Starting phenix.real_space_refine on Wed Nov 19 05:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e2f_8961/11_2025/6e2f_8961.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e2f_8961/11_2025/6e2f_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_8961/11_2025/6e2f_8961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e2f_8961/11_2025/6e2f_8961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e2f_8961/11_2025/6e2f_8961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e2f_8961/11_2025/6e2f_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 4.80, per 1000 atoms: 0.23 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: 1.74 Conformation dependent library (CDL) restraints added in 823.5 milliseconds 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: 0.61 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: 2.74 Time building geometry restraints manager: 2.35 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: 0.950 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: 0.030 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.860 Find NCS groups from input model: 0.330 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 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 covalent geometry : bond 0.00971 (21666) covalent geometry : angle 1.36385 (29370) hydrogen bonds : bond 0.31610 ( 848) hydrogen bonds : angle 9.20345 ( 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 : 0.815 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: 0.9219 (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: 0.9154 (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: 0.9207 (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: 0.9158 (pt0) cc_final: 0.8745 (pm20) REVERT: B 637 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8457 (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: 0.8155 (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: 0.9463 (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 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: 0.1464 time to fit residues: 110.3711 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 : 0.731 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.066703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.050011 restraints weight = 83717.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.051855 restraints weight = 45487.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.053109 restraints weight = 30361.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.053980 restraints weight = 22892.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.054606 restraints weight = 18749.838| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21666 Z= 0.186 Angle : 0.848 13.090 29370 Z= 0.431 Chirality : 0.044 0.202 3323 Planarity : 0.005 0.038 3736 Dihedral : 7.025 58.358 2918 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.78 % Favored : 90.07 % Rotamer: Outliers : 4.02 % Allowed : 11.18 % Favored : 84.80 % 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: -2.97 (0.15), residues: 2628 helix: -1.15 (0.12), residues: 1430 sheet: -4.23 (0.35), residues: 82 loop : -2.86 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 643 TYR 0.018 0.001 TYR C 324 PHE 0.029 0.002 PHE A 493 TRP 0.019 0.002 TRP D 495 HIS 0.007 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00401 (21666) covalent geometry : angle 0.84783 (29370) hydrogen bonds : bond 0.05357 ( 848) hydrogen bonds : angle 4.95605 ( 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 459 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 367 time to evaluate : 0.859 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: 0.9632 (mt) cc_final: 0.9311 (pp) REVERT: A 128 GLN cc_start: 0.9167 (tt0) cc_final: 0.7890 (tm-30) REVERT: A 209 LYS cc_start: 0.9264 (mttp) cc_final: 0.8977 (mmtt) REVERT: A 315 GLU cc_start: 0.8825 (mp0) cc_final: 0.8459 (mp0) REVERT: A 414 ARG cc_start: 0.9104 (tpp80) cc_final: 0.8736 (tpt170) REVERT: A 437 LEU cc_start: 0.9462 (mp) cc_final: 0.8848 (mm) REVERT: A 440 MET cc_start: 0.9014 (tmm) cc_final: 0.8703 (ppp) REVERT: A 474 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.9022 (ppp) REVERT: A 485 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8971 (ttm) REVERT: A 515 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8647 (tp30) REVERT: A 528 MET cc_start: 0.9344 (tpt) cc_final: 0.8800 (tpp) REVERT: A 557 ILE cc_start: 0.9681 (mt) cc_final: 0.9374 (tp) REVERT: A 603 MET cc_start: 0.9460 (ttp) cc_final: 0.8850 (tmm) REVERT: B 38 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9447 (tp) REVERT: B 57 ASP cc_start: 0.9194 (m-30) cc_final: 0.8716 (m-30) REVERT: B 110 MET cc_start: 0.8781 (mtm) cc_final: 0.8529 (mtm) REVERT: B 130 MET cc_start: 0.8673 (mmm) cc_final: 0.8363 (mmm) REVERT: B 168 SER cc_start: 0.9805 (m) cc_final: 0.9536 (p) REVERT: B 345 MET cc_start: 0.8925 (mmm) cc_final: 0.8571 (tmm) REVERT: B 464 ASN cc_start: 0.9393 (OUTLIER) cc_final: 0.8752 (t0) REVERT: B 542 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6317 (m-30) REVERT: B 591 GLU cc_start: 0.9259 (pt0) cc_final: 0.8719 (pm20) REVERT: B 637 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8340 (tm-30) REVERT: B 641 ARG cc_start: 0.9164 (mtt180) cc_final: 0.8848 (mmp80) REVERT: C 38 LEU cc_start: 0.9662 (mt) cc_final: 0.9301 (tt) REVERT: C 96 MET cc_start: 0.9357 (mmm) cc_final: 0.9123 (mmm) REVERT: C 99 MET cc_start: 0.9557 (mmt) cc_final: 0.9107 (mmm) REVERT: C 110 MET cc_start: 0.7994 (mtp) cc_final: 0.7661 (mtm) REVERT: C 130 MET cc_start: 0.8372 (mmt) cc_final: 0.8043 (mmm) REVERT: C 284 ASP cc_start: 0.8855 (t70) cc_final: 0.8512 (t0) REVERT: C 315 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.8890 (mp0) REVERT: C 410 MET cc_start: 0.7903 (mtp) cc_final: 0.7334 (ttp) REVERT: C 491 MET cc_start: 0.9102 (tpt) cc_final: 0.8773 (tpp) REVERT: C 515 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8632 (tp30) REVERT: C 528 MET cc_start: 0.9285 (ttm) cc_final: 0.9027 (tpp) REVERT: C 532 SER cc_start: 0.9793 (t) cc_final: 0.9446 (p) REVERT: C 577 MET cc_start: 0.9225 (tmt) cc_final: 0.8908 (tmm) REVERT: C 591 GLU cc_start: 0.8965 (pt0) cc_final: 0.8623 (pm20) REVERT: C 603 MET cc_start: 0.9304 (ttp) cc_final: 0.8891 (tmm) REVERT: D 35 GLU cc_start: 0.9539 (tt0) cc_final: 0.9062 (mt-10) REVERT: D 38 LEU cc_start: 0.9711 (mt) cc_final: 0.9507 (tp) REVERT: D 61 LEU cc_start: 0.9598 (mt) cc_final: 0.9368 (mt) REVERT: D 85 ILE cc_start: 0.9818 (mm) cc_final: 0.9554 (tp) REVERT: D 99 MET cc_start: 0.9478 (mmt) cc_final: 0.8863 (mmm) REVERT: D 183 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9310 (mt) REVERT: D 184 GLU cc_start: 0.8786 (mp0) cc_final: 0.8448 (mm-30) REVERT: D 282 GLU cc_start: 0.8240 (mp0) cc_final: 0.7989 (mp0) REVERT: D 289 GLU cc_start: 0.8187 (mp0) cc_final: 0.7957 (pm20) REVERT: D 331 MET cc_start: 0.9036 (tmm) cc_final: 0.8766 (mmt) REVERT: D 364 ASP cc_start: 0.9452 (m-30) cc_final: 0.8375 (m-30) REVERT: D 483 GLN cc_start: 0.8931 (tt0) cc_final: 0.8574 (tm-30) REVERT: D 491 MET cc_start: 0.8990 (tpt) cc_final: 0.8503 (tmm) REVERT: D 492 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7961 (ptt180) REVERT: D 577 MET cc_start: 0.9236 (tmt) cc_final: 0.9000 (tmm) REVERT: D 603 MET cc_start: 0.9275 (ttp) cc_final: 0.8828 (tmm) REVERT: D 625 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9325 (tm) REVERT: E 8 GLN cc_start: 0.8895 (mt0) cc_final: 0.8653 (mt0) REVERT: E 14 GLU cc_start: 0.9610 (mm-30) cc_final: 0.9329 (tm-30) REVERT: E 18 LEU cc_start: 0.9299 (tt) cc_final: 0.9090 (pp) REVERT: E 36 MET cc_start: 0.9194 (ttt) cc_final: 0.8844 (tpp) REVERT: E 49 GLN cc_start: 0.9092 (pt0) cc_final: 0.8772 (pm20) REVERT: E 116 LEU cc_start: 0.8980 (mt) cc_final: 0.8515 (tp) REVERT: E 143 GLN cc_start: 0.6773 (mt0) cc_final: 0.6290 (tm-30) REVERT: E 144 MET cc_start: 0.7875 (mmp) cc_final: 0.7207 (mtt) REVERT: E 148 LYS cc_start: 0.6820 (pmtt) cc_final: 0.5962 (mmtm) outliers start: 92 outliers final: 28 residues processed: 434 average time/residue: 0.1301 time to fit residues: 90.4291 Evaluate side-chains 319 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 499 VAL 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 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 542 ASP Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 613 TRP 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 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 183 ILE Chi-restraints excluded: chain D residue 189 ILE 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 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: 0.7980 chunk 192 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 241 optimal weight: 0.0060 chunk 33 optimal weight: 8.9990 chunk 245 optimal weight: 0.0370 chunk 165 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 208 ASN B 217 ASN B 582 HIS C 165 HIS C 230 GLN C 582 HIS C 587 HIS D 91 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.053843 restraints weight = 82950.