Starting phenix.real_space_refine on Wed Jun 18 13:33:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e2f_8961/06_2025/6e2f_8961.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e2f_8961/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6e2f_8961/06_2025/6e2f_8961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e2f_8961/06_2025/6e2f_8961.map" model { file = "/net/cci-nas-00/data/ceres_data/6e2f_8961/06_2025/6e2f_8961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e2f_8961/06_2025/6e2f_8961.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.97, per 1000 atoms: 0.56 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: 5.13 Conformation dependent library (CDL) restraints added in 3.0 seconds 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4984 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 4 sheets defined 63.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 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: 5.89 Time building geometry restraints manager: 6.15 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 46.100 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.210 ------------------------------------------------------------------------------- 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 : 4.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.038 0.004 TRP D 629 HIS 0.012 0.003 HIS A 522 PHE 0.034 0.003 PHE B 211 TYR 0.026 0.003 TYR B 524 ARG 0.016 0.001 ARG B 492 Details of bonding type rmsd hydrogen bonds : bond 0.31610 ( 848) hydrogen bonds : angle 9.20345 ( 2439) covalent geometry : bond 0.00971 (21666) covalent geometry : angle 1.36385 (29370) *********************** 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 : 2.480 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: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.8343 (t60) cc_final: 0.8042 (t60) REVERT: A 61 LEU cc_start: 0.9648 (mt) cc_final: 0.9211 (pp) REVERT: A 105 LEU cc_start: 0.9650 (mt) cc_final: 0.9265 (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: 0.9199 (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: 0.8795 (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: 0.9326 (mmm) REVERT: B 577 MET cc_start: 0.9318 (tmt) cc_final: 0.8135 (tmt) REVERT: B 591 GLU cc_start: 0.9158 (pt0) cc_final: 0.8745 (pm20) REVERT: B 600 THR cc_start: 0.9511 (m) cc_final: 0.9310 (p) REVERT: B 637 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8459 (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: 0.9038 (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: 0.9154 (t80) REVERT: C 491 MET cc_start: 0.9227 (tpt) cc_final: 0.8879 (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: 0.8764 (tmm) REVERT: D 35 GLU cc_start: 0.9495 (tt0) cc_final: 0.9168 (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 367 LEU cc_start: 0.9137 (tt) cc_final: 0.8755 (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: 0.8888 (tppp) REVERT: D 491 MET cc_start: 0.8958 (tpt) cc_final: 0.8592 (tmm) REVERT: D 492 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7842 (ptt90) REVERT: D 535 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8874 (mm-30) REVERT: D 569 LEU cc_start: 0.9471 (tp) cc_final: 0.9211 (tt) REVERT: D 577 MET cc_start: 0.9269 (tmt) cc_final: 0.8120 (tmt) REVERT: D 603 MET cc_start: 0.9173 (ttp) cc_final: 0.8464 (tmm) REVERT: D 625 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9350 (tm) REVERT: E 8 GLN cc_start: 0.8816 (mt0) cc_final: 0.8564 (mt0) REVERT: E 14 GLU cc_start: 0.9616 (mm-30) cc_final: 0.9205 (tm-30) REVERT: E 18 LEU cc_start: 0.9239 (tt) cc_final: 0.8981 (pp) REVERT: E 30 LYS cc_start: 0.9496 (ttmp) cc_final: 0.9290 (tttt) REVERT: E 71 MET cc_start: 0.9583 (ttt) cc_final: 0.9160 (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: 0.8675 (tp) REVERT: E 124 MET cc_start: 0.6819 (mtp) cc_final: 0.6501 (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: 0.6031 (mmtm) outliers start: 32 outliers final: 7 residues processed: 489 average time/residue: 0.3838 time to fit residues: 294.0734 Evaluate side-chains 303 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 293 time to evaluate : 2.375 ------------------------------------------------------------------------------- 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 220 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 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 91 ASN D 165 HIS D 365 ASN D 370 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.050664 restraints weight = 82457.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.052532 restraints weight = 44687.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053810 restraints weight = 29785.009| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21666 Z= 0.165 Angle : 0.840 13.253 29370 Z= 0.425 Chirality : 0.043 0.200 3323 Planarity : 0.005 0.038 3736 Dihedral : 7.011 59.857 2918 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.74 % Favored : 90.11 % Rotamer: Outliers : 3.76 % Allowed : 11.44 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.15), residues: 2628 helix: -1.28 (0.12), residues: 1426 sheet: -4.22 (0.35), residues: 82 loop : -2.90 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 495 HIS 0.007 0.001 HIS C 582 PHE 0.029 0.002 PHE A 493 TYR 0.015 0.001 TYR A 526 ARG 0.006 0.001 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.05645 ( 848) hydrogen bonds : angle 4.93697 ( 2439) covalent geometry : bond 0.00347 (21666) covalent geometry : angle 0.83952 (29370) *********************** 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 460 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 374 time to evaluate : 2.416 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: 0.9628 (mt) cc_final: 0.9298 (pp) REVERT: A 128 GLN cc_start: 0.9187 (tt0) cc_final: 0.7871 (tm-30) REVERT: A 209 LYS cc_start: 0.9256 (mttp) cc_final: 0.8962 (mmtt) REVERT: A 315 GLU cc_start: 0.8819 (mp0) cc_final: 0.8465 (mp0) REVERT: A 414 ARG cc_start: 0.9136 (tpp80) cc_final: 0.8656 (tpt90) REVERT: A 437 LEU cc_start: 0.9458 (mp) cc_final: 0.8878 (mm) REVERT: A 440 MET cc_start: 0.9023 (tmm) cc_final: 0.8675 (ppp) REVERT: A 474 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9036 (ppp) REVERT: A 485 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.9033 (ttm) REVERT: A 489 ASP cc_start: 0.8677 (m-30) cc_final: 0.8368 (t70) REVERT: A 515 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8670 (tp30) REVERT: A 528 MET cc_start: 0.9362 (tpt) cc_final: 0.8813 (tpp) REVERT: A 542 ASP cc_start: 0.6918 (t0) cc_final: 0.6648 (m-30) REVERT: A 557 ILE cc_start: 0.9679 (mt) cc_final: 0.9390 (tp) REVERT: A 577 MET cc_start: 0.9364 (tmt) cc_final: 0.8693 (tmm) REVERT: A 578 MET cc_start: 0.9573 (OUTLIER) cc_final: 0.9352 (tpp) REVERT: A 603 MET cc_start: 0.9472 (ttp) cc_final: 0.8873 (tmm) REVERT: B 38 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9416 (tp) REVERT: B 57 ASP cc_start: 0.9201 (m-30) cc_final: 0.8712 (m-30) REVERT: B 110 MET cc_start: 0.8767 (mtm) cc_final: 0.8528 (mtm) REVERT: B 130 MET cc_start: 0.8649 (mmm) cc_final: 0.8434 (mmm) REVERT: B 168 SER cc_start: 0.9784 (m) cc_final: 0.9494 (p) REVERT: B 260 MET cc_start: 0.9684 (tpp) cc_final: 0.9234 (tpp) REVERT: B 345 MET cc_start: 0.8942 (mmm) cc_final: 0.8560 (tmm) REVERT: B 464 ASN cc_start: 0.9389 (OUTLIER) cc_final: 0.8760 (t0) REVERT: B 489 ASP cc_start: 0.8579 (t0) cc_final: 0.8106 (t0) REVERT: B 