 0.9583 (mp) cc_final: 0.8906 (mm) REVERT: A 440 MET cc_start: 0.9043 (tmm) cc_final: 0.8757 (ppp) REVERT: A 485 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8916 (ttm) REVERT: A 489 ASP cc_start: 0.8344 (t0) cc_final: 0.7668 (t70) REVERT: A 491 MET cc_start: 0.8921 (ttm) cc_final: 0.8529 (tmm) REVERT: A 497 MET cc_start: 0.9308 (ttp) cc_final: 0.9090 (ttp) REVERT: A 515 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8022 (mp0) REVERT: A 528 MET cc_start: 0.9295 (tpt) cc_final: 0.8862 (tpp) REVERT: A 535 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8490 (tt0) REVERT: A 557 ILE cc_start: 0.9730 (mt) cc_final: 0.9437 (tp) REVERT: A 570 MET cc_start: 0.9158 (mmm) cc_final: 0.8858 (mmm) REVERT: A 577 MET cc_start: 0.9160 (tmt) cc_final: 0.8929 (tmm) REVERT: A 603 MET cc_start: 0.9429 (ttp) cc_final: 0.8842 (tmm) REVERT: B 57 ASP cc_start: 0.9127 (m-30) cc_final: 0.8637 (m-30) REVERT: B 168 SER cc_start: 0.9807 (m) cc_final: 0.9545 (p) REVERT: B 260 MET cc_start: 0.9560 (tpp) cc_final: 0.9147 (tpp) REVERT: B 301 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8852 (mtpt) REVERT: B 302 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.7319 (tpp-160) REVERT: B 305 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8351 (mtm-85) REVERT: B 345 MET cc_start: 0.8960 (mmm) cc_final: 0.8582 (tmm) REVERT: B 386 LEU cc_start: 0.9751 (tp) cc_final: 0.9398 (mm) REVERT: B 408 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: B 464 ASN cc_start: 0.9355 (OUTLIER) cc_final: 0.8798 (t0) REVERT: B 528 MET cc_start: 0.9208 (tpp) cc_final: 0.8747 (tpp) REVERT: B 591 GLU cc_start: 0.9160 (pt0) cc_final: 0.8888 (mm-30) REVERT: B 637 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8375 (tm-30) REVERT: B 641 ARG cc_start: 0.9155 (mtt180) cc_final: 0.8851 (mmp80) REVERT: C 99 MET cc_start: 0.9537 (mmt) cc_final: 0.9150 (mmm) REVERT: C 284 ASP cc_start: 0.8756 (t70) cc_final: 0.8532 (t70) REVERT: C 315 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8859 (mp0) REVERT: C 345 MET cc_start: 0.8490 (mmt) cc_final: 0.8126 (tpp) REVERT: C 410 MET cc_start: 0.8406 (mtp) cc_final: 0.7666 (ttp) REVERT: C 432 TYR cc_start: 0.8750 (t80) cc_final: 0.8325 (t80) REVERT: C 454 MET cc_start: 0.9541 (mmm) cc_final: 0.9340 (tpt) REVERT: C 491 MET cc_start: 0.9069 (tpt) cc_final: 0.8267 (tpp) REVERT: C 515 GLU cc_start: 0.8832 (mm-30) cc_final: 0.7938 (mp0) REVERT: C 550 ASP cc_start: 0.8989 (t70) cc_final: 0.8502 (t0) REVERT: C 603 MET cc_start: 0.9307 (ttp) cc_final: 0.8892 (tmm) REVERT: D 35 GLU cc_start: 0.9541 (tt0) cc_final: 0.9137 (mt-10) REVERT: D 61 LEU cc_start: 0.9533 (mt) cc_final: 0.9305 (mt) REVERT: D 85 ILE cc_start: 0.9850 (mm) cc_final: 0.9561 (tp) REVERT: D 114 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9149 (tp) REVERT: D 184 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8580 (mm-30) REVERT: D 345 MET cc_start: 0.9124 (mmp) cc_final: 0.8476 (tmm) REVERT: D 371 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9034 (ttpp) REVERT: D 378 MET cc_start: 0.8697 (pmm) cc_final: 0.8400 (pmm) REVERT: D 442 MET cc_start: 0.9234 (tpp) cc_final: 0.8901 (ttm) REVERT: D 491 MET cc_start: 0.9013 (tpt) cc_final: 0.8512 (tmm) REVERT: D 492 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8467 (ptt180) REVERT: D 577 MET cc_start: 0.9126 (tmt) cc_final: 0.8896 (tmm) REVERT: D 603 MET cc_start: 0.9335 (ttp) cc_final: 0.8905 (tmm) REVERT: D 625 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9341 (tm) REVERT: E 8 GLN cc_start: 0.9058 (mt0) cc_final: 0.8782 (mt0) REVERT: E 14 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9350 (tm-30) REVERT: E 30 LYS cc_start: 0.9433 (ttmp) cc_final: 0.9162 (tttt) REVERT: E 36 MET cc_start: 0.9235 (ttt) cc_final: 0.8835 (tpp) REVERT: E 71 MET cc_start: 0.9569 (ttt) cc_final: 0.9250 (ttt) REVERT: E 72 MET cc_start: 0.8830 (mmp) cc_final: 0.8457 (mmm) REVERT: E 148 LYS cc_start: 0.6759 (pmtt) cc_final: 0.5804 (mmtm) outliers start: 86 outliers final: 39 residues processed: 354 average time/residue: 0.1371 time to fit residues: 78.2318 Evaluate side-chains 322 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 51 optimal weight: 0.0970 chunk 252 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 HIS ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.067265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.050583 restraints weight = 84520.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.052404 restraints weight = 46417.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.053658 restraints weight = 31125.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.054522 restraints weight = 23516.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.055076 restraints weight = 19277.503| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21666 Z= 0.159 Angle : 0.783 15.625 29370 Z= 0.378 Chirality : 0.042 0.197 3323 Planarity : 0.003 0.037 3736 Dihedral : 5.803 50.607 2904 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.36 % Favored : 90.49 % Rotamer: Outliers : 3.93 % Allowed : 16.07 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.84 (0.17), residues: 2628 helix: 0.94 (0.14), residues: 1448 sheet: -3.58 (0.49), residues: 76 loop : -2.47 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 106 TYR 0.010 0.001 TYR C 432 PHE 0.015 0.001 PHE B 472 TRP 0.016 0.001 TRP A 613 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (21666) covalent geometry : angle 0.78295 / 0.38 (29370) hydrogen bonds : bond 0.03436 / 2.21 ( 848) hydrogen bonds : angle 4.01330 / 2.79 ( 2439) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 282 