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.055746 restraints weight = 45237.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.057054 restraints weight = 30158.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.057962 restraints weight = 22662.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.058559 restraints weight = 18504.488| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3718 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= 0.126 Angle : 0.791 14.431 29370 Z= 0.383 Chirality : 0.041 0.208 3323 Planarity : 0.004 0.041 3736 Dihedral : 6.184 52.063 2908 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.25 % Favored : 90.60 % Rotamer: Outliers : 3.28 % Allowed : 14.72 % Favored : 82.01 % 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: -1.91 (0.16), residues: 2628 helix: -0.09 (0.13), residues: 1428 sheet: -3.72 (0.41), residues: 80 loop : -2.69 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 363 TYR 0.021 0.001 TYR A 324 PHE 0.023 0.001 PHE E 141 TRP 0.013 0.001 TRP A 613 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00269 (21666) covalent geometry : angle 0.79116 (29370) hydrogen bonds : bond 0.03942 ( 848) hydrogen bonds : angle 4.19430 ( 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 407 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 332 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9600 (mt) cc_final: 0.9271 (pp) REVERT: A 128 GLN cc_start: 0.9133 (tt0) cc_final: 0.7839 (tm-30) REVERT: A 209 LYS cc_start: 0.9048 (mttp) cc_final: 0.8785 (mmtt) REVERT: A 311 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8128 (p) REVERT: A 315 GLU cc_start: 0.8933 (mp0) cc_final: 0.8615 (mp0) REVERT: A 410 MET cc_start: 0.8238 (mpp) cc_final: 0.7884 (mpp) REVERT: A 414 ARG cc_start: 0.9045 (tpp80) cc_final: 0.8614 (tpt90) REVERT: A 437 LEU cc_start: 0.9561 (mp) cc_final: 0.8885 (mm) REVERT: A 440 MET cc_start: 0.8972 (tmm) cc_final: 0.8640 (ppp) REVERT: A 454 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.8912 (tpp) REVERT: A 464 ASN cc_start: 0.9494 (OUTLIER) cc_final: 0.8860 (t0) REVERT: A 489 ASP cc_start: 0.8307 (t0) cc_final: 0.7861 (t0) REVERT: A 515 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8478 (tp30) REVERT: A 528 MET cc_start: 0.9254 (tpt) cc_final: 0.8822 (tpp) REVERT: A 535 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8642 (tt0) REVERT: A 557 ILE cc_start: 0.9695 (mt) cc_final: 0.9411 (tp) REVERT: A 570 MET cc_start: 0.9104 (mmm) cc_final: 0.8891 (mmm) REVERT: A 577 MET cc_start: 0.9235 (tmt) cc_final: 0.8917 (tmm) REVERT: A 603 MET cc_start: 0.9434 (ttp) cc_final: 0.8840 (tmm) REVERT: A 635 ASP cc_start: 0.8358 (t70) cc_final: 0.7989 (p0) REVERT: B 57 ASP cc_start: 0.9126 (m-30) cc_final: 0.8674 (m-30) REVERT: B 130 MET cc_start: 0.8515 (mmm) cc_final: 0.8288 (mmm) REVERT: B 168 SER cc_start: 0.9777 (m) cc_final: 0.9503 (p) REVERT: B 241 LEU cc_start: 0.9437 (mt) cc_final: 0.9219 (mp) REVERT: B 260 MET cc_start: 0.9510 (tpp) cc_final: 0.9213 (tpp) REVERT: B 302 ARG cc_start: 0.8081 (tpt170) cc_final: 0.7777 (tpp-160) REVERT: B 345 MET cc_start: 0.8966 (mmm) cc_final: 0.8475 (tmm) REVERT: B 398 ILE cc_start: 0.9624 (tt) cc_final: 0.9397 (pt) REVERT: B 489 ASP cc_start: 0.8558 (t0) cc_final: 0.8004 (t0) REVERT: B 528 MET cc_start: 0.9183 (tpp) cc_final: 0.8786 (tpp) REVERT: B 637 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8391 (tm-30) REVERT: B 641 ARG cc_start: 0.9157 (mtt180) cc_final: 0.8860 (mmp80) REVERT: C 99 MET cc_start: 0.9466 (mmt) cc_final: 0.9175 (mmp) REVERT: C 284 ASP cc_start: 0.8727 (t70) cc_final: 0.8490 (t70) REVERT: C 400 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.8977 (pp) REVERT: C 410 MET cc_start: 0.8253 (mtp) cc_final: 0.7522 (ttp) REVERT: C 432 TYR cc_start: 0.8718 (t80) cc_final: 0.8501 (t80) REVERT: C 491 MET cc_start: 0.9067 (tpt) cc_final: 0.8275 (tpp) REVERT: C 492 ARG cc_start: 0.9288 (ptt180) cc_final: 0.8634 (ptt-90) REVERT: C 515 GLU cc_start: 0.8780 (mm-30) cc_final: 0.7852 (mp0) REVERT: C 528 MET cc_start: 0.9330 (ttm) cc_final: 0.9071 (tpp) REVERT: C 532 SER cc_start: 0.9777 (t) cc_final: 0.9369 (p) REVERT: C 603 MET cc_start: 0.9291 (ttp) cc_final: 0.8904 (tmm) REVERT: D 35 GLU cc_start: 0.9484 (tt0) cc_final: 0.9106 (mt-10) REVERT: D 61 LEU cc_start: 0.9554 (mt) cc_final: 0.9320 (mt) REVERT: D 85 ILE cc_start: 0.9838 (mm) cc_final: 0.9527 (tp) REVERT: D 99 MET cc_start: 0.9448 (mmt) cc_final: 0.8846 (mmm) REVERT: D 282 GLU cc_start: 0.8227 (mp0) cc_final: 0.7976 (mp0) REVERT: D 345 MET cc_start: 0.9129 (tpp) cc_final: 0.8230 (tmm) REVERT: D 483 GLN cc_start: 0.8926 (tt0) cc_final: 0.8497 (tm-30) REVERT: D 491 MET cc_start: 0.9034 (tpt) cc_final: 0.8537 (tmm) REVERT: D 492 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8442 (ptt180) REVERT: D 535 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8546 (mt-10) REVERT: D 577 MET cc_start: 0.9158 (tmt) cc_final: 0.8942 (tmm) REVERT: D 603 MET cc_start: 0.9248 (ttp) cc_final: 0.8894 (tmm) REVERT: D 625 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9324 (tm) REVERT: E 8 GLN cc_start: 0.8938 (mt0) cc_final: 0.8687 (mt0) REVERT: E 14 GLU cc_start: 0.9571 (mm-30) cc_final: 0.9292 (tm-30) REVERT: E 36 MET cc_start: 0.9232 (ttt) cc_final: 0.8813 (tpp) REVERT: E 63 ILE cc_start: 0.9183 (mp) cc_final: 0.8930 (mm) REVERT: E 144 MET cc_start: 0.7750 (mmp) cc_final: 0.7543 (tpp) REVERT: E 145 MET cc_start: 0.8302 (mmm) cc_final: 0.8076 (mmm) REVERT: E 148 LYS cc_start: 0.6759 (pmtt) cc_final: 0.5916 (mmtm) outliers start: 75 outliers final: 21 residues processed: 379 average time/residue: 0.1269 time to fit residues: 77.4396 Evaluate side-chains 312 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 454 MET Chi-restraints excluded: chain A residue 464 ASN 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 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 346 CYS 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 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: 5.9990 chunk 224 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 73 HIS A 217 ASN A 258 HIS A 464 ASN A 572 ASN B 73 HIS B 267 GLN C 158 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.065870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.049118 restraints weight = 85829.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.050937 restraints weight = 46076.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.052205 restraints weight = 30647.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.053076 restraints weight = 23044.