542 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6364 (m-30) REVERT: B 591 GLU cc_start: 0.9263 (pt0) cc_final: 0.8711 (pm20) REVERT: B 637 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8353 (tm-30) REVERT: B 641 ARG cc_start: 0.9134 (mtt180) cc_final: 0.8816 (mmp80) REVERT: C 35 GLU cc_start: 0.9334 (tt0) cc_final: 0.8995 (pp20) REVERT: C 38 LEU cc_start: 0.9606 (mt) cc_final: 0.9256 (tt) REVERT: C 99 MET cc_start: 0.9586 (mmt) cc_final: 0.9145 (mmm) REVERT: C 110 MET cc_start: 0.8156 (mtp) cc_final: 0.7848 (mtm) REVERT: C 130 MET cc_start: 0.8334 (mmt) cc_final: 0.8007 (mmm) REVERT: C 284 ASP cc_start: 0.8892 (t70) cc_final: 0.8557 (t70) REVERT: C 315 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8877 (mp0) REVERT: C 410 MET cc_start: 0.7898 (mtp) cc_final: 0.7363 (ttp) REVERT: C 489 ASP cc_start: 0.8906 (m-30) cc_final: 0.8548 (m-30) REVERT: C 528 MET cc_start: 0.9287 (ttm) cc_final: 0.9004 (tpp) REVERT: C 532 SER cc_start: 0.9790 (t) cc_final: 0.9350 (p) REVERT: C 535 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8935 (mp0) REVERT: C 577 MET cc_start: 0.9279 (tmm) cc_final: 0.8374 (tmm) REVERT: C 591 GLU cc_start: 0.8952 (pt0) cc_final: 0.8613 (pm20) REVERT: C 603 MET cc_start: 0.9301 (ttp) cc_final: 0.8914 (tmm) REVERT: D 35 GLU cc_start: 0.9544 (tt0) cc_final: 0.9068 (mt-10) REVERT: D 38 LEU cc_start: 0.9693 (mt) cc_final: 0.9486 (tp) REVERT: D 61 LEU cc_start: 0.9596 (mt) cc_final: 0.9356 (mt) REVERT: D 85 ILE cc_start: 0.9818 (mm) cc_final: 0.9546 (tp) REVERT: D 99 MET cc_start: 0.9501 (mmt) cc_final: 0.8810 (mmm) REVERT: D 184 GLU cc_start: 0.8778 (mp0) cc_final: 0.8549 (mp0) REVERT: D 289 GLU cc_start: 0.8190 (mp0) cc_final: 0.7960 (pm20) REVERT: D 315 GLU cc_start: 0.9278 (mm-30) cc_final: 0.9072 (mm-30) REVERT: D 331 MET cc_start: 0.9058 (tmm) cc_final: 0.8766 (mmt) REVERT: D 364 ASP cc_start: 0.9425 (m-30) cc_final: 0.9015 (m-30) REVERT: D 483 GLN cc_start: 0.8880 (tt0) cc_final: 0.8553 (tm-30) REVERT: D 491 MET cc_start: 0.8961 (tpt) cc_final: 0.8507 (tmm) REVERT: D 577 MET cc_start: 0.9113 (tmt) cc_final: 0.8614 (tmt) REVERT: D 588 GLU cc_start: 0.9316 (tt0) cc_final: 0.9096 (tt0) REVERT: D 603 MET cc_start: 0.9244 (ttp) cc_final: 0.8834 (tmm) REVERT: D 625 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9297 (tm) REVERT: E 8 GLN cc_start: 0.8898 (mt0) cc_final: 0.8655 (mt0) REVERT: E 14 GLU cc_start: 0.9558 (mm-30) cc_final: 0.9277 (tm-30) REVERT: E 18 LEU cc_start: 0.9295 (tt) cc_final: 0.9052 (pp) REVERT: E 30 LYS cc_start: 0.9340 (ttmp) cc_final: 0.9094 (tttt) REVERT: E 36 MET cc_start: 0.9223 (ttt) cc_final: 0.8903 (tpp) REVERT: E 37 ARG cc_start: 0.8995 (ptt90) cc_final: 0.8740 (ptt-90) REVERT: E 49 GLN cc_start: 0.9096 (pt0) cc_final: 0.8793 (pm20) REVERT: E 71 MET cc_start: 0.9561 (ttt) cc_final: 0.9114 (ttt) REVERT: E 72 MET cc_start: 0.8859 (mmp) cc_final: 0.8248 (mmm) REVERT: E 116 LEU cc_start: 0.9029 (mt) cc_final: 0.8550 (tp) REVERT: E 143 GLN cc_start: 0.6749 (mt0) cc_final: 0.6261 (tm-30) REVERT: E 144 MET cc_start: 0.7820 (mmp) cc_final: 0.7167 (mtt) REVERT: E 148 LYS cc_start: 0.6824 (pmtt) cc_final: 0.5972 (mmtm) outliers start: 86 outliers final: 27 residues processed: 438 average time/residue: 0.2918 time to fit residues: 203.8322 Evaluate side-chains 312 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 2.236 ------------------------------------------------------------------------------- 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 371 LYS Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 551 LEU 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 615 ARG Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 38 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 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 625 LEU Chi-restraints excluded: chain D residue 160 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 613 TRP Chi-restraints excluded: chain D residue 615 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 149 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 194 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 143 optimal weight: 6.