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9599 (mt) cc_final: 0.9292 (pp) REVERT: A 96 MET cc_start: 0.9285 (mmm) cc_final: 0.9045 (mmm) REVERT: A 99 MET cc_start: 0.9505 (mmm) cc_final: 0.8976 (mmm) REVERT: A 128 GLN cc_start: 0.9079 (tt0) cc_final: 0.8120 (tm-30) REVERT: A 209 LYS cc_start: 0.9190 (mttp) cc_final: 0.8908 (mmtt) REVERT: A 215 MET cc_start: 0.9178 (ttm) cc_final: 0.8900 (ttm) REVERT: A 311 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 315 GLU cc_start: 0.9061 (mp0) cc_final: 0.8693 (mp0) REVERT: A 410 MET cc_start: 0.8251 (mpp) cc_final: 0.7926 (mpp) REVERT: A 414 ARG cc_start: 0.9081 (tpp80) cc_final: 0.8694 (tpt170) REVERT: A 437 LEU cc_start: 0.9562 (mp) cc_final: 0.8969 (mm) REVERT: A 440 MET cc_start: 0.9186 (tmm) cc_final: 0.8882 (ppp) REVERT: A 474 MET cc_start: 0.9196 (ppp) cc_final: 0.8719 (ppp) REVERT: A 485 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8980 (ttm) REVERT: A 491 MET cc_start: 0.8898 (ttm) cc_final: 0.8487 (tmm) REVERT: A 497 MET cc_start: 0.9390 (ttp) cc_final: 0.9111 (ttp) REVERT: A 528 MET cc_start: 0.9261 (tpt) cc_final: 0.8827 (tpp) REVERT: A 535 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8629 (tt0) REVERT: A 554 MET cc_start: 0.8552 (tpp) cc_final: 0.8087 (tpp) REVERT: A 557 ILE cc_start: 0.9707 (mt) cc_final: 0.9486 (tp) REVERT: A 603 MET cc_start: 0.9444 (ttp) cc_final: 0.8878 (tmm) REVERT: B 38 LEU cc_start: 0.9697 (tp) cc_final: 0.9264 (tt) REVERT: B 57 ASP cc_start: 0.9182 (m-30) cc_final: 0.8685 (m-30) REVERT: B 130 MET cc_start: 0.8407 (mmm) cc_final: 0.7957 (mmm) REVERT: B 168 SER cc_start: 0.9799 (m) cc_final: 0.9552 (p) REVERT: B 260 MET cc_start: 0.9610 (tpp) cc_final: 0.9258 (tpp) REVERT: B 294 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8546 (pt0) REVERT: B 301 LYS cc_start: 0.9295 (mtpp) cc_final: 0.9042 (mtpt) REVERT: B 345 MET cc_start: 0.8975 (mmm) cc_final: 0.8586 (tmm) REVERT: B 408 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: B 464 ASN cc_start: 0.9376 (OUTLIER) cc_final: 0.8825 (t0) REVERT: B 528 MET cc_start: 0.9121 (tpp) cc_final: 0.8658 (tpp) REVERT: B 577 MET cc_start: 0.9045 (tmt) cc_final: 0.8813 (tmm) REVERT: B 591 GLU cc_start: 0.9136 (pt0) cc_final: 0.8871 (mm-30) REVERT: B 637 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8471 (tm-30) REVERT: B 641 ARG cc_start: 0.9205 (mtt180) cc_final: 0.8736 (tpt170) REVERT: C 38 LEU cc_start: 0.9676 (mt) cc_final: 0.9304 (tt) REVERT: C 99 MET cc_start: 0.9614 (mmt) cc_final: 0.9204 (mmm) REVERT: C 114 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8480 (tp) REVERT: C 284 ASP cc_start: 0.8861 (t70) cc_final: 0.8547 (t0) REVERT: C 345 MET cc_start: 0.8470 (mmt) cc_final: 0.8148 (tpp) REVERT: C 410 MET cc_start: 0.8386 (mtp) cc_final: 0.7606 (ttp) REVERT: C 432 TYR cc_start: 0.8724 (t80) cc_final: 0.8331 (t80) REVERT: C 454 MET cc_start: 0.9562 (mmm) cc_final: 0.9175 (tpt) REVERT: C 491 MET cc_start: 0.8955 (tpt) cc_final: 0.8529 (tmm) REVERT: C 515 GLU cc_start: 0.8959 (mm-30) cc_final: 0.7935 (mp0) REVERT: C 603 MET cc_start: 0.9283 (ttp) cc_final: 0.8830 (tmm) REVERT: D 35 GLU cc_start: 0.9564 (tt0) cc_final: 0.9189 (mt-10) REVERT: D 61 LEU cc_start: 0.9538 (mt) cc_final: 0.9307 (mt) REVERT: D 85 ILE cc_start: 0.9828 (mm) cc_final: 0.9559 (tp) REVERT: D 99 MET cc_start: 0.9456 (mmt) cc_final: 0.8846 (mmm) REVERT: D 114 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9105 (tp) REVERT: D 184 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8578 (mm-30) REVERT: D 345 MET cc_start: 0.8986 (mmp) cc_final: 0.8306 (tmm) REVERT: D 371 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9009 (ttpp) REVERT: D 378 MET cc_start: 0.8743 (pmm) cc_final: 0.8425 (pmm) REVERT: D 442 MET cc_start: 0.9244 (tpp) cc_final: 0.8846 (ttm) REVERT: D 491 MET cc_start: 0.8895 (tpt) cc_final: 0.8391 (tmm) REVERT: D 492 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8339 (ptt180) REVERT: D 497 MET cc_start: 0.9363 (ttp) cc_final: 0.8677 (tmm) REVERT: D 535 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8714 (mt-10) REVERT: D 577 MET cc_start: 0.9029 (tmt) cc_final: 0.8734 (tmm) REVERT: D 603 MET cc_start: 0.9326 (ttp) cc_final: 0.8862 (tmm) REVERT: D 608 LEU cc_start: 0.9613 (tt) cc_final: 0.9372 (tt) REVERT: D 625 LEU cc_start: 0.9700 (OUTLIER) cc_final: 0.9334 (tm) REVERT: E 8 GLN cc_start: 0.9031 (mt0) cc_final: 0.8780 (mt0) REVERT: E 14 GLU cc_start: 0.9613 (mm-30) cc_final: 0.9310 (tm-30) REVERT: E 30 LYS cc_start: 0.9398 (ttmp) cc_final: 0.9141 (tttt) REVERT: E 36 MET cc_start: 0.9203 (ttt) cc_final: 0.8840 (tpp) REVERT: E 71 MET cc_start: 0.9576 (ttt) cc_final: 0.9272 (ttt) REVERT: E 72 MET cc_start: 0.8887 (mmp) cc_final: 0.8409 (mmm) REVERT: E 145 MET cc_start: 0.8107 (mmm) cc_final: 0.7715 (mmm) REVERT: E 148 LYS cc_start: 0.6711 (pmtt) cc_final: 0.5811 (mmtm) outliers start: 90 outliers final: 48 residues processed: 352 average time/residue: 0.1402 time to fit residues: 79.3275 Evaluate side-chains 329 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 175 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 GLN B 426 HIS ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.067648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.051062 restraints weight = 84451.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.052900 restraints weight = 46244.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054163 restraints weight = 30957.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.055031 restraints weight = 23340.