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.053648 restraints weight = 18849.201| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21666 Z= 0.228 Angle : 0.828 15.618 29370 Z= 0.407 Chirality : 0.044 0.206 3323 Planarity : 0.004 0.036 3736 Dihedral : 6.148 51.230 2908 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.63 % Favored : 90.22 % Rotamer: Outliers : 4.06 % Allowed : 15.85 % Favored : 80.09 % 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: -1.23 (0.17), residues: 2628 helix: 0.60 (0.14), residues: 1455 sheet: -3.91 (0.42), residues: 78 loop : -2.63 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 302 TYR 0.025 0.002 TYR A 324 PHE 0.015 0.001 PHE A 493 TRP 0.020 0.002 TRP A 613 HIS 0.009 0.002 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00502 (21666) covalent geometry : angle 0.82782 (29370) hydrogen bonds : bond 0.03918 ( 848) hydrogen bonds : angle 4.39383 ( 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 377 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 284 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9613 (mt) cc_final: 0.9298 (pp) REVERT: A 99 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.9049 (mmm) REVERT: A 128 GLN cc_start: 0.9121 (tt0) cc_final: 0.7803 (tm-30) REVERT: A 209 LYS cc_start: 0.9216 (mttp) cc_final: 0.8935 (mmtt) REVERT: A 311 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8215 (p) REVERT: A 315 GLU cc_start: 0.9028 (mp0) cc_final: 0.8682 (mp0) REVERT: A 410 MET cc_start: 0.8234 (mpp) cc_final: 0.7888 (mpp) REVERT: A 414 ARG cc_start: 0.9115 (tpp80) cc_final: 0.8619 (tpt90) REVERT: A 437 LEU cc_start: 0.9573 (mp) cc_final: 0.8965 (mm) REVERT: A 440 MET cc_start: 0.9149 (tmm) cc_final: 0.8879 (ppp) REVERT: A 454 MET cc_start: 0.9557 (OUTLIER) cc_final: 0.9182 (tpp) REVERT: A 491 MET cc_start: 0.8937 (ttm) cc_final: 0.8559 (tmm) REVERT: A 515 GLU cc_start: 0.9024 (mm-30) cc_final: 0.7987 (mp0) REVERT: A 528 MET cc_start: 0.9312 (tpt) cc_final: 0.8844 (tpp) REVERT: A 535 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8909 (tt0) REVERT: A 557 ILE cc_start: 0.9738 (mt) cc_final: 0.9495 (tp) REVERT: A 603 MET cc_start: 0.9460 (ttp) cc_final: 0.8928 (tmm) REVERT: B 38 LEU cc_start: 0.9687 (tp) cc_final: 0.9335 (tp) REVERT: B 57 ASP cc_start: 0.9136 (m-30) cc_final: 0.8638 (m-30) REVERT: B 130 MET cc_start: 0.8857 (mmm) cc_final: 0.8642 (mmm) REVERT: B 168 SER cc_start: 0.9823 (m) cc_final: 0.9581 (p) REVERT: B 260 MET cc_start: 0.9618 (tpp) cc_final: 0.9276 (tpp) REVERT: B 301 LYS cc_start: 0.9228 (mtpp) cc_final: 0.9007 (mtpp) REVERT: B 302 ARG cc_start: 0.8561 (tpt170) cc_final: 0.8176 (tpp-160) REVERT: B 345 MET cc_start: 0.9042 (mmm) cc_final: 0.8633 (tmm) REVERT: B 377 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7834 (m-10) REVERT: B 398 ILE cc_start: 0.9593 (tt) cc_final: 0.9378 (pt) REVERT: B 408 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: B 464 ASN cc_start: 0.9418 (OUTLIER) cc_final: 0.8834 (t0) REVERT: B 515 GLU cc_start: 0.8960 (tp30) cc_final: 0.8298 (mp0) REVERT: B 528 MET cc_start: 0.9135 (tpp) cc_final: 0.8722 (tpp) REVERT: B 637 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8331 (tm-30) REVERT: B 641 ARG cc_start: 0.9192 (mtt180) cc_final: 0.8860 (mmp80) REVERT: C 38 LEU cc_start: 0.9681 (mt) cc_final: 0.9332 (tt) REVERT: C 99 MET cc_start: 0.9613 (mmt) cc_final: 0.9215 (mmm) REVERT: C 284 ASP cc_start: 0.8848 (t70) cc_final: 0.8528 (t0) REVERT: C 315 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.8961 (mp0) REVERT: C 410 MET cc_start: 0.8414 (mtp) cc_final: 0.7759 (ttp) REVERT: C 432 TYR cc_start: 0.8827 (t80) cc_final: 0.8542 (t80) REVERT: C 454 MET cc_start: 0.9541 (mmm) cc_final: 0.9340 (tpt) REVERT: C 474 MET cc_start: 0.8504 (pmm) cc_final: 0.8277 (pmm) REVERT: C 491 MET cc_start: 0.9083 (tpt) cc_final: 0.8302 (tpp) REVERT: C 515 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8034 (mp0) REVERT: C 528 MET cc_start: 0.9343 (ttm) cc_final: 0.8961 (tpp) REVERT: C 532 SER cc_start: 0.9685 (t) cc_final: 0.9452 (p) REVERT: C 603 MET cc_start: 0.9317 (ttp) cc_final: 0.8839 (tmm) REVERT: D 35 GLU cc_start: 0.9562 (tt0) cc_final: 0.9123 (mt-10) REVERT: D 61 LEU cc_start: 0.9556 (mt) cc_final: 0.9327 (mt) REVERT: D 85 ILE cc_start: 0.9838 (mm) cc_final: 0.9589 (tp) REVERT: D 99 MET cc_start: 0.9466 (mmt) cc_final: 0.8947 (mmm) REVERT: D 114 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9022 (tp) REVERT: D 289 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: D 345 MET cc_start: 0.9083 (tpp) cc_final: 0.8252 (tmm) REVERT: D 371 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8817 (ttpp) REVERT: D 378 MET cc_start: 0.8807 (pmm) cc_final: 0.8525 (pmm) REVERT: D 442 MET cc_start: 0.9486 (tpp) cc_final: 0.9037 (ttm) REVERT: D 491 MET cc_start: 0.8979 (tpt) cc_final: 0.8441 (tmm) REVERT: D 492 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8345 (ptt180) REVERT: D 577 MET cc_start: 0.9126 (tmt) cc_final: 0.8847 (tmm) REVERT: D 603 MET cc_start: 0.9336 (ttp) cc_final: 0.8840 (tmm) REVERT: D 625 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9381 (tm) REVERT: E 8 GLN cc_start: 0.8805 (mt0) cc_final: 0.8603 (mt0) REVERT: E 14 GLU cc_start: 0.9619 (mm-30) cc_final: 0.9316 (tm-30) REVERT: E 36 MET cc_start: 0.9227 (ttt) cc_final: 0.8850 (tpp) REVERT: E 77 LYS cc_start: 0.6071 (tppt) cc_final: 0.5793 (tppt) REVERT: E 148 LYS cc_start: 0.6740 (pmtt) cc_final: 0.5911 (mmtm) outliers start: 93 outliers final: 51 residues processed: 348 average time/residue: 0.1306 time to fit residues: 73.0703 Evaluate side-chains 326 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 263 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 215 MET 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 454 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 572 ASN 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 377 TYR 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 520 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 315 GLU 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 387 VAL 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 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 575 ILE 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 289 GLU Chi-restraints excluded: chain D residue 338 LEU 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 492 ARG Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 575 ILE 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 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: 4.9990 chunk 75 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 chunk 29 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 572 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 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 = 0.3052 r_free = 0.3052 target = 0.065783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.049487 restraints weight = 83984.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.051299 restraints weight = 45255.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.052555 restraints weight = 30035.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.053424 restraints weight = 22516.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054044 restraints weight = 18338.473| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21666 Z= 0.181 Angle : 0.797 15.444 29370 Z= 0.387 Chirality : 0.043 0.230 3323 Planarity : 0.004 0.038 3736 Dihedral : 5.958 51.705 2904 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.78 % Favored : 90.07 % Rotamer: Outliers : 4.54 % Allowed : 16.64 % Favored : 78.82 % 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: -0.94 (0.17), residues: 2628 helix: 0.88 (0.14), residues: 1453 sheet: -3.79 (0.46), residues: 76 loop : -2.55 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 302 TYR 0.013 0.001 TYR C 623 PHE 0.017 0.001 PHE A 493 TRP 0.019 0.001 TRP A 613 HIS 0.008 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00405 (21666) covalent geometry : angle 0.79740 (29370) hydrogen bonds : bond 0.03652 ( 848) hydrogen bonds : angle 4.21359 ( 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 378 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 274 time to evaluate : 0.594 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: 0.9601 (mt) cc_final: 0.9312 (pp) REVERT: A 99 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.8985 (mmm) REVERT: A 128 GLN cc_start: 0.9129 (tt0) cc_final: 0.7770 (tm-30) REVERT: A 209 LYS cc_start: 0.9237 (mttp) cc_final: 0.8956 (mmtt) REVERT: A 311 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 315 GLU cc_start: 0.9087 (mp0) cc_final: 0.8712 (mp0) REVERT: A 410 MET cc_start: 0.8266 (mpp) cc_final: 0.7975 (mpp) REVERT: A 414 ARG cc_start: 0.9080 (tpp80) cc_final: 0.8694 (tpt170) REVERT: A 437 LEU cc_start: 0.9551 (mp) cc_final: 0.8938 (mm) REVERT: A 440 MET cc_start: 0.9191 (tmm) cc_final: 0.8901 (ppp) REVERT: A 454 MET cc_start: 0.9564 (OUTLIER) cc_final: 0.9113 (tpp) REVERT: A 474 MET cc_start: 0.9195 (ppp) cc_final: 0.8620 (ppp) REVERT: A 491 MET cc_start: 0.8894 (ttm) cc_final: 0.8507 (tmm) REVERT: A 515 