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- 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 A 572 ASN B 217 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 HIS D 91 ASN D 374 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.051743 restraints weight = 82164.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.053649 restraints weight = 44083.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.054969 restraints weight = 29211.593| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21666 Z= 0.130 Angle : 0.787 13.976 29370 Z= 0.383 Chirality : 0.042 0.207 3323 Planarity : 0.004 0.039 3736 Dihedral : 6.210 56.538 2912 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.28 % Favored : 90.56 % Rotamer: Outliers : 3.58 % Allowed : 14.54 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.16), residues: 2628 helix: 0.01 (0.13), residues: 1433 sheet: -3.62 (0.41), residues: 84 loop : -2.71 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 613 HIS 0.007 0.001 HIS A 582 PHE 0.025 0.001 PHE E 68 TYR 0.015 0.001 TYR C 432 ARG 0.008 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 848) hydrogen bonds : angle 4.23678 ( 2439) covalent geometry : bond 0.00281 (21666) covalent geometry : angle 0.78704 (29370) *********************** 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 402 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 320 time to evaluate : 5.687 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: 0.9625 (mt) cc_final: 0.9312 (pp) REVERT: A 128 GLN cc_start: 0.9126 (tt0) cc_final: 0.7854 (tm-30) REVERT: A 209 LYS cc_start: 0.9135 (mttp) cc_final: 0.8836 (mmtt) REVERT: A 311 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 315 GLU cc_start: 0.8983 (mp0) cc_final: 0.8636 (mp0) REVERT: A 410 MET cc_start: 0.8171 (mpp) cc_final: 0.7746 (mpp) REVERT: A 414 ARG cc_start: 0.9110 (tpp80) cc_final: 0.8618 (tpt90) REVERT: A 437 LEU cc_start: 0.9509 (mp) cc_final: 0.8938 (mm) REVERT: A 440 MET cc_start: 0.9113 (tmm) cc_final: 0.8731 (ppp) REVERT: A 485 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8980 (ttm) REVERT: A 515 GLU cc_start: 0.9012 (mm-30) cc_final: 0.7976 (mp0) REVERT: A 528 MET cc_start: 0.9241 (tpt) cc_final: 0.8798 (tpp) REVERT: A 535 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8719 (tt0) REVERT: A 557 ILE cc_start: 0.9681 (mt) cc_final: 0.9407 (tp) REVERT: A 570 MET cc_start: 0.9150 (mmm) cc_final: 0.8904 (mmm) REVERT: A 603 MET cc_start: 0.9481 (ttp) cc_final: 0.8871 (tmm) REVERT: A 635 ASP cc_start: 0.8410 (t70) cc_final: 0.7949 (p0) REVERT: B 57 ASP cc_start: 0.9179 (m-30) cc_final: 0.8699 (m-30) REVERT: B 110 MET cc_start: 0.8541 (mtm) cc_final: 0.8313 (mtm) REVERT: B 130 MET cc_start: 0.8611 (mmm) cc_final: 0.8251 (mmm) REVERT: B 168 SER cc_start: 0.9803 (m) cc_final: 0.9548 (p) REVERT: B 241 LEU cc_start: 0.9381 (mt) cc_final: 0.9171 (mp) REVERT: B 260 MET cc_start: 0.9610 (tpp) cc_final: 0.9265 (tpp) REVERT: B 302 ARG cc_start: 0.8156 (tpt170) cc_final: 0.7908 (tpp-160) REVERT: B 345 MET cc_start: 0.8982 (mmm) cc_final: 0.8443 (tmm) REVERT: B 485 MET cc_start: 0.9173 (mmm) cc_final: 0.8036 (tpp) REVERT: B 489 ASP cc_start: 0.8424 (t0) cc_final: 0.7527 (t0) REVERT: B 528 MET cc_start: 0.9121 (tpp) cc_final: 0.8735 (tpp) REVERT: B 591 GLU cc_start: 0.9165 (pt0) cc_final: 