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.055602 restraints weight = 19130.522| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21666 Z= 0.142 Angle : 0.773 15.674 29370 Z= 0.372 Chirality : 0.042 0.218 3323 Planarity : 0.003 0.035 3736 Dihedral : 5.710 52.460 2904 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.13 % Favored : 90.72 % Rotamer: Outliers : 3.76 % Allowed : 16.77 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2628 helix: 1.10 (0.14), residues: 1451 sheet: -3.42 (0.51), residues: 76 loop : -2.41 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 106 TYR 0.010 0.001 TYR C 555 PHE 0.017 0.001 PHE D 162 TRP 0.013 0.001 TRP A 613 HIS 0.010 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21666) covalent geometry : angle 0.77252 / 0.37 (29370) hydrogen bonds : bond 0.03287 / 2.10 ( 848) hydrogen bonds : angle 3.90019 / 2.71 ( 2439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 295 time to evaluate : 0.909 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: A 61 LEU cc_start: 0.9591 (mt) cc_final: 0.9308 (pp) REVERT: A 99 MET cc_start: 0.9508 (mmm) cc_final: 0.8980 (mmm) REVERT: A 128 GLN cc_start: 0.9064 (tt0) cc_final: 0.8143 (tm-30) REVERT: A 209 LYS cc_start: 0.9173 (mttp) cc_final: 0.8893 (mmtt) REVERT: A 215 MET cc_start: 0.9161 (ttm) cc_final: 0.8910 (ttm) REVERT: A 311 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 315 GLU cc_start: 0.9078 (mp0) cc_final: 0.8699 (mp0) REVERT: A 410 MET cc_start: 0.8237 (mpp) cc_final: 0.7926 (mpp) REVERT: A 414 ARG cc_start: 0.9093 (tpp80) cc_final: 0.8688 (tpt170) REVERT: A 437 LEU cc_start: 0.9573 (mp) cc_final: 0.8960 (mt) REVERT: A 440 MET cc_start: 0.9210 (tmm) cc_final: 0.8974 (ppp) REVERT: A 474 MET cc_start: 0.9142 (ppp) cc_final: 0.8734 (ppp) REVERT: A 485 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9112 (ttm) REVERT: A 491 MET cc_start: 0.8789 (ttm) cc_final: 0.8307 (tmm) REVERT: A 497 MET cc_start: 0.9385 (ttp) cc_final: 0.9079 (ttp) REVERT: A 528 MET cc_start: 0.9273 (tpt) cc_final: 0.8835 (tpp) REVERT: A 535 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8627 (tt0) REVERT: A 557 ILE cc_start: 0.9665 (mt) cc_final: 0.9447 (tp) REVERT: A 577 MET cc_start: 0.9320 (tmm) cc_final: 0.9040 (tmm) REVERT: A 603 MET cc_start: 0.9437 (ttp) cc_final: 0.8939 (tmm) REVERT: B 38 LEU cc_start: 0.9732 (tp) cc_final: 0.9280 (tt) REVERT: B 57 ASP cc_start: 0.9179 (m-30) cc_final: 0.8691 (m-30) REVERT: B 130 MET cc_start: 0.8402 (mmm) cc_final: 0.7978 (mmm) REVERT: B 168 SER cc_start: 0.9785 (m) cc_final: 0.9534 (p) REVERT: B 260 MET cc_start: 0.9546 (tpp) cc_final: 0.9224 (tpp) REVERT: B 294 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8857 (mt-10) REVERT: B 301 LYS cc_start: 0.9257 (mtpp) cc_final: 0.8983 (mtpt) REVERT: B 324 TYR cc_start: 0.8432 (m-10) cc_final: 0.8213 (m-10) REVERT: B 345 MET cc_start: 0.9017 (mmm) cc_final: 0.8634 (tmm) REVERT: B 386 LEU cc_start: 0.9760 (tp) cc_final: 0.9393 (mm) REVERT: B 389 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: B 390 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9483 (mm) REVERT: B 408 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: B 464 ASN cc_start: 0.9372 (OUTLIER) cc_final: 0.8863 (t0) REVERT: B 474 MET cc_start: 0.9043 (ttp) cc_final: 0.8587 (ttp) REVERT: B 528 MET cc_start: 0.9100 (tpp) cc_final: 0.8608 (tpp) REVERT: B 591 GLU cc_start: 0.9078 (pt0) cc_final: 0.8869 (mm-30) REVERT: B 641 ARG cc_start: 0.9219 (mtt180) cc_final: 0.8715 (tpt170) REVERT: C 67 TYR cc_start: 0.8543 (t80) cc_final: 0.8186 (t80) REVERT: C 99 MET cc_start: 0.9617 (mmt) cc_final: 0.9201 (mmm) REVERT: C 114 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8382 (tp) REVERT: C 284 ASP cc_start: 0.8844 (t70) cc_final: 0.8543 (t0) REVERT: C 345 MET cc_start: 0.8497 (mmt) cc_final: 0.8181 (tpp) REVERT: C 410 MET cc_start: 0.8383 (mtp) cc_final: 0.7622 (ttp) REVERT: C 432 TYR cc_start: 0.8691 (t80) cc_final: 0.8304 (t80) REVERT: C 454 MET cc_start: 0.9487 (mmm) cc_final: 0.9160 (tpt) REVERT: C 491 MET cc_start: 0.8852 (tpt) cc_final: 0.8567 (ttt) REVERT: C 515 GLU cc_start: 0.8921 (mm-30) cc_final: 0.7869 (mp0) REVERT: C 535 GLU cc_start: 0.8927 (mp0) cc_final: 0.8635 (mp0) REVERT: C 584 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8594 (tpp80) REVERT: C 603 MET cc_start: 0.9270 (ttp) cc_final: 0.8807 (tmm) REVERT: D 35 GLU cc_start: 0.9564 (tt0) cc_final: 0.9171 (mt-10) REVERT: D 61 LEU cc_start: 0.9534 (mt) cc_final: 0.9309 (mt) REVERT: D 85 ILE cc_start: 0.9834 (mm) cc_final: 0.9562 (tp) REVERT: D 99 MET cc_start: 0.9461 (mmt) cc_final: 0.8872 (mmm) REVERT: D 114 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9086 (tp) REVERT: D 181 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9442 (tm) REVERT: D 345 MET cc_start: 0.9007 (mmp) cc_final: 0.8316 (tmm) REVERT: D 364 ASP cc_start: 0.9385 (m-30) cc_final: 0.8708 (p0) REVERT: D 371 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9109 (ttpp) REVERT: D 378 MET cc_start: 0.8742 (pmm) cc_final: 0.8417 (pmm) REVERT: D 442 MET cc_start: 0.9259 (tpp) cc_final: 0.8843 (ttm) REVERT: D 485 MET cc_start: 0.8892 (ttm) cc_final: 0.8252 (ttm) REVERT: D 491 MET cc_start: 0.8875 (tpt) cc_final: 0.8386 (tmm) REVERT: D 492 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8332 (ptt180) REVERT: D 535 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8684 (mt-10) REVERT: D 577 MET cc_start: 0.9048 (tmt) cc_final: 0.8748 (tmm) REVERT: D 603 MET cc_start: 0.9320 (ttp) cc_final: 0.8855 (tmm) REVERT: E 8 GLN cc_start: 0.8986 (mt0) cc_final: 0.8765 (mt0) REVERT: E 14 GLU cc_start: 0.9636 (mm-30) cc_final: 0.9334 (tm-30) REVERT: E 30 LYS cc_start: 0.9406 (ttmp) cc_final: 0.9131 (tttp) REVERT: E 36 MET cc_start: 0.9214 (ttt) cc_final: 0.8889 (tpp) REVERT: E 37 ARG cc_start: 0.8902 (ptt90) cc_final: 0.8548 (ptt-90) REVERT: E 71 MET cc_start: 0.9567 (ttt) cc_final: 0.9278 (ttt) REVERT: E 72 MET cc_start: 0.8875 (mmp) cc_final: 0.8414 (mmm) REVERT: E 148 LYS cc_start: 0.6556 (pmtt) cc_final: 0.5647 (mmtm) outliers start: 86 outliers final: 53 residues processed: 358 average time/residue: 0.1383 time to fit residues: 80.1985 Evaluate side-chains 332 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 267 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 613 TRP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 241 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 GLN B 426 HIS B 464 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.069484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.052784 restraints weight = 82973.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.054697 restraints weight = 44995.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.056015 restraints weight = 29965.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.056928 restraints weight = 22516.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.057574 restraints weight = 18353.822| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21666 Z= 0.114 Angle : 0.783 15.219 29370 Z= 0.368 Chirality : 0.041 0.218 3323 Planarity : 0.003 0.036 3736 Dihedral : 5.524 53.910 2904 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.71 % Favored : 91.17 % Rotamer: Outliers : 3.23 % Allowed : 17.82 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2628 helix: 1.24 (0.14), residues: 1447 sheet: -3.14 (0.54), residues: 76 loop : -2.39 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 302 TYR 0.040 0.001 TYR A 324 PHE 0.017 0.001 PHE B 472 TRP 0.011 0.001 TRP A 613 HIS 0.008 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (21666) covalent geometry : angle 0.78281 / 0.37 (29370) hydrogen bonds : bond 0.02976 / 1.92 ( 848) hydrogen bonds : angle 3.71842 / 2.58 ( 2439) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 321 time to evaluate : 0.857 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: A 61 LEU cc_start: 0.9572 (mt) cc_final: 0.9296 (pp) REVERT: A 99 MET cc_start: 0.9506 (mmm) cc_final: 0.9068 (mmm) REVERT: A 114 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8781 (tp) REVERT: A 128 GLN cc_start: 0.8998 (tt0) cc_final: 0.8064 (tm-30) REVERT: A 209 LYS cc_start: 0.9081 (mttp) cc_final: 0.8769 (mmtt) REVERT: A 311 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8105 (p) REVERT: A 315 GLU cc_start: 0.9061 (mp0) cc_final: 0.8737 (mp0) REVERT: A 410 MET cc_start: 0.8248 (mpp) cc_final: 0.7954 (mpp) REVERT: A 414 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8614 (tpt90) REVERT: A 437 LEU cc_start: 0.9568 (mp) cc_final: 0.8930 (mm) REVERT: A 440 MET cc_start: 0.9223 (tmm) cc_final: 0.8939 (ppp) REVERT: A 474 MET cc_start: 0.9080 (ppp) cc_final: 0.8865 (ppp) REVERT: A 485 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.9162 (ttm) REVERT: A 491 MET cc_start: 0.8785 (ttm) cc_final: 0.8248 (tmm) REVERT: A 497 MET cc_start: 0.9417 (ttp) cc_final: 0.9103 (ttp) REVERT: A 528 MET cc_start: 0.9222 (tpt) cc_final: 0.8765 (tpp) REVERT: A 557 ILE cc_start: 0.9586 (mt) cc_final: 0.9353 (tp) REVERT: A 603 MET cc_start: 0.9429 (ttp) cc_final: 0.8921 (tmm) REVERT: A 634 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8685 (mp0) REVERT: B 38 LEU cc_start: 0.9689 (tp) cc_final: 0.9314 (tt) REVERT: B 57 ASP cc_start: 0.9163 (m-30) cc_final: 0.8708 (m-30) REVERT: B 130 MET cc_start: 0.8325 (mmm) cc_final: 0.7875 (mmm) REVERT: B 168 SER cc_start: 0.9763 (m) cc_final: 0.9502 (p) REVERT: B 241 LEU cc_start: 0.9304 (mt) cc_final: 0.9074 (mp) REVERT: B 260 MET cc_start: 0.9460 (tpp) cc_final: 0.9195 (tpp) REVERT: B 294 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8800 (pt0) REVERT: B 301 LYS cc_start: 0.9246 (mtpp) cc_final: 0.8899 (mtpt) REVERT: B 345 MET cc_start: 0.9011 (mmm) cc_final: 0.8559 (tmm) REVERT: B 386 LEU cc_start: 0.9731 (tp) cc_final: 0.9375 (mm) REVERT: B 390 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9492 (mm) REVERT: B 408 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: B 464 ASN cc_start: 0.9208 (t0) cc_final: 0.8953 (t0) REVERT: B 474 MET cc_start: 0.9056 (ttp) cc_final: 0.8692 (ttp) REVERT: B 577 MET cc_start: 0.8913 (tmm) cc_final: 0.8532 (tmm) REVERT: B 584 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8744 (mmt90) REVERT: B 591 GLU cc_start: 0.9042 (pt0) cc_final: 0.8822 (mm-30) REVERT: B 641 ARG cc_start: 0.9261 (mtt180) cc_final: 0.8753 (tpt170) REVERT: C 99 MET cc_start: 0.9657 (mmt) cc_final: 0.9244 (mmm) REVERT: C 114 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8333 (tp) REVERT: C 284 ASP cc_start: 0.8820 (t70) cc_final: 0.8513 (t0) REVERT: C 331 MET cc_start: 0.8675 (mmt) cc_final: 0.8452 (mmp) REVERT: C 345 MET cc_start: 0.8397 (mmt) cc_final: 0.8148 (tpp) REVERT: C 400 LEU cc_start: 0.9335 (mt) cc_final: 0.8912 (pp) REVERT: C 410 MET cc_start: 0.8325 (mtp) cc_final: 0.7581 (ttp) REVERT: C 432 TYR cc_start: 0.8505 (t80) cc_final: 0.8264 (t80) REVERT: C 485 MET cc_start: 0.9405 (tpp) cc_final: 0.9194 (ttm) REVERT: C 491 MET cc_start: 0.8810 (tpt) cc_final: 0.8559 (ttt) REVERT: C 515 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8306 (mm-30) REVERT: C 535 GLU cc_start: 0.8812 (mp0) cc_final: 0.8078 (mp0) REVERT: C 584 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8478 (tpp80) REVERT: C 603 MET cc_start: 0.9204 (ttp) cc_final: 0.8784 (tmm) REVERT: D 35 GLU cc_start: 0.9552 (tt0) cc_final: 