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8830 (tp30) REVERT: A 528 MET cc_start: 0.9295 (tpt) cc_final: 0.8811 (tpp) REVERT: A 557 ILE cc_start: 0.9707 (mt) cc_final: 0.9481 (tp) REVERT: A 577 MET cc_start: 0.9396 (tmt) cc_final: 0.9176 (tmm) REVERT: A 603 MET cc_start: 0.9446 (ttp) cc_final: 0.8934 (tmm) REVERT: B 38 LEU cc_start: 0.9710 (tp) cc_final: 0.9390 (tt) REVERT: B 57 ASP cc_start: 0.9072 (m-30) cc_final: 0.8568 (m-30) REVERT: B 168 SER cc_start: 0.9821 (m) cc_final: 0.9580 (p) REVERT: B 260 MET cc_start: 0.9588 (tpp) cc_final: 0.9251 (tpp) REVERT: B 294 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8704 (mp0) REVERT: B 301 LYS cc_start: 0.9200 (mtpp) cc_final: 0.9000 (mtpp) REVERT: B 345 MET cc_start: 0.9042 (mmm) cc_final: 0.8761 (tmm) REVERT: B 377 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7949 (m-10) REVERT: B 398 ILE cc_start: 0.9590 (tt) cc_final: 0.9384 (pt) REVERT: B 408 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: B 464 ASN cc_start: 0.9399 (OUTLIER) cc_final: 0.8836 (t0) REVERT: B 528 MET cc_start: 0.9104 (tpp) cc_final: 0.8663 (tpp) REVERT: B 637 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8442 (tm-30) REVERT: B 641 ARG cc_start: 0.9154 (mtt180) cc_final: 0.8734 (tpt170) REVERT: C 38 LEU cc_start: 0.9685 (mt) cc_final: 0.9330 (tt) REVERT: C 99 MET cc_start: 0.9624 (mmt) cc_final: 0.9228 (mmm) REVERT: C 114 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8500 (tp) REVERT: C 284 ASP cc_start: 0.8846 (t70) cc_final: 0.8528 (t0) REVERT: C 345 MET cc_start: 0.8704 (mmt) cc_final: 0.8417 (tpp) REVERT: C 410 MET cc_start: 0.8400 (mtp) cc_final: 0.7647 (ttp) REVERT: C 432 TYR cc_start: 0.8771 (t80) cc_final: 0.8404 (t80) REVERT: C 454 MET cc_start: 0.9494 (mmm) cc_final: 0.9111 (tpt) REVERT: C 491 MET cc_start: 0.9055 (tpt) cc_final: 0.8330 (tpp) REVERT: C 515 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8031 (mp0) REVERT: C 528 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8947 (tpp) REVERT: C 550 ASP cc_start: 0.9079 (t70) cc_final: 0.8639 (t0) REVERT: C 603 MET cc_start: 0.9333 (ttp) cc_final: 0.8880 (tmm) REVERT: D 35 GLU cc_start: 0.9582 (tt0) cc_final: 0.9199 (mt-10) REVERT: D 61 LEU cc_start: 0.9531 (mt) cc_final: 0.9291 (mt) REVERT: D 85 ILE cc_start: 0.9835 (mm) cc_final: 0.9583 (tp) REVERT: D 99 MET cc_start: 0.9459 (mmt) cc_final: 0.8970 (mmm) REVERT: D 114 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8993 (tp) REVERT: D 289 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: D 345 MET cc_start: 0.9093 (tpp) cc_final: 0.8271 (tmm) REVERT: D 371 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9088 (ttpp) REVERT: D 378 MET cc_start: 0.8758 (pmm) cc_final: 0.8440 (pmm) REVERT: D 442 MET cc_start: 0.9488 (tpp) cc_final: 0.9037 (ttm) REVERT: D 491 MET cc_start: 0.8902 (tpt) cc_final: 0.8404 (tmm) REVERT: D 497 MET cc_start: 0.9387 (ttp) cc_final: 0.8679 (tmm) REVERT: D 577 MET cc_start: 0.9078 (tmt) cc_final: 0.8789 (tmm) REVERT: D 603 MET cc_start: 0.9352 (ttp) cc_final: 0.8843 (tmm) REVERT: D 625 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9340 (tm) REVERT: E 14 GLU cc_start: 0.9605 (mm-30) cc_final: 0.9313 (tm-30) REVERT: E 36 MET cc_start: 0.9240 (ttt) cc_final: 0.8855 (tpp) REVERT: E 51 MET cc_start: 0.8289 (mmt) cc_final: 0.7866 (tpp) REVERT: E 71 MET cc_start: 0.9254 (ttt) cc_final: 0.8957 (tmm) REVERT: E 76 MET cc_start: 0.9125 (pmm) cc_final: 0.8652 (pmm) REVERT: E 122 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8711 (m-30) REVERT: E 145 MET cc_start: 0.8154 (mmm) cc_final: 0.7590 (mmm) REVERT: E 148 LYS cc_start: 0.6700 (pmtt) cc_final: 0.5688 (mmtm) outliers start: 104 outliers final: 57 residues processed: 344 average time/residue: 0.1340 time to fit residues: 73.2444 Evaluate side-chains 327 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 257 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 215 MET 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 452 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 572 ASN 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 348 ILE Chi-restraints excluded: chain B residue 377 TYR 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 520 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 387 VAL 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 499 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 538 LEU 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 189 ILE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU 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 492 ARG Chi-restraints excluded: chain D residue 575 ILE 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 122 ASP 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: 0.7980 chunk 67 optimal weight: 8.9990 chunk 259 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 129 optimal weight: 0.0050 chunk 138 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 147 optimal weight: 0.0470 overall best weight: 1.9696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 572 ASN B 267 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.050497 restraints weight = 84663.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.052332 restraints weight = 45992.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.053607 restraints weight = 30728.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.054488 restraints weight = 23156.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.055125 restraints weight = 18950.708| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21666 Z= 0.137 Angle : 0.771 15.341 29370 Z= 0.371 Chirality : 0.042 0.208 3323 Planarity : 0.003 0.059 3736 Dihedral : 5.779 53.478 2904 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.51 % Favored : 90.33 % Rotamer: Outliers : 3.84 % Allowed : 17.64 % Favored : 78.52 % 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: -0.60 (0.17), residues: 2628 helix: 1.15 (0.14), residues: 1448 sheet: -3.33 (0.51), residues: 78 loop : -2.41 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 37 TYR 0.010 0.001 TYR A 324 PHE 0.016 0.001 PHE B 472 TRP 0.015 0.001 TRP A 613 HIS 0.008 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00308 (21666) covalent geometry : angle 0.77098 (29370) hydrogen bonds : bond 0.03293 ( 848) hydrogen bonds : angle 3.94683 ( 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 379 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 291 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9593 (mt) cc_final: 0.9313 (pp) REVERT: A 96 MET cc_start: 0.9265 (mmm) cc_final: 0.9046 (mmm) REVERT: A 99 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.8971 (mmm) REVERT: A 128 GLN cc_start: 0.9058 (tt0) cc_final: 0.7999 (tm-30) REVERT: A 209 LYS cc_start: 0.9186 (mttp) cc_final: 0.8889 (mmtt) REVERT: A 311 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 315 GLU cc_start: 0.9092 (mp0) cc_final: 0.8708 (mp0) REVERT: A 410 MET cc_start: 0.8253 (mpp) cc_final: 0.7846 (mpp) REVERT: A 437 LEU cc_start: 0.9562 (mp) cc_final: 0.8985 (mt) REVERT: A 440 MET cc_start: 0.9206 (tmm) cc_final: 0.8915 (ppp) REVERT: A 454 MET cc_start: 0.9544 (mmm) cc_final: 0.9036 (tpp) REVERT: A 474 MET cc_start: 0.9193 (ppp) cc_final: 0.8586 (ppp) REVERT: A 489 ASP cc_start: 0.8755 (t0) cc_final: 0.7973 (t0) REVERT: A 491 MET cc_start: 0.8870 (ttm) cc_final: 0.8379 (tmm) REVERT: A 528 MET cc_start: 0.9288 (tpt) cc_final: 0.8795 (tpp) REVERT: A 535 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8649 (tt0) REVERT: A 557 ILE cc_start: 0.9640 (mt) cc_final: 0.9378 (tp) REVERT: A 577 MET cc_start: 0.9336 (tmt) cc_final: 0.9073 (tmm) REVERT: A 603 MET cc_start: 0.9439 (ttp) cc_final: 0.8927 (tmm) REVERT: B 38 LEU cc_start: 0.9706 (tp) cc_final: 0.9400 (tp) REVERT: B 57 ASP cc_start: 0.8985 (m-30) cc_final: 0.8487 (m-30) REVERT: B 130 MET cc_start: 0.8448 (mmm) cc_final: 0.8099 (mmm) REVERT: B 168 SER cc_start: 0.9781 (m) cc_final: 0.9537 (p) REVERT: B 260 MET cc_start: 0.9518 (tpp) cc_final: 0.9222 (tpp) REVERT: B 301 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8916 (mtpt) REVERT: B 345 MET cc_start: 0.9051 (mmm) cc_final: 0.8635 (tmm) REVERT: B 377 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: B 386 LEU cc_start: 0.9765 (tp) cc_final: 0.9413 (mm) REVERT: B 390 LEU cc_start: 0.9738 (OUTLIER) cc_final: 0.9504 (mm) REVERT: B 408 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: B 464 ASN cc_start: 0.9376 (OUTLIER) cc_final: 0.8854 (t0) REVERT: B 474 MET cc_start: 0.9232 (ptm) cc_final: 0.9024 (ttp) REVERT: B 489 ASP cc_start: 0.8279 (t0) cc_final: 0.7955 (t0) REVERT: B 528 MET cc_start: 0.9088 (tpp) cc_final: 0.8612 (tpp) REVERT: B 584 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8861 (mmt90) REVERT: B 637 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8589 (tm-30) REVERT: B 641 ARG cc_start: 0.9226 (mtt180) cc_final: 0.8729 (tpt170) REVERT: C 67 TYR cc_start: 0.8533 (t80) cc_final: 0.8169 (t80) REVERT: C 99 MET cc_start: 0.9608 (mmt) cc_final: 0.9207 (mmm) REVERT: C 114 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8556 (tp) REVERT: C 284 ASP cc_start: 0.8819 (t70) cc_final: 0.8522 (t0) REVERT: C 345 MET cc_start: 0.8701 (mmt) cc_final: 0.8419 (tpp) REVERT: C 410 MET cc_start: 0.8384 (mtp) cc_final: 0.7615 (ttp) REVERT: C 432 TYR cc_start: 0.8698 (t80) cc_final: 0.8375 (t80) REVERT: C 454 MET cc_start: 0.9453 (mmm) cc_final: 0.9165 (tpt) REVERT: C 491 MET cc_start: 0.8890 (tpt) cc_final: 0.8557 (tmm) REVERT: C 515 GLU cc_start: 0.8965 (mm-30) cc_final: 0.7889 (mp0) REVERT: C 584 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8587 (tpp80) REVERT: C 603 MET cc_start: 0.9272 (ttp) cc_final: 0.8837 (tmm) REVERT: D 35 GLU cc_start: 0.9562 (tt0) cc_final: 0.9163 (mt-10) REVERT: D 61 LEU cc_start: 0.9525 (mt) cc_final: 0.9291 (mt) REVERT: D 85 ILE cc_start: 0.9834 (mm) cc_final: 0.9567 (tp) REVERT: D 114 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9076 (tp) REVERT: D 181 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9429 (tm) REVERT: D 289 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: D 345 MET cc_start: 0.9095 (tpp) cc_final: 0.8302 (tmm) REVERT: D 371 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9108 (ttpp) REVERT: D 378 MET cc_start: 0.8751 (pmm) cc_final: 0.8420 (pmm) REVERT: D 442 MET cc_start: 0.9369 (tpp) cc_final: 0.8893 (ttm) REVERT: D 491 MET cc_start: 0.8878 (tpt) cc_final: 0.8394 (tmm) REVERT: D 497 MET cc_start: 0.9403 (ttp) cc_final: 0.8657 (tmm) REVERT: D 577 MET cc_start: 0.8950 (tmt) cc_final: 0.8662 (tmm) REVERT: D 603 MET cc_start: 0.9337 (ttp) cc_final: 0.9136 (tmm) REVERT: E 14 GLU cc_start: 0.9594 (mm-30) cc_final: 0.9318 (tm-30) REVERT: E 36 MET cc_start: 0.9218 (ttt) cc_final: 0.8895 (tpp) REVERT: E 51 MET cc_start: 0.8352 (mmt) cc_final: 0.8004 (mmt) REVERT: E 71 MET cc_start: 0.9272 (ttt) cc_final: 0.9032 (tmm) REVERT: E 76 MET cc_start: 0.9073 (pmm) cc_final: 0.8636 (pmm) REVERT: E 122 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8716 (m-30) REVERT: E 145 MET cc_start: 0.8178 (mmm) cc_final: 0.7966 (mmm) REVERT: E 148 LYS cc_start: 0.6622 (pmtt) cc_final: 0.5677 (mmtm) outliers start: 88 outliers final: 45 residues processed: 350 average time/residue: 0.1322 time to fit residues: 73.6936 Evaluate side-chains 320 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 261 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET 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 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP 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 297 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 377 TYR 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 464 ASN Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 377 TYR 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 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 289 GLU 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 492 ARG Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 575 ILE 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 116 LEU Chi-restraints excluded: chain E residue 122 ASP 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: 0.0470 chunk 86 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 239 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 17 optimal weight: 0.0030 chunk 62 optimal weight: 2.9990 overall best weight: 0.3266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN B 426 HIS C 40 GLN D 206 GLN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.053067 restraints weight = 82354.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.054960 restraints weight = 45058.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.056275 restraints weight = 30093.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.057176 restraints weight = 22563.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.057779 restraints weight = 18404.679| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21666 Z= 0.117 Angle : 0.781 15.913 29370 Z= 0.367 Chirality : 0.041 0.199 3323 Planarity : 0.003 0.037 3736 Dihedral : 5.581 54.896 2904 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.25 % Favored : 90.64 % Rotamer: Outliers : 3.19 % Allowed : 18.86 % Favored : 77.95 % 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: -0.48 (0.17), residues: 2628 helix: 1.26 (0.14), residues: 1451 sheet: -3.26 (0.51), residues: 76 loop : -2.38 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 302 TYR 0.019 0.001 TYR A 432 PHE 0.021 0.001 PHE B 472 TRP 0.010 0.001 TRP D 462 HIS 0.008 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00253 (21666) covalent geometry : angle 0.78083 (29370) hydrogen bonds : bond 0.02945 ( 848) hydrogen bonds : angle 3.72671 ( 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 404 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 331 time to evaluate : 0.678 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: 0.9583 (mt) cc_final: 0.9318 (pp) REVERT: A 99 MET cc_start: 0.9484 (OUTLIER) cc_final: 0.8939 (mmm) REVERT: A 128 GLN cc_start: 0.8902 (tt0) cc_final: 0.7972 (tm-30) REVERT: A 209 LYS cc_start: 0.9069 (mttp) cc_final: 0.8723 (mmtt) REVERT: A 255 MET cc_start: 0.9514 (mmt) cc_final: 0.9266 (mmm) REVERT: A 311 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8098 (p) REVERT: A 315 GLU cc_start: 0.9056 (mp0) cc_final: 0.8736 (mp0) REVERT: A 345 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.9006 (tpp) REVERT: A 369 GLN cc_start: 0.8833 (tt0) cc_final: 0.8611 (mp-120) REVERT: A 410 MET cc_start: 0.8280 (mpp) cc_final: 0.7864 (mpp) REVERT: A 437 LEU cc_start: 0.9575 (mp) cc_final: 0.8946 (mm) REVERT: A 440 MET cc_start: 0.9213 (tmm) cc_final: 0.8937 (ppp) REVERT: A 454 MET cc_start: 0.9498 (mmm) cc_final: 0.9042 (tpp) REVERT: A 474 MET cc_start: 0.9066 (ppp) cc_final: 0.8791 (ppp) REVERT: A 489 ASP cc_start: 0.8686 (t0) cc_final: 0.7870 (t0) REVERT: A 491 MET cc_start: 0.8842 (ttm) cc_final: 0.8282 (tmm) REVERT: A 515 GLU cc_start: 0.9091 (tp30) cc_final: 0.8358 (mp0) REVERT: A 528 MET cc_start: 0.9217 (tpt) cc_final: 0.8754 (tpp) REVERT: A 557 ILE cc_start: 0.9582 (mt) cc_final: 0.9299 (tp) REVERT: A 577 MET cc_start: 0.9302 (tmt) cc_final: 0.9040 (tmm) REVERT: A 603 MET cc_start: 0.9423 (ttp) cc_final: 0.8911 (tmm) REVERT: A 634 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8625 (mp0) REVERT: B 57 ASP cc_start: 0.8958 (m-30) cc_final: 0.8447 (m-30) REVERT: B 130 MET cc_start: 0.8354 (mmm) cc_final: 0.7936 (mmm) REVERT: B 168 SER cc_start: 0.9741 (m) cc_final: 0.9499 (p) REVERT: B 193 ASP cc_start: 0.9308 (p0) cc_final: 0.9103 (p0) REVERT: B 260 MET cc_start: 0.9451 (tpp) cc_final: 0.9248 (tpp) REVERT: B 345 MET cc_start: 0.9021 (mmm) cc_final: 0.8578 (tmm) REVERT: B 377 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.8018 (m-10) REVERT: B 386 LEU cc_start: 0.9753 (tp) cc_final: 0.9387 (mm) REVERT: B 408 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: B 464 ASN cc_start: 0.9306 (OUTLIER) cc_final: 0.8894 (t0) REVERT: B 474 MET cc_start: 0.9143 (ptm) cc_final: 0.8559 (ttp) REVERT: B 584 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8761 (mmt90) REVERT: B 637 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8508 (tm-30) REVERT: B 641 ARG cc_start: 0.9227 (mtt180) cc_final: 0.8757 (tpt170) REVERT: C 67 TYR cc_start: 0.8511 (t80) cc_final: 0.8134 (t80) REVERT: C 99 MET cc_start: 0.9661 (mmt) cc_final: 0.9258 (mmm) REVERT: C 284 ASP cc_start: 0.8769 (t70) cc_final: 0.8480 (t70) REVERT: C 331 MET cc_start: 0.8650 (mmt) cc_final: 0.8442 (mmp) REVERT: C 345 MET cc_start: 0.8614 (mmt) cc_final: 0.8319 (tpp) REVERT: C 400 LEU cc_start: 0.9353 (mt) cc_final: 0.8908 (pp) REVERT: C 410 MET cc_start: 0.8282 (mtp) cc_final: 0.7595 (ttp) REVERT: C 432 TYR cc_start: 0.8516 (t80) cc_final: 0.8232 (t80) REVERT: C 454 MET cc_start: 0.9420 (mmm) cc_final: 0.9138 (tpt) REVERT: C 491 MET cc_start: 0.8823 (tpt) cc_final: 0.8574 (ttt) REVERT: C 515 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8179 (mm-30) REVERT: C 584 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8482 (tpp80) REVERT: C 603 MET cc_start: 0.9212 (ttp) cc_final: 0.8769 (tmm) REVERT: C 608 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9277 (tt) REVERT: D 35 GLU cc_start: 0.9543 (tt0) cc_final: 0.9141 (mt-10) REVERT: D 61 LEU cc_start: 0.9529 (mt) cc_final: 0.9299 (mt) REVERT: D 85 ILE cc_start: 0.9795 (mm) cc_final: 0.9474 (tp) REVERT: D 99 MET cc_start: 0.9475 (mmt) cc_final: 0.9016 (mmm) REVERT: D 114 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9050 (tp) REVERT: D 345 MET cc_start: 0.9093 (tpp) cc_final: 0.8294 (tmm) REVERT: D 371 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9150 (ttpp) REVERT: D 378 MET cc_start: 0.8728 (pmm) cc_final: 0.8391 (pmm) REVERT: D 442 MET cc_start: 0.9264 (tpp) cc_final: 0.8848 (ttm) REVERT: D 474 MET cc_start: 0.8506 (pmm) cc_final: 0.8206 (ppp) REVERT: D 491 MET cc_start: 0.8845 (tpt) cc_final: 0.8415 (tmm) REVERT: D 492 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8259 (ptp90) REVERT: D 497 MET cc_start: 0.9373 (ttp) cc_final: 0.8638 (tmm) REVERT: D 535 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8723 (mt-10) REVERT: D 577 MET cc_start: 0.8905 (tmt) cc_final: 0.8585 (tmm) REVERT: D 603 MET cc_start: 0.9309 (ttp) cc_final: 0.8667 (tmm) REVERT: D 608 LEU cc_start: 0.9604 (tt) cc_final: 0.9352 (tt) REVERT: E 36 MET cc_start: 0.9157 (ttt) cc_final: 0.8719 (tpp) REVERT: E 51 MET cc_start: 0.8364 (mmt) cc_final: 0.8008 (mmt) REVERT: E 112 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6274 (mm) REVERT: E 122 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8732 (m-30) REVERT: E 148 LYS cc_start: 0.6502 (pmtt) cc_final: 0.5591 (mmtm) outliers start: 73 outliers final: 32 residues processed: 377 average time/residue: 0.1300 time to fit residues: 78.6103 Evaluate side-chains 333 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 287 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 499 VAL 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 181 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 536 LEU 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 C residue 440 MET 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 C residue 608 LEU 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 492 ARG Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 575 ILE 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 112 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 59 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 192 optimal weight: 0.0040 chunk 105 optimal weight: 0.9990 chunk 154 optimal weight: 0.1980 chunk 149 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 464 ASN C 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 = 0.3137 r_free = 0.3137 target = 0.069597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.052991 restraints weight = 83168.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.054882 restraints weight = 45263.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.056200 restraints weight = 30177.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.057087 restraints weight = 22675.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.057688 restraints weight = 18557.857| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21666 Z= 0.117 Angle : 0.788 15.442 29370 Z= 0.371 Chirality : 0.041 0.247 3323 Planarity : 0.003 0.035 3736 Dihedral : 5.367 41.611 2902 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.51 % Favored : 90.41 % Rotamer: Outliers : 2.58 % Allowed : 19.56 % Favored : 77.86 % 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: -0.36 (0.17), residues: 2628 helix: 1.34 (0.14), residues: 1445 sheet: -3.03 (0.56), residues: 76 loop : -2.28 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 302 TYR 0.015 0.001 TYR D 432 PHE 0.020 0.001 PHE B 472 TRP 0.009 0.001 TRP A 613 HIS 0.010 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00266 (21666) covalent geometry : angle 0.78830 (29370) hydrogen bonds : bond 0.02933 ( 848) hydrogen bonds : angle 3.70203 ( 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 358 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 0.861 Fit side-chains 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: 0.9312 (pp) REVERT: A 99 MET cc_start: 0.9488 (OUTLIER) cc_final: 0.9054 (mmm) REVERT: A 128 GLN cc_start: 0.8989 (tt0) cc_final: 0.8024 (tm-30) REVERT: A 209 LYS cc_start: 0.9047 (mttp) cc_final: 0.8737 (mmtt) REVERT: A 311 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8138 (p) REVERT: A 315 GLU cc_start: 0.9048 (mp0) cc_final: 0.8730 (mp0) REVERT: A 410 MET cc_start: 0.8362 (mpp) cc_final: 0.8057 (mpp) REVERT: A 414 ARG cc_start: 0.9050 (tpp80) cc_final: 0.8604 (tpt90) REVERT: A 437 LEU cc_start: 0.9576 (mp) cc_final: 0.8931 (mm) REVERT: A 440 MET cc_start: 0.9230 (tmm) cc_final: 0.8935 (ppp) REVERT: A 454 MET cc_start: 0.9491 (mmm) cc_final: 0.9052 (tpp) REVERT: A 489 ASP cc_start: 0.8620 (t0) cc_final: 0.8153 (t0) REVERT: A 497 MET cc_start: 0.9374 (ttp) cc_final: 0.9093 (ttm) REVERT: A 515 GLU cc_start: 0.9144 (tp30) cc_final: 0.8402 (mp0) REVERT: A 528 MET cc_start: 0.9218 (tpt) cc_final: 0.8885 (tpp) REVERT: A 557 ILE cc_start: 0.9563 (mt) cc_final: 0.9291 (tp) REVERT: A 603 MET cc_start: 0.9433 (ttp) cc_final: 0.8913 (tmm) REVERT: A 634 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8713 (mp0) REVERT: B 57 ASP cc_start: 0.8978 (m-30) cc_final: 0.8464 (m-30) REVERT: B 130 MET cc_start: 0.8244 (mmm) cc_final: 0.7849 (mmm) REVERT: B 168 SER cc_start: 0.9780 (m) cc_final: 0.9543 (p) REVERT: B 345 MET cc_start: 0.8863 (mmm) cc_final: 0.8511 (tmm) REVERT: B 386 LEU cc_start: 0.9726 (tp) cc_final: 0.9375 (mm) REVERT: B 464 ASN cc_start: 0.9328 (t0) cc_final: 0.8984 (t0) REVERT: B 474 MET cc_start: 0.9114 (ptm) cc_final: 0.8557 (ttp) REVERT: B 515 GLU cc_start: 0.8799 (mm-30) cc_final: 0.7864 (mp0) REVERT: B 637 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8484 (tm-30) REVERT: B 641 ARG cc_start: 0.9256 (mtt180) cc_final: 0.8767 (tpt170) REVERT: C 67 TYR cc_start: 0.8551 (t80) cc_final: 0.8160 (t80) REVERT: C 99 MET cc_start: 0.9675 (mmt) cc_final: 0.9246 (mmm) REVERT: C 284 ASP cc_start: 0.8808 (t70) cc_final: 0.8483 (t0) REVERT: C 306 GLN cc_start: 0.9465 (tp-100) cc_final: 0.8945 (tp40) REVERT: C 331 MET cc_start: 0.8576 (mmt) cc_final: 0.8335 (mmp) REVERT: C 345 MET cc_start: 0.8619 (mmt) cc_final: 0.8330 (tpp) REVERT: C 363 ARG cc_start: 0.8753 (pmt-80) cc_final: 0.8247 (ptt90) REVERT: C 400 LEU cc_start: 0.9348 (mt) cc_final: 0.8901 (pp) REVERT: C 410 MET cc_start: 0.8312 (mtp) cc_final: 0.7635 (ttp) REVERT: C 432 TYR cc_start: 0.8502 (t80) cc_final: 0.8188 (t80) REVERT: C 491 MET cc_start: 0.8801 (tpt) cc_final: 0.8557 (ttt) REVERT: C 515 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8213 (mm-30) REVERT: C 535 GLU cc_start: 0.8799 (mp0) cc_final: 0.8396 (mp0) REVERT: C 603 MET cc_start: 0.9206 (ttp) cc_final: 0.8740 (tmm) REVERT: D 35 GLU cc_start: 0.9548 (tt0) cc_final: 0.9146 (mt-10) REVERT: D 61 LEU cc_start: 0.9530 (mt) cc_final: 0.9298 (mt) REVERT: D 85 ILE cc_start: 0.9787 (mm) cc_final: 0.9491 (tp) REVERT: D 99 MET cc_start: 0.9482 (mmt) cc_final: 0.9056 (mmm) REVERT: D 181 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9435 (tm) REVERT: D 331 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7758 (mmp) REVERT: D 345 MET cc_start: 0.9079 (tpp) cc_final: 0.8296 (tmm) REVERT: D 364 ASP cc_start: 0.9391 (m-30) cc_final: 0.8692 (p0) REVERT: D 371 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.9179 (ttpp) REVERT: D 378 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8399 (pmm) REVERT: D 442 MET cc_start: 0.9253 (tpp) cc_final: 