0.8758 (pm20) REVERT: B 637 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8305 (tm-30) REVERT: B 641 ARG cc_start: 0.9192 (mtt180) cc_final: 0.8875 (mmp80) REVERT: C 99 MET cc_start: 0.9609 (mmt) cc_final: 0.9228 (mmm) REVERT: C 284 ASP cc_start: 0.8873 (t70) cc_final: 0.8549 (t70) REVERT: C 410 MET cc_start: 0.8157 (mtp) cc_final: 0.7461 (ttp) REVERT: C 432 TYR cc_start: 0.8661 (t80) cc_final: 0.8323 (t80) REVERT: C 489 ASP cc_start: 0.8910 (m-30) cc_final: 0.8394 (m-30) REVERT: C 491 MET cc_start: 0.8928 (tpp) cc_final: 0.8713 (ttt) REVERT: C 515 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8018 (mp0) REVERT: C 528 MET cc_start: 0.9310 (ttm) cc_final: 0.8988 (tpp) REVERT: C 532 SER cc_start: 0.9756 (t) cc_final: 0.9392 (p) REVERT: C 535 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8841 (mp0) REVERT: C 577 MET cc_start: 0.9207 (tmm) cc_final: 0.8475 (tmm) REVERT: C 603 MET cc_start: 0.9308 (ttp) cc_final: 0.8899 (tmm) REVERT: D 35 GLU cc_start: 0.9526 (tt0) cc_final: 0.9096 (mt-10) REVERT: D 61 LEU cc_start: 0.9557 (mt) cc_final: 0.9334 (mt) REVERT: D 85 ILE cc_start: 0.9828 (mm) cc_final: 0.9580 (tp) REVERT: D 99 MET cc_start: 0.9507 (mmt) cc_final: 0.8917 (mmm) REVERT: D 184 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8590 (mm-30) REVERT: D 363 ARG cc_start: 0.8679 (tpp80) cc_final: 0.8142 (tpp80) REVERT: D 364 ASP cc_start: 0.9311 (m-30) cc_final: 0.8973 (m-30) REVERT: D 378 MET cc_start: 0.8812 (pmm) cc_final: 0.8567 (pmm) REVERT: D 483 GLN cc_start: 0.8844 (tt0) cc_final: 0.8440 (tm-30) REVERT: D 491 MET cc_start: 0.8923 (tpt) cc_final: 0.8420 (tmm) REVERT: D 570 MET cc_start: 0.9223 (tpp) cc_final: 0.9013 (mmm) REVERT: D 603 MET cc_start: 0.9308 (ttp) cc_final: 0.8885 (tmm) REVERT: D 625 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9344 (tm) REVERT: E 8 GLN cc_start: 0.8958 (mt0) cc_final: 0.8736 (mt0) REVERT: E 14 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9278 (tm-30) REVERT: E 18 LEU cc_start: 0.9317 (tt) cc_final: 0.9081 (pp) REVERT: E 30 LYS cc_start: 0.9347 (ttmp) cc_final: 0.9130 (tttt) REVERT: E 36 MET cc_start: 0.9257 (ttt) cc_final: 0.8907 (tpp) REVERT: E 37 ARG cc_start: 0.8981 (ptt90) cc_final: 0.8762 (ptt-90) REVERT: E 68 PHE cc_start: 0.9148 (t80) cc_final: 0.8887 (t80) REVERT: E 69 LEU cc_start: 0.9737 (mt) cc_final: 0.9516 (mt) REVERT: E 71 MET cc_start: 0.9563 (ttt) cc_final: 0.9188 (ttt) REVERT: E 72 MET cc_start: 0.8839 (mmp) cc_final: 0.8236 (mmm) REVERT: E 116 LEU cc_start: 0.8893 (mt) cc_final: 0.8649 (mm) REVERT: E 145 MET cc_start: 0.8245 (mmm) cc_final: 0.7995 (mmm) REVERT: E 148 LYS cc_start: 0.6761 (pmtt) cc_final: 0.5921 (mmtm) outliers start: 82 outliers final: 29 residues processed: 379 average time/residue: 0.3947 time to fit residues: 237.6852 Evaluate side-chains 321 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 288 time to evaluate : 3.457 ------------------------------------------------------------------------------- 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 331 MET Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 241 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 257 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- 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 206 GLN A 217 ASN A 258 HIS A 464 ASN B 73 HIS B 267 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN D 37 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.048736 restraints weight = 86065.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.050536 restraints weight = 46861.