0.9148 (mt-10) REVERT: D 61 LEU cc_start: 0.9531 (mt) cc_final: 0.9299 (mt) REVERT: D 85 ILE cc_start: 0.9808 (mm) cc_final: 0.9489 (tp) REVERT: D 99 MET cc_start: 0.9499 (mmt) cc_final: 0.9062 (mmm) REVERT: D 114 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9045 (tp) REVERT: D 345 MET cc_start: 0.8980 (mmp) cc_final: 0.8337 (tmm) REVERT: D 364 ASP cc_start: 0.9349 (m-30) cc_final: 0.8655 (p0) REVERT: D 371 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9146 (ttpp) REVERT: D 378 MET cc_start: 0.8726 (pmm) cc_final: 0.8406 (pmm) REVERT: D 474 MET cc_start: 0.8478 (pmm) cc_final: 0.8191 (ppp) REVERT: D 491 MET cc_start: 0.8819 (tpt) cc_final: 0.8373 (tmm) REVERT: D 492 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8294 (ptt180) REVERT: D 497 MET cc_start: 0.9414 (ttp) cc_final: 0.8681 (tmm) REVERT: D 535 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8667 (mt-10) REVERT: D 577 MET cc_start: 0.8890 (tmt) cc_final: 0.8688 (tmm) REVERT: D 603 MET cc_start: 0.9303 (ttp) cc_final: 0.8669 (tmm) REVERT: D 608 LEU cc_start: 0.9591 (tt) cc_final: 0.9337 (tt) REVERT: E 8 GLN cc_start: 0.9001 (mt0) cc_final: 0.8753 (mt0) REVERT: E 14 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9341 (tm-30) REVERT: E 30 LYS cc_start: 0.9413 (ttmp) cc_final: 0.9088 (tttt) REVERT: E 36 MET cc_start: 0.9207 (ttt) cc_final: 0.8835 (tpp) REVERT: E 37 ARG cc_start: 0.8877 (ptt90) cc_final: 0.8554 (ptt-90) REVERT: E 71 MET cc_start: 0.9561 (ttt) cc_final: 0.9237 (ttt) REVERT: E 72 MET cc_start: 0.8784 (mmp) cc_final: 0.8030 (mmm) REVERT: E 144 MET cc_start: 0.7936 (tpp) cc_final: 0.7582 (tpp) REVERT: E 148 LYS cc_start: 0.6492 (pmtt) cc_final: 0.5621 (mmtm) outliers start: 74 outliers final: 42 residues processed: 373 average time/residue: 0.1367 time to fit residues: 82.4204 Evaluate side-chains 335 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 136 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 59 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN B 290 GLN B 426 HIS ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.068701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.052241 restraints weight = 82488.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.054170 restraints weight = 43856.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.055499 restraints weight = 28858.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.056415 restraints weight = 21432.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.057067 restraints weight = 17346.013| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21666 Z= 0.125 Angle : 0.797 16.473 29370 Z= 0.373 Chirality : 0.042 0.274 3323 Planarity : 0.003 0.034 3736 Dihedral : 5.478 54.400 2904 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.25 % Favored : 90.64 % Rotamer: Outliers : 3.01 % Allowed : 18.43 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -0.38 (0.17), residues: 2628 helix: 1.37 (0.14), residues: 1446 sheet: -3.07 (0.56), residues: 76 loop : -2.38 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 302 TYR 0.017 0.001 TYR B 216 PHE 0.023 0.001 PHE B 472 TRP 0.011 0.001 TRP A 613 HIS 0.010 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (21666) covalent geometry : angle 0.79674 / 0.37 (29370) hydrogen bonds : bond 0.03013 / 1.93 ( 848) hydrogen bonds : angle 3.75725 / 2.61 ( 2439) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 292 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9580 (mt) cc_final: 0.9323 (pp) REVERT: A 99 MET cc_start: 0.9539 (OUTLIER) cc_final: 0.9041 (mmm) REVERT: A 114 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8785 (tp) REVERT: A 128 GLN cc_start: 0.9050 (tt0) cc_final: 0.8071 (tm-30) REVERT: A 209 LYS cc_start: 0.9059 (mttp) cc_final: 0.8752 (mmtt) REVERT: A 311 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8140 (p) REVERT: A 315 GLU cc_start: 0.9052 (mp0) cc_final: 0.8743 (mp0) REVERT: A 410 MET cc_start: 0.8345 (mpp) cc_final: 0.8043 (mpp) REVERT: A 414 ARG cc_start: 0.9035 (tpp80) cc_final: 0.8606 (tpt90) REVERT: A 437 LEU cc_start: 0.9582 (mp) cc_final: 0.8933 (mm) REVERT: A 440 MET cc_start: 0.9229 (tmm) cc_final: 0.8950 (ppp) REVERT: A 485 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9120 (ttm) REVERT: A 491 MET cc_start: 0.8800 (ttm) cc_final: 0.8256 (tmm) REVERT: A 497 MET cc_start: 0.9393 (ttp) cc_final: 0.9065 (ttp) REVERT: A 528 MET cc_start: 0.9251 (tpt) cc_final: 0.8785 (tpp) REVERT: A 535 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8586 (tt0) REVERT: A 557 ILE cc_start: 0.9605 (mt) cc_final: 0.9358 (tp) REVERT: A 603 MET cc_start: 0.9436 (ttp) cc_final: 0.8925 (tmm) REVERT: B 57 ASP cc_start: 0.9107 (m-30) cc_final: 0.8631 (m-30) REVERT: B 130 MET cc_start: 0.8348 (mmm) cc_final: 0.8092 (mmm) REVERT: B 168 SER cc_start: 0.9779 (m) cc_final: 0.9534 (p) REVERT: B 255 MET cc_start: 0.9670 (mmm) cc_final: 0.9466 (mmt) REVERT: B 282 GLU cc_start: 0.8652 (mp0) cc_final: 0.8228 (mp0) REVERT: B 294 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8766 (pt0) REVERT: B 345 MET cc_start: 0.8950 (mmm) cc_final: 0.8543 (tmm) REVERT: B 386 LEU cc_start: 0.9736 (tp) cc_final: 0.9375 (mm) REVERT: B 390 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9484 (mm) REVERT: B 408 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: B 464 ASN cc_start: 0.9206 (t0) cc_final: 0.9003 (t0) REVERT: B 474 MET cc_start: 0.9004 (ttp) cc_final: 0.8695 (ttp) REVERT: B 515 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7810 (mp0) REVERT: B 584 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8812 (mmt90) REVERT: B 641 ARG cc_start: 0.9264 (mtt180) cc_final: 0.8753 (tpt170) REVERT: C 67 TYR cc_start: 0.8547 (t80) cc_final: 0.8185 (t80) REVERT: C 99 MET cc_start: 0.9668 (mmt) cc_final: 0.9257 (mmm) REVERT: C 114 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8446 (tp) REVERT: C 284 ASP cc_start: 0.8835 (t70) cc_final: 0.8540 (t0) REVERT: C 331 MET cc_start: 0.8642 (mmt) cc_final: 0.8410 (mmp) REVERT: C 345 MET cc_start: 0.8479 (mmt) cc_final: 0.8162 (tpp) REVERT: C 410 MET cc_start: 0.8371 (mtp) cc_final: 0.7614 (ttp) REVERT: C 432 TYR cc_start: 0.8580 (t80) cc_final: 0.8324 (t80) REVERT: C 491 MET cc_start: 0.8815 (tpt) cc_final: 0.8548 (ttt) REVERT: C 515 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8239 (mm-30) REVERT: C 535 GLU cc_start: 0.8813 (mp0) cc_final: 0.8606 (mp0) REVERT: C 584 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8526 (tpp80) REVERT: C 603 MET cc_start: 0.9214 (ttp) cc_final: 0.8774 (tmm) REVERT: D 35 GLU cc_start: 0.9552 (tt0) cc_final: 0.9161 (mt-10) REVERT: D 61 LEU cc_start: 0.9544 (mt) cc_final: 0.9309 (mt) REVERT: D 85 ILE cc_start: 0.9816 (mm) cc_final: 0.9513 (tp) REVERT: D 99 MET cc_start: 0.9480 (mmt) cc_final: 0.9053 (mmm) REVERT: D 114 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9060 (tp) REVERT: D 181 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9457 (tm) REVERT: D 183 ILE cc_start: 0.9685 (tp) cc_final: 0.9376 (pt) REVERT: D 345 MET cc_start: 0.8998 (mmp) cc_final: 0.8358 (tmm) REVERT: D 364 ASP cc_start: 0.9330 (m-30) cc_final: 0.8665 (p0) REVERT: D 371 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9213 (ttpp) REVERT: D 378 MET cc_start: 0.8702 (pmm) cc_final: 0.8382 (pmm) REVERT: D 491 MET cc_start: 0.8815 (tpt) cc_final: 0.8387 (tmm) REVERT: D 492 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8297 (ptp90) REVERT: D 535 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8700 (mt-10) REVERT: D 577 MET cc_start: 0.8966 (tmt) cc_final: 0.8695 (tmm) REVERT: D 603 MET cc_start: 0.9321 (ttp) cc_final: 0.8669 (tmm) REVERT: D 608 LEU cc_start: 0.9598 (tt) cc_final: 0.9343 (tt) REVERT: D 625 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9369 (mm) REVERT: E 8 GLN cc_start: 0.8987 (mt0) cc_final: 0.8755 (mt0) REVERT: E 14 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9347 (tm-30) REVERT: E 30 LYS cc_start: 0.9425 (ttmp) cc_final: 0.9150 (tttt) REVERT: E 36 MET cc_start: 0.9158 (ttt) cc_final: 0.8774 (tpp) REVERT: E 37 ARG cc_start: 0.8850 (ptt90) cc_final: 0.8546 (ptt-90) REVERT: E 71 MET cc_start: 0.9597 (ttt) cc_final: 0.9287 (ttt) REVERT: E 72 MET cc_start: 0.8742 (mmp) cc_final: 0.8207 (mmm) REVERT: E 145 MET cc_start: 0.8076 (mmm) cc_final: 0.7614 (mmm) REVERT: E 148 LYS cc_start: 0.6522 (pmtt) cc_final: 0.5616 (mmtm) outliers start: 69 outliers final: 44 residues processed: 340 average time/residue: 0.1407 time to fit residues: 77.4137 Evaluate side-chains 338 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 280 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 107 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 GLN ** D 230 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 = 0.3141 r_free = 0.3141 target = 0.069875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.053548 restraints weight = 82686.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.055488 restraints weight = 43792.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.056812 restraints weight = 28726.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.057742 restraints weight = 21256.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.058391 restraints weight = 17154.006| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21666 Z= 0.121 Angle : 0.811 17.411 29370 Z= 0.378 Chirality : 0.042 0.254 3323 Planarity : 0.003 0.036 3736 Dihedral : 5.396 54.939 2904 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.75 % Favored : 91.17 % Rotamer: Outliers : 2.93 % Allowed : 19.00 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2628 helix: 1.41 (0.14), residues: 1440 sheet: -2.96 (0.57), residues: 76 loop : -2.34 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 302 TYR 0.040 0.001 TYR A 324 PHE 0.023 0.001 PHE B 472 TRP 0.010 0.001 TRP A 613 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21666) covalent geometry : angle 0.81073 / 0.38 (29370) hydrogen bonds : bond 0.02957 / 1.90 ( 848) hydrogen bonds : angle 3.74318 / 2.61 ( 2439) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 291 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9566 (mt) cc_final: 0.9311 (pp) REVERT: A 99 MET cc_start: 0.9537 (OUTLIER) cc_final: 0.9066 (mmm) REVERT: A 114 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8827 (tp) REVERT: A 128 GLN cc_start: 0.9076 (tt0) cc_final: 0.8116 (tm-30) REVERT: A 209 LYS cc_start: 0.9031 (mttp) cc_final: 0.8706 (mmtt) REVERT: A 311 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8147 (p) REVERT: A 315 GLU cc_start: 0.9052 (mp0) cc_final: 0.8737 (mp0) REVERT: A 410 MET cc_start: 0.8329 (mpp) cc_final: 0.8032 (mpp) REVERT: A 414 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8606 (tpt90) REVERT: A 437 LEU cc_start: 0.9580 (mp) cc_final: 0.8929 (mm) REVERT: A 440 MET cc_start: 0.9240 (tmm) cc_final: 0.8957 (ppp) REVERT: A 485 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9097 (ttm) REVERT: A 497 MET cc_start: 0.9388 (ttp) cc_final: 0.9052 (ttp) REVERT: A 528 MET cc_start: 0.9247 (tpt) cc_final: 0.8906 (tpp) REVERT: A 535 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8567 (tt0) REVERT: A 557 ILE cc_start: 0.9601 (mt) cc_final: 0.9353 (tp) REVERT: A 577 MET cc_start: 0.9348 (ttp) cc_final: 0.8791 (tmm) REVERT: A 603 MET cc_start: 0.9428 (ttp) cc_final: 0.8983 (tmm) REVERT: B 57 ASP cc_start: 0.9129 (m-30) cc_final: 0.8650 (m-30) REVERT: B 168 SER cc_start: 0.9772 (m) cc_final: 0.9529 (p) REVERT: B 241 LEU cc_start: 0.9328 (mt) cc_final: 0.9064 (mp) REVERT: B 294 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8801 (pt0) REVERT: B 345 MET cc_start: 0.8868 (mmm) cc_final: 0.8512 (tmm) REVERT: B 386 LEU cc_start: 0.9740 (tp) cc_final: 0.9372 (mm) REVERT: B 390 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9505 (mm) REVERT: B 408 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: B 464 ASN cc_start: 0.9214 (t0) cc_final: 0.8966 (t0) REVERT: B 474 MET cc_start: 0.9003 (ttp) cc_final: 0.8702 (ttp) REVERT: B 584 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8825 (mmt90) REVERT: B 641 ARG cc_start: 0.9263 (mtt180) cc_final: 0.8767 (tpt170) REVERT: C 99 MET cc_start: 0.9661 (mmt) cc_final: 0.9241 (mmm) REVERT: C 114 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8461 (tp) REVERT: C 284 ASP cc_start: 0.8860 (t70) cc_final: 0.8547 (t0) REVERT: C 331 MET cc_start: 0.8651 (mmt) cc_final: 0.8425 (mmp) REVERT: C 345 MET cc_start: 0.8674 (mmt) cc_final: 0.8377 (tpp) REVERT: C 363 ARG cc_start: 0.8710 (pmt-80) cc_final: 0.8257 (ptt90) REVERT: C 400 LEU cc_start: 0.9439 (mt) cc_final: 0.8902 (pp) REVERT: C 410 MET cc_start: 0.8356 (mtp) cc_final: 0.7590 (ttp) REVERT: C 432 TYR cc_start: 0.8547 (t80) cc_final: 0.8208 (t80) REVERT: C 491 MET cc_start: 0.8791 (tpt) cc_final: 0.8510 (ttt) REVERT: C 515 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8270 (mm-30) REVERT: C 535 GLU cc_start: 0.8772 (mp0) cc_final: 0.8553 (mp0) REVERT: C 584 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8548 (tpp80) REVERT: C 603 MET cc_start: 0.9191 (ttp) cc_final: 0.8792 (tmm) REVERT: D 35 GLU cc_start: 0.9555 (tt0) cc_final: 0.9160 (mt-10) REVERT: D 61 LEU cc_start: 0.9556 (mt) cc_final: 0.9325 (mt) REVERT: D 85 ILE cc_start: 0.9832 (mm) cc_final: 0.9565 (tp) REVERT: D 99 MET cc_start: 0.9472 (mmt) cc_final: 0.9077 (mmm) REVERT: D 181 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9468 (tm) REVERT: D 345 MET cc_start: 0.8988 (mmp) cc_final: 0.8352 (tmm) REVERT: D 364 ASP cc_start: 0.9311 (m-30) cc_final: 0.8617 (p0) REVERT: D 371 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9238 (ttpp) REVERT: D 378 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8366 (pmm) REVERT: D 491 MET cc_start: 0.8809 (tpt) cc_final: 0.8402 (tmm) REVERT: D 492 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8299 (ptp90) REVERT: D 577 MET cc_start: 0.8796 (tmt) cc_final: 0.8592 (tmm) REVERT: D 603 MET cc_start: 0.9317 (ttp) cc_final: 0.8658 (tmm) REVERT: D 608 LEU cc_start: 0.9590 (tt) cc_final: 0.9335 (tt) REVERT: D 625 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9379 (mm) REVERT: E 8 GLN cc_start: 0.9006 (mt0) cc_final: 0.8747 (mt0) REVERT: E 30 LYS cc_start: 0.9425 (ttmp) cc_final: 0.9151 (tttt) REVERT: E 36 MET cc_start: 0.9140 (ttt) cc_final: 0.8780 (tpp) REVERT: E 37 ARG cc_start: 0.8783 (ptt90) cc_final: 0.8542 (ptt-90) REVERT: E 145 MET cc_start: 0.8070 (mmm) cc_final: 0.7758 (mmm) REVERT: E 148 LYS cc_start: 0.6542 (pmtt) cc_final: 0.5595 (mmtm) outliers start: 67 outliers final: 45 residues processed: 339 average time/residue: 0.1422 time to fit residues: 77.7174 Evaluate side-chains 342 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 283 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 160 optimal weight: 6.9990 chunk 145 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 206 optimal weight: 0.0770 chunk 85 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 0.0370 chunk 238 optimal weight: 0.1980 chunk 141 optimal weight: 8.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 522 HIS B 158 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.054975 restraints weight = 82655.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.056921 restraints weight = 45155.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.058281 restraints weight = 30073.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.059234 restraints weight = 22507.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.059895 restraints weight = 18314.651| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21666 Z= 0.121 Angle : 0.830 16.943 29370 Z= 0.382 Chirality : 0.042 0.240 3323 Planarity : 0.003 0.036 3736 Dihedral : 5.305 55.893 2904 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.58 % Allowed : 19.26 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.18), residues: 2628 helix: 1.38 (0.14), residues: 1444 sheet: -2.76 (0.58), residues: 76 loop : -2.28 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 302 TYR 0.015 0.001 TYR A 432 PHE 0.026 0.001 PHE B 472 TRP 0.010 0.001 TRP D 462 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (21666) covalent geometry : angle 0.83049 / 0.38 (29370) hydrogen bonds : bond 0.02774 / 1.77 ( 848) hydrogen bonds : angle 3.67195 / 2.55 ( 2439) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 330 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9558 (mt) cc_final: 0.9307 (pp) REVERT: A 114 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8769 (tp) REVERT: A 128 GLN cc_start: 0.9003 (tt0) cc_final: 0.8125 (tm-30) REVERT: A 209 LYS cc_start: 0.8967 (mttp) cc_final: 0.8632 (mmtt) REVERT: A 302 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7924 (ttp80) REVERT: A 311 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8092 (p) REVERT: A 315 GLU cc_start: 0.9049 (mp0) cc_final: 0.8699 (mp0) REVERT: A 410 MET cc_start: 0.8333 (mpp) cc_final: 0.8032 (mpp) REVERT: A 414 ARG cc_start: 0.9055 (tpp80) cc_final: 0.8615 (tpt90) REVERT: A 437 LEU cc_start: 0.9564 (mp) cc_final: 0.8925 (mm) REVERT: A 440 MET cc_start: 0.9259 (tmm) cc_final: 0.8998 (ppp) REVERT: A 464 ASN cc_start: 0.9378 (OUTLIER) cc_final: 0.8766 (t0) REVERT: A 485 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9128 (ttm) REVERT: A 497 MET cc_start: 0.9384 (ttp) cc_final: 0.9044 (ttp) REVERT: A 515 GLU cc_start: 0.9043 (tp30) cc_final: 0.8289 (mp0) REVERT: A 528 MET cc_start: 0.9218 (tpt) cc_final: 0.8856 (tpp) REVERT: A 557 ILE cc_start: 0.9548 (mt) cc_final: 0.9315 (tp) REVERT: A 577 MET cc_start: 0.9236 (ttp) cc_final: 0.8716 (tmm) REVERT: A 603 MET cc_start: 0.9432 (ttp) cc_final: 0.8923 (tmm) REVERT: B 57 ASP cc_start: 0.9071 (m-30) cc_final: 0.8596 (m-30) REVERT: B 168 SER cc_start: 0.9745 (m) cc_final: 0.9506 (p) REVERT: B 241 LEU cc_start: 0.9252 (mt) cc_final: 0.9032 (mp) REVERT: B 282 GLU cc_start: 0.8657 (mp0) cc_final: 0.8211 (mp0) REVERT: B 345 MET cc_start: 0.8873 (mmm) cc_final: 0.8521 (tmm) REVERT: B 386 LEU cc_start: 0.9734 (tp) cc_final: 0.9354 (mm) REVERT: B 390 LEU cc_start: 0.9700 (OUTLIER) cc_final: 0.9494 (mm) REVERT: B 408 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: B 474 MET cc_start: 0.9017 (ttp) cc_final: 0.8762 (ttp) REVERT: B 584 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8769 (mmt90) REVERT: B 641 ARG cc_start: 0.9269 (mtt180) cc_final: 0.8756 (tpt170) REVERT: C 99 MET cc_start: 0.9678 (mmt) cc_final: 0.9243 (mmm) REVERT: C 114 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8486 (tp) REVERT: C 284 ASP cc_start: 0.8823 (t70) cc_final: 0.8493 (t0) REVERT: C 306 GLN cc_start: 0.9438 (tp-100) cc_final: 0.8915 (tp40) REVERT: C 314 LYS cc_start: 0.9155 (ttpt) cc_final: 0.8734 (ttmm) REVERT: C 331 MET cc_start: 0.8634 (mmt) cc_final: 0.8395 (mmp) REVERT: C 345 MET cc_start: 0.8387 (mmt) cc_final: 0.8009 (tpp) REVERT: C 363 ARG cc_start: 0.8752 (pmt-80) cc_final: 0.8311 (ptt90) REVERT: C 410 MET cc_start: 0.8356 (mtp) cc_final: 0.7661 (ttp) REVERT: C 491 MET cc_start: 0.8762 (tpt) cc_final: 0.8514 (ttt) REVERT: C 515 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8516 (mm-30) REVERT: C 535 GLU cc_start: 0.8755 (mp0) cc_final: 0.8213 (mp0) REVERT: C 603 MET cc_start: 0.9138 (ttp) cc_final: 0.8748 (tmm) REVERT: D 35 GLU cc_start: 0.9546 (tt0) cc_final: 0.9134 (mt-10) REVERT: D 61 LEU cc_start: 0.9536 (mt) cc_final: 0.9311 (mt) REVERT: D 85 ILE cc_start: 0.9813 (mm) cc_final: 0.9528 (tp) REVERT: D 99 MET cc_start: 0.9480 (mmt) cc_final: 0.9103 (mmm) REVERT: D 173 VAL cc_start: 0.8075 (t) cc_final: 0.7813 (p) REVERT: D 181 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9457 (tt) REVERT: D 345 MET cc_start: 0.8932 (mmp) cc_final: 0.8336 (tmm) REVERT: D 364 ASP cc_start: 0.9286 (m-30) cc_final: 0.8511 (p0) REVERT: D 371 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9214 (ttpp) REVERT: D 378 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8414 (pmm) REVERT: D 440 MET cc_start: 0.9257 (tpp) cc_final: 0.8887 (mmp) REVERT: D 491 MET cc_start: 0.8664 (tpt) cc_final: 0.8299 (tmm) REVERT: D 554 MET cc_start: 0.8736 (mmm) cc_final: 0.8528 (mtt) REVERT: D 603 MET cc_start: 0.9265 (ttp) cc_final: 0.8605 (tmm) REVERT: D 608 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9319 (tt) REVERT: D 625 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9492 (mm) REVERT: E 8 GLN cc_start: 0.8945 (mt0) cc_final: 0.8694 (mt0) REVERT: E 30 LYS cc_start: 0.9399 (ttmp) cc_final: 0.9132 (tttt) REVERT: E 36 MET cc_start: 0.9116 (ttt) cc_final: 0.8789 (tpp) REVERT: E 37 ARG cc_start: 0.8748 (ptt90) cc_final: 0.8517 (ptt-90) REVERT: E 71 MET cc_start: 0.9485 (ttt) cc_final: 0.9063 (tmm) REVERT: E 148 LYS cc_start: 0.6534 (pmtt) cc_final: 0.5623 (mmtm) outliers start: 59 outliers final: 39 residues processed: 373 average time/residue: 0.1354 time to fit residues: 81.6487 Evaluate side-chains 335 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 283 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 27 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 219 optimal weight: 0.0980 chunk 69 optimal weight: 0.0970 chunk 153 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 128 optimal weight: 9.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.055031 restraints weight = 82104.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.057026 restraints weight = 44230.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.058398 restraints weight = 29217.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.059355 restraints weight = 21824.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.060035 restraints weight = 17678.969| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21666 Z= 0.119 Angle : 0.824 17.137 29370 Z= 0.381 Chirality : 0.042 0.222 3323 Planarity : 0.003 0.038 3736 Dihedral : 5.068 56.055 2900 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.53 % Allowed : 19.74 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.29 (0.17), residues: 2628 helix: 1.34 (0.14), residues: 1452 sheet: -2.45 (0.59), residues: 78 loop : -2.23 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 302 TYR 0.036 0.001 TYR A 324 PHE 0.026 0.001 PHE B 472 TRP 0.007 0.001 TRP D 462 HIS 0.008 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21666) covalent geometry : angle 0.82443 / 0.38 (29370) hydrogen bonds : bond 0.02793 / 1.80 ( 848) hydrogen bonds : angle 3.68807 / 2.57 ( 2439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.87 seconds wall clock time: 61 minutes 44.28 seconds (3704.28 seconds total)