0.8988 (ttm) REVERT: D 491 MET cc_start: 0.8817 (tpt) cc_final: 0.8385 (tmm) REVERT: D 492 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8175 (ptp90) REVERT: D 497 MET cc_start: 0.9376 (ttp) cc_final: 0.8674 (tmm) REVERT: D 535 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8681 (mt-10) REVERT: D 577 MET cc_start: 0.9026 (tmt) cc_final: 0.8699 (tmm) REVERT: D 603 MET cc_start: 0.9279 (ttp) cc_final: 0.8628 (tmm) REVERT: D 608 LEU cc_start: 0.9596 (tt) cc_final: 0.9340 (tt) REVERT: E 36 MET cc_start: 0.9168 (ttt) cc_final: 0.8597 (tpp) REVERT: E 51 MET cc_start: 0.8197 (mmt) cc_final: 0.7907 (mmt) REVERT: E 71 MET cc_start: 0.9355 (tmm) cc_final: 0.9130 (ppp) REVERT: E 76 MET cc_start: 0.9068 (pmm) cc_final: 0.8863 (pmm) REVERT: E 122 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8762 (m-30) REVERT: E 148 LYS cc_start: 0.6482 (pmtt) cc_final: 0.5614 (mmtm) outliers start: 59 outliers final: 32 residues processed: 338 average time/residue: 0.1309 time to fit residues: 71.6377 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 : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL 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 181 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 440 MET 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 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 331 MET 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 404 VAL Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 568 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 116 LEU Chi-restraints excluded: chain E residue 122 ASP 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: 2.9990 chunk 245 optimal weight: 0.9990 chunk 174 optimal weight: 0.0370 chunk 228 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.053851 restraints weight = 82748.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.055787 restraints weight = 45072.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.057094 restraints weight = 30045.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.058019 restraints weight = 22572.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.058682 restraints weight = 18414.347| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21666 Z= 0.118 Angle : 0.813 16.853 29370 Z= 0.377 Chirality : 0.042 0.239 3323 Planarity : 0.003 0.034 3736 Dihedral : 5.258 39.567 2902 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.79 % Favored : 91.13 % Rotamer: Outliers : 2.27 % Allowed : 20.13 % Favored : 77.60 % 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: -0.31 (0.17), residues: 2628 helix: 1.36 (0.14), residues: 1449 sheet: -2.88 (0.57), residues: 76 loop : -2.27 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 302 TYR 0.017 0.001 TYR D 115 PHE 0.019 0.001 PHE B 472 TRP 0.008 0.001 TRP D 462 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00266 (21666) covalent geometry : angle 0.81275 (29370) hydrogen bonds : bond 0.02821 ( 848) hydrogen bonds : angle 3.68579 ( 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 363 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9583 (mt) cc_final: 0.9306 (pp) REVERT: A 99 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9007 (mmm) REVERT: A 128 GLN cc_start: 0.8995 (tt0) cc_final: 0.8079 (tm-30) REVERT: A 209 LYS cc_start: 0.9020 (mttp) cc_final: 0.8723 (mmtt) REVERT: A 302 ARG cc_start: 0.8211 (ttp80) cc_final: 0.8004 (ttp80) REVERT: A 311 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8125 (p) REVERT: A 315 GLU cc_start: 0.9044 (mp0) cc_final: 0.8720 (mp0) REVERT: A 410 MET cc_start: 0.8325 (mpp) cc_final: 0.8039 (mpp) REVERT: A 414 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8610 (tpt90) REVERT: A 437 LEU cc_start: 0.9559 (mp) cc_final: 0.8929 (mm) REVERT: A 440 MET cc_start: 0.9263 (tmm) cc_final: 0.8961 (ppp) REVERT: A 454 MET cc_start: 0.9469 (mmm) cc_final: 0.9098 (tpp) REVERT: A 489 ASP cc_start: 0.8492 (t0) cc_final: 0.8238 (t70) REVERT: A 497 MET cc_start: 0.9380 (ttp) cc_final: 0.9077 (ttm) REVERT: A 515 GLU cc_start: 0.9109 (tp30) cc_final: 0.8344 (mp0) REVERT: A 528 MET cc_start: 0.9222 (tpt) cc_final: 0.8867 (tpp) REVERT: A 557 ILE cc_start: 0.9547 (mt) cc_final: 0.9285 (tp) REVERT: A 577 MET cc_start: 0.9242 (tmm) cc_final: 0.8954 (tmm) REVERT: A 603 MET cc_start: 0.9428 (ttp) cc_final: 0.8971 (tmm) REVERT: A 634 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8681 (mp0) REVERT: B 57 ASP cc_start: 0.8980 (m-30) cc_final: 0.8464 (m-30) REVERT: B 130 MET cc_start: 0.8129 (mmm) cc_final: 0.7808 (mmm) REVERT: B 168 SER cc_start: 0.9770 (m) cc_final: 0.9533 (p) REVERT: B 345 MET cc_start: 0.8846 (mmm) cc_final: 0.8520 (tmm) REVERT: B 386 LEU cc_start: 0.9689 (tp) cc_final: 0.9355 (mm) REVERT: B 474 MET cc_start: 0.9133 (ptm) cc_final: 0.8697 (ttp) REVERT: B 515 GLU cc_start: 0.8842 (mm-30) cc_final: 0.7656 (mp0) REVERT: B 584 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8743 (mmt90) REVERT: B 641 ARG cc_start: 0.9263 (mtt180) cc_final: 0.8772 (tpt170) REVERT: C 67 TYR cc_start: 0.8565 (t80) cc_final: 0.8192 (t80) REVERT: C 99 MET cc_start: 0.9674 (mmt) cc_final: 0.9236 (mmm) REVERT: C 114 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8619 (tp) REVERT: C 284 ASP cc_start: 0.8741 (t70) cc_final: 0.8387 (t0) REVERT: C 306 GLN cc_start: 0.9443 (tp-100) cc_final: 0.8897 (tp40) REVERT: C 331 MET cc_start: 0.8576 (mmt) cc_final: 0.8342 (mmp) REVERT: C 345 MET cc_start: 0.8602 (mmt) cc_final: 0.8236 (tpp) REVERT: C 363 ARG cc_start: 0.8802 (pmt-80) cc_final: 0.8312 (ptt90) REVERT: C 410 MET cc_start: 0.8351 (mtp) cc_final: 0.7704 (ttp) REVERT: C 454 MET cc_start: 0.9399 (tpp) cc_final: 0.9071 (tpt) REVERT: C 491 MET cc_start: 0.8817 (tpt) cc_final: 0.8577 (ttt) REVERT: C 535 GLU cc_start: 0.8813 (mp0) cc_final: 0.8401 (mp0) REVERT: C 603 MET cc_start: 0.9190 (ttp) cc_final: 0.8738 (tmm) REVERT: D 35 GLU cc_start: 0.9546 (tt0) cc_final: 0.9135 (mt-10) REVERT: D 61 LEU cc_start: 0.9524 (mt) cc_final: 0.9291 (mt) REVERT: D 85 ILE cc_start: 0.9813 (mm) cc_final: 0.9559 (tp) REVERT: D 99 MET cc_start: 0.9486 (mmt) cc_final: 0.9073 (mmm) REVERT: D 173 VAL cc_start: 0.8169 (t) cc_final: 0.7946 (p) REVERT: D 331 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7797 (mmp) REVERT: D 345 MET cc_start: 0.9058 (tpp) cc_final: 0.8302 (tmm) REVERT: D 364 ASP cc_start: 0.9376 (m-30) cc_final: 0.8689 (p0) REVERT: D 371 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9185 (ttpp) REVERT: D 378 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8390 (pmm) REVERT: D 442 MET cc_start: 0.9231 (tpp) cc_final: 0.8987 (ttm) REVERT: D 491 MET cc_start: 0.8703 (tpt) cc_final: 0.8310 (tmm) REVERT: D 492 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8289 (ptt180) REVERT: D 497 MET cc_start: 0.9377 (ttp) cc_final: 0.8642 (tmm) REVERT: D 535 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8652 (mt-10) REVERT: D 577 MET cc_start: 0.9046 (tmt) cc_final: 0.8778 (tmm) REVERT: D 603 MET cc_start: 0.9276 (ttp) cc_final: 0.8616 (tmm) REVERT: D 608 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9332 (tt) REVERT: E 36 MET cc_start: 0.9101 (ttt) cc_final: 0.8553 (tpp) REVERT: E 51 MET cc_start: 0.8346 (mmt) cc_final: 0.8127 (mmt) REVERT: E 71 MET cc_start: 0.9371 (tmm) cc_final: 0.9105 (ppp) REVERT: E 122 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8766 (m-30) REVERT: E 148 LYS cc_start: 0.6450 (pmtt) cc_final: 0.5602 (mmtm) outliers start: 52 outliers final: 31 residues processed: 343 average time/residue: 0.1308 time to fit residues: 72.5358 Evaluate side-chains 334 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL 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 181 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 426 HIS 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 C residue 114 LEU Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET 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 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 331 MET 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 404 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 608 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 116 LEU Chi-restraints excluded: chain E residue 122 ASP 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: 0.9980 chunk 145 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 572 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 426 HIS ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.053580 restraints weight = 83113.