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.051785 restraints weight = 31437.147| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21666 Z= 0.248 Angle : 0.841 15.830 29370 Z= 0.416 Chirality : 0.044 0.301 3323 Planarity : 0.004 0.041 3736 Dihedral : 6.020 49.693 2902 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.89 % Favored : 89.95 % Rotamer: Outliers : 4.10 % Allowed : 15.59 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2628 helix: 0.53 (0.14), residues: 1455 sheet: -3.75 (0.44), residues: 82 loop : -2.66 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 613 HIS 0.009 0.002 HIS E 107 PHE 0.024 0.002 PHE E 68 TYR 0.027 0.002 TYR A 324 ARG 0.009 0.001 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 848) hydrogen bonds : angle 4.49028 ( 2439) covalent geometry : bond 0.00544 (21666) covalent geometry : angle 0.84144 (29370) *********************** 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 380 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 286 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9614 (mt) cc_final: 0.9323 (pp) REVERT: A 96 MET cc_start: 0.9245 (mpp) cc_final: 0.9035 (mpp) REVERT: A 128 GLN cc_start: 0.9129 (tt0) cc_final: 0.7833 (tm-30) REVERT: A 209 LYS cc_start: 0.9236 (mttp) cc_final: 0.8944 (mmtt) REVERT: A 215 MET cc_start: 0.9208 (ttm) cc_final: 0.8935 (ttm) REVERT: A 311 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8277 (p) REVERT: A 315 GLU cc_start: 0.9060 (mp0) cc_final: 0.8711 (mp0) REVERT: A 410 MET cc_start: 0.8233 (mpp) cc_final: 0.7895 (mpp) REVERT: A 414 ARG cc_start: 0.9141 (tpp80) cc_final: 0.8733 (tpt170) REVERT: A 434 PHE cc_start: 0.9021 (t80) cc_final: 0.8783 (t80) REVERT: A 437 LEU cc_start: 0.9569 (mp) cc_final: 0.8993 (mm) REVERT: A 440 MET cc_start: 0.9176 (tmm) cc_final: 0.8900 (ppp) REVERT: A 485 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.9038 (ttm) REVERT: A 489 ASP cc_start: 0.8421 (t0) cc_final: 0.7819 (t0) REVERT: A 491 MET cc_start: 0.8906 (ttm) cc_final: 0.8546 (tmm) REVERT: A 497 MET cc_start: 0.9429 (ttp) cc_final: 0.9166 (ttp) REVERT: A 515 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8057 (mp0) REVERT: A 528 MET cc_start: 0.9318 (tpt) cc_final: 0.8837 (tpp) REVERT: A 535 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8819 (tt0) REVERT: A 557 ILE cc_start: 0.9743 (mt) cc_final: 0.9501 (tp) REVERT: A 570 MET cc_start: 0.9286 (mmm) cc_final: 0.8985 (mmm) REVERT: A 577 MET cc_start: 0.9339 (tmt) cc_final: 0.8917 (tmm) REVERT: A 603 MET cc_start: 0.9480 (ttp) cc_final: 0.8961 (tmm) REVERT: B 38 LEU cc_start: 0.9710 (tp) cc_final: 0.9322 (tp) REVERT: B 57 ASP cc_start: 0.9191 (m-30) cc_final: 0.8678 (m-30) REVERT: B 110 MET cc_start: 0.8566 (mtm) cc_final: 0.8364 (mtm) REVERT: B 130 MET cc_start: 0.8941 (mmm) cc_final: 0.8680 (mmm) REVERT: B 168 SER cc_start: 0.9832 (m) cc_final: 0.9588 (p) REVERT: B 260 MET cc_start: 0.9622 (tpp) cc_final: 0.9259 (tpp) REVERT: B 290 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7627 (tm-30) REVERT: B 294 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8690 (pt0) REVERT: B 345 MET cc_start: 0.9051 (mmm) cc_final: 0.8644 (tmm) REVERT: B 377 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7979 (m-10) REVERT: B 408 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: B 464 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.8842 (t0) REVERT: B 528 MET cc_start: 0.9142 (tpp) cc_final: 0.8730 (tpp) REVERT: B 578 MET cc_start: 0.9495 (mmm) cc_final: 0.9285 (mmm) REVERT: B 637 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8373 (tm-30) REVERT: B 641 ARG cc_start: 0.9214 (mtt180) cc_final: 0.8877 (mmp80) REVERT: C 38 LEU cc_start: 0.9671 (mt) cc_final: 0.9309 (tt) REVERT: C 99 MET cc_start: 0.9656 (mmt) cc_final: 0.9271 (mmm) REVERT: C 284 ASP cc_start: 0.8866 (t70) cc_final: 0.8524 (t0) REVERT: C 410 MET cc_start: 0.8420 (mtp) cc_final: 0.7750 (ttp) REVERT: C 432 TYR cc_start: 0.8855 (t80) cc_final: 0.8579 (t80) REVERT: C 489 ASP cc_start: 0.8881 (m-30) cc_final: 0.8313 (m-30) REVERT: C 515 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8132 (mp0) REVERT: C 528 MET cc_start: 0.9356 (ttm) cc_final: 0.9007 (tpp) REVERT: C 532 SER cc_start: 0.9814 (t) cc_final: 0.9577 (p) REVERT: C 535 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9036 (mp0) REVERT: C 550 ASP cc_start: 0.9102 (t70) cc_final: 0.8674 (t0) REVERT: C 577 MET cc_start: 0.9229 (tmm) cc_final: 0.8224 (tmm) REVERT: C 603 MET cc_start: 0.9366 (ttp) cc_final: 0.8893 (tmm) REVERT: D 35 GLU cc_start: 0.9604 (tt0) cc_final: 0.9188 (mt-10) REVERT: D 61 LEU cc_start: 0.9530 (mt) cc_final: 0.9289 (mt) REVERT: D 85 ILE cc_start: 0.9851 (mm) cc_final: 0.9632 (tp) REVERT: D 99 MET cc_start: 0.9483 (mmt) cc_final: 0.8936 (mmm) REVERT: D 114 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8976 (tp) REVERT: D 184 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8652 (mm-30) REVERT: D 345 MET cc_start: 0.9060 (tpp) cc_final: 0.8248 (tmm) REVERT: D 363 ARG cc_start: 0.8771 (tpp80) cc_final: 0.8327 (tpp80) REVERT: D 364 ASP cc_start: 0.9345 (m-30) cc_final: 0.9026 (m-30) REVERT: D 371 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8861 (ttpp) REVERT: D 378 MET cc_start: 0.8874 (pmm) cc_final: 0.8573 (pmm) REVERT: D 464 ASN cc_start: 0.9510 (t0) cc_final: 0.9301 (t0) REVERT: D 491 MET cc_start: 0.8954 (tpt) cc_final: 0.8481 (tmm) REVERT: D 603 MET cc_start: 0.9363 (ttp) cc_final: 0.8981 (tmm) REVERT: D 625 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9375 (tm) REVERT: E 8 GLN cc_start: 0.9006 (mt0) cc_final: 0.8765 (mt0) REVERT: E 14 GLU cc_start: 0.9601 (mm-30) cc_final: 0.9330 (tm-30) REVERT: E 30 LYS cc_start: 0.9430 (ttmp) cc_final: 0.9195 (tttt) REVERT: E 36 MET cc_start: 0.9251 (ttt) cc_final: 0.8915 (tpp) REVERT: E 37 ARG cc_start: 0.8971 (ptt90) cc_final: 0.8768 (ptt90) REVERT: E 71 MET cc_start: 0.9556 (ttt) cc_final: 0.9246 (ttt) REVERT: E 72 MET cc_start: 0.8986 (mmp) cc_final: 0.8545 (mmm) REVERT: E 116 LEU cc_start: 0.8916 (mt) cc_final: 0.8705 (tp) REVERT: E 148 LYS cc_start: 0.6791 (pmtt) cc_final: 0.5910 (mmtm) outliers start: 94 outliers final: 50 residues processed: 354 average time/residue: 0.3146 time to fit residues: 177.9578 Evaluate side-chains 325 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 266 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 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 444 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 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 D residue 114 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 404 VAL 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 63 ILE Chi-restraints excluded: chain E residue 105 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 134 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 81 optimal weight: 0.4980 chunk 233 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN B 267 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.050322 restraints weight = 84356.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.052158 restraints weight = 45651.