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.055528 restraints weight = 44431.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.056863 restraints weight = 29329.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.057802 restraints weight = 21895.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.058464 restraints weight = 17759.974| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5332 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= 0.122 Angle : 0.815 16.805 29370 Z= 0.381 Chirality : 0.042 0.221 3323 Planarity : 0.003 0.034 3736 Dihedral : 5.223 40.102 2902 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.25 % Favored : 90.68 % Rotamer: Outliers : 2.05 % Allowed : 20.52 % Favored : 77.42 % 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: -0.25 (0.18), residues: 2628 helix: 1.40 (0.14), residues: 1452 sheet: -2.81 (0.57), residues: 76 loop : -2.24 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 302 TYR 0.021 0.001 TYR C 432 PHE 0.026 0.001 PHE B 472 TRP 0.009 0.001 TRP A 613 HIS 0.008 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00279 (21666) covalent geometry : angle 0.81513 (29370) hydrogen bonds : bond 0.02870 ( 848) hydrogen bonds : angle 3.71715 ( 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 343 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9576 (mt) cc_final: 0.9295 (pp) REVERT: A 99 MET cc_start: 0.9503 (OUTLIER) cc_final: 0.8946 (mmm) REVERT: A 128 GLN cc_start: 0.9071 (tt0) cc_final: 0.8122 (tm-30) REVERT: A 189 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9085 (mm) REVERT: A 209 LYS cc_start: 0.8993 (mttp) cc_final: 0.8703 (mmtt) REVERT: A 311 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8170 (p) REVERT: A 315 GLU cc_start: 0.9019 (mp0) cc_final: 0.8718 (mp0) REVERT: A 410 MET cc_start: 0.8367 (mpp) cc_final: 0.8090 (mpp) REVERT: A 414 ARG cc_start: 0.9015 (tpp80) cc_final: 0.8618 (tpt90) REVERT: A 437 LEU cc_start: 0.9607 (mp) cc_final: 0.8958 (mm) REVERT: A 440 MET cc_start: 0.9221 (tmm) cc_final: 0.8955 (ppp) REVERT: A 474 MET cc_start: 0.8822 (ttt) cc_final: 0.8592 (tmm) REVERT: A 497 MET cc_start: 0.9327 (ttp) cc_final: 0.9014 (ttm) REVERT: A 515 GLU cc_start: 0.8971 (tp30) cc_final: 0.8358 (mp0) REVERT: A 528 MET cc_start: 0.9276 (tpt) cc_final: 0.8938 (tpp) REVERT: A 557 ILE cc_start: 0.9576 (mt) cc_final: 0.9318 (tp) REVERT: A 577 MET cc_start: 0.9288 (tmm) cc_final: 0.8993 (tmm) REVERT: A 603 MET cc_start: 0.9442 (ttp) cc_final: 0.8945 (tmm) REVERT: B 57 ASP cc_start: 0.8999 (m-30) cc_final: 0.8483 (m-30) REVERT: B 130 MET cc_start: 0.8139 (mmm) cc_final: 0.7868 (mmm) REVERT: B 168 SER cc_start: 0.9778 (m) cc_final: 0.9537 (p) REVERT: B 282 GLU cc_start: 0.8766 (mp0) cc_final: 0.8326 (mp0) REVERT: B 345 MET cc_start: 0.8909 (mmm) cc_final: 0.8537 (tmm) REVERT: B 386 LEU cc_start: 0.9698 (tp) cc_final: 0.9346 (mm) REVERT: B 408 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7825 (m-10) REVERT: B 474 MET cc_start: 0.9048 (ptm) cc_final: 0.8664 (ttp) REVERT: B 584 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8855 (mmt90) REVERT: B 641 ARG cc_start: 0.9336 (mtt180) cc_final: 0.8817 (tpt170) REVERT: C 67 TYR cc_start: 0.8535 (t80) cc_final: 0.8162 (t80) REVERT: C 99 MET cc_start: 0.9621 (mmt) cc_final: 0.9211 (mmm) REVERT: C 110 MET cc_start: 0.8025 (mmm) cc_final: 0.7758 (mmm) REVERT: C 114 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8710 (tp) REVERT: C 284 ASP cc_start: 0.8698 (t70) cc_final: 0.8403 (t0) REVERT: C 306 GLN cc_start: 0.9451 (tp-100) cc_final: 0.8906 (tp40) REVERT: C 314 LYS cc_start: 0.9279 (ttpt) cc_final: 0.8830 (ttmm) REVERT: C 331 MET cc_start: 0.8592 (mmt) cc_final: 0.8344 (mmp) REVERT: C 345 MET cc_start: 0.8689 (mmt) cc_final: 0.8393 (tpp) REVERT: C 363 ARG cc_start: 0.8704 (pmt-80) cc_final: 0.8305 (ptt90) REVERT: C 410 MET cc_start: 0.8419 (mtp) cc_final: 0.7752 (ttp) REVERT: C 454 MET cc_start: 0.9388 (tpp) cc_final: 0.9085 (tpt) REVERT: C 485 MET cc_start: 0.9199 (ttm) cc_final: 0.8965 (ttm) REVERT: C 491 MET cc_start: 0.8825 (tpt) cc_final: 0.8573 (ttt) REVERT: C 535 GLU cc_start: 0.8785 (mp0) cc_final: 0.8430 (mp0) REVERT: C 603 MET cc_start: 0.9221 (ttp) cc_final: 0.8766 (tmm) REVERT: D 35 GLU cc_start: 0.9549 (tt0) cc_final: 0.9155 (mt-10) REVERT: D 61 LEU cc_start: 0.9534 (mt) cc_final: 0.9297 (mt) REVERT: D 85 ILE cc_start: 0.9850 (mm) cc_final: 0.9582 (tp) REVERT: D 99 MET cc_start: 0.9457 (mmt) cc_final: 0.9078 (mmm) REVERT: D 331 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7719 (mmp) REVERT: D 345 MET cc_start: 0.9102 (tpp) cc_final: 0.8334 (tmm) REVERT: D 364 ASP cc_start: 0.9346 (m-30) cc_final: 0.8693 (p0) REVERT: D 371 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9274 (ttpp) REVERT: D 378 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8336 (pmm) REVERT: D 410 MET cc_start: 0.8585 (mmp) cc_final: 0.8265 (mtt) REVERT: D 432 TYR cc_start: 0.9040 (t80) cc_final: 0.8758 (t80) REVERT: D 442 MET cc_start: 0.9264 (tpp) cc_final: 0.9063 (ttm) REVERT: D 491 MET cc_start: 0.8789 (tpt) cc_final: 0.8393 (tmm) REVERT: D 535 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8650 (mt-10) REVERT: D 577 MET cc_start: 0.8959 (tmt) cc_final: 0.8756 (tmm) REVERT: D 603 MET cc_start: 0.9332 (ttp) cc_final: 0.8633 (tmm) REVERT: D 608 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9361 (tt) REVERT: E 36 MET cc_start: 0.9032 (ttt) cc_final: 0.8418 (tpp) REVERT: E 51 MET cc_start: 0.8339 (mmt) cc_final: 0.8085 (mmt) REVERT: E 71 MET cc_start: 0.9386 (tmm) cc_final: 0.9087 (ppp) REVERT: E 148 LYS cc_start: 0.6500 (pmtt) cc_final: 0.5598 (mmtm) outliers start: 47 outliers final: 29 residues processed: 328 average time/residue: 0.1324 time to fit residues: 70.0021 Evaluate side-chains 323 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 426 HIS 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 C residue 114 LEU Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET 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 132 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 331 MET 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 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 27 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 219 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 259 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 chunk 128 optimal weight: 9.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 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 = 0.3162 r_free = 0.3162 target = 0.070153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.053646 restraints weight = 82866.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.055588 restraints weight = 44602.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.056902 restraints weight = 29544.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057834 restraints weight = 22116.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.058499 restraints weight = 17987.441| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 21666 Z= 0.199 Angle : 1.013 59.198 29370 Z= 0.543 Chirality : 0.045 0.833 3323 Planarity : 0.005 0.148 3736 Dihedral : 5.170 42.583 2898 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.36 % Favored : 90.56 % Rotamer: Outliers : 1.97 % Allowed : 20.70 % Favored : 77.34 % Cbeta Deviations : 0.12 % 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: -0.27 (0.17), residues: 2628 helix: 1.39 (0.14), residues: 1452 sheet: -2.80 (0.57), residues: 76 loop : -2.24 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.000 ARG D 323 TYR 0.050 0.001 TYR D 324 PHE 0.024 0.001 PHE B 472 TRP 0.009 0.001 TRP A 613 HIS 0.234 0.004 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00406 (21666) covalent geometry : angle 1.01306 (29370) hydrogen bonds : bond 0.02961 ( 848) hydrogen bonds : angle 3.72066 ( 2439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3129.54 seconds wall clock time: 54 minutes 58.99 seconds (3298.99 seconds total)