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.053434 restraints weight = 30447.990| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21666 Z= 0.144 Angle : 0.779 15.175 29370 Z= 0.377 Chirality : 0.042 0.208 3323 Planarity : 0.003 0.038 3736 Dihedral : 5.737 51.954 2900 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.36 % Favored : 90.49 % Rotamer: Outliers : 3.58 % Allowed : 16.94 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2628 helix: 0.88 (0.14), residues: 1458 sheet: -3.77 (0.47), residues: 76 loop : -2.55 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 613 HIS 0.009 0.001 HIS E 107 PHE 0.017 0.001 PHE B 472 TYR 0.013 0.001 TYR A 324 ARG 0.007 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 848) hydrogen bonds : angle 4.07828 ( 2439) covalent geometry : bond 0.00327 (21666) covalent geometry : angle 0.77879 (29370) *********************** 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 369 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 287 time to evaluate : 2.403 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: 0.9595 (mt) cc_final: 0.9304 (pp) REVERT: A 96 MET cc_start: 0.9259 (mpp) cc_final: 0.8952 (mpp) REVERT: A 128 GLN cc_start: 0.9010 (tt0) cc_final: 0.7772 (tm-30) REVERT: A 209 LYS cc_start: 0.9198 (mttp) cc_final: 0.8897 (mmtt) REVERT: A 215 MET cc_start: 0.9194 (ttm) cc_final: 0.8973 (ttm) REVERT: A 311 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8233 (p) REVERT: A 315 GLU cc_start: 0.9098 (mp0) cc_final: 0.8713 (mp0) REVERT: A 410 MET cc_start: 0.8246 (mpp) cc_final: 0.7964 (mpp) REVERT: A 414 ARG cc_start: 0.9113 (tpp80) cc_final: 0.8631 (tpt90) REVERT: A 434 PHE cc_start: 0.9053 (t80) cc_final: 0.8830 (t80) REVERT: A 437 LEU cc_start: 0.9549 (mp) cc_final: 0.8940 (mm) REVERT: A 440 MET cc_start: 0.9202 (tmm) cc_final: 0.8900 (ppp) REVERT: A 485 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.9034 (ttm) REVERT: A 491 MET cc_start: 0.8881 (ttm) cc_final: 0.8469 (tmm) REVERT: A 497 MET cc_start: 0.9402 (ttp) cc_final: 0.9103 (ttp) REVERT: A 515 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8874 (tp30) REVERT: A 528 MET cc_start: 0.9270 (tpt) cc_final: 0.8775 (tpp) REVERT: A 535 GLU cc_start: 0.9368 (mt-10) cc_final: 0.8862 (tt0) REVERT: A 554 MET cc_start: 0.8624 (tpp) cc_final: 0.8136 (tpp) REVERT: A 557 ILE cc_start: 0.9707 (mt) cc_final: 0.9498 (tp) REVERT: A 603 MET cc_start: 0.9450 (ttp) cc_final: 0.8948 (tmm) REVERT: B 38 LEU cc_start: 0.9707 (tp) cc_final: 0.9387 (tt) REVERT: B 57 ASP cc_start: 0.9169 (m-30) cc_final: 0.8696 (m-30) REVERT: B 110 MET cc_start: 0.8479 (mtm) cc_final: 0.8262 (mtm) REVERT: B 130 MET cc_start: 0.8774 (mmm) cc_final: 0.8489 (mmm) REVERT: B 168 SER cc_start: 0.9807 (m) cc_final: 0.9562 (p) REVERT: B 260 MET cc_start: 0.9561 (tpp) cc_final: 0.9237 (tpp) REVERT: B 294 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8688 (pt0) REVERT: B 302 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.7944 (tpp-160) REVERT: B 345 MET cc_start: 0.8985 (mmm) cc_final: 0.8591 (tmm) REVERT: B 386 LEU cc_start: 0.9762 (tp) cc_final: 0.9425 (mm) REVERT: B 390 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9509 (mm) REVERT: B 408 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: B 464 ASN cc_start: 0.9402 (OUTLIER) cc_final: 0.8855 (t0) REVERT: B 485 MET cc_start: 0.9459 (tpp) cc_final: 0.8585 (tpp) REVERT: B 515 GLU cc_start: 0.9022 (tp30) cc_final: 0.8777 (tp30) REVERT: B 528 MET cc_start: 0.9119 (tpp) cc_final: 0.8670 (tpp) REVERT: B 577 MET cc_start: 0.9060 (tmt) cc_final: 0.8760 (tmm) REVERT: B 578 MET cc_start: 0.9409 (mmm) cc_final: 0.9157 (mmm) REVERT: B 637 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8480 (tm-30) REVERT: B 641 ARG cc_start: 0.9191 (mtt180) cc_final: 0.8723 (tpt170) REVERT: C 38 LEU cc_start: 0.9658 (mt) cc_final: 0.9281 (tt) REVERT: C 99 MET cc_start: 0.9634 (mmt) cc_final: 0.9227 (mmm) REVERT: C 114 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8459 (tp) REVERT: C 284 ASP cc_start: 0.8901 (t70) cc_final: 0.8583 (t0) REVERT: C 345 MET cc_start: 0.8624 (mmt) cc_final: 0.8334 (tpp) REVERT: C 410 MET cc_start: 0.8356 (mtp) cc_final: 0.7612 (ttp) REVERT: C 432 TYR cc_start: 0.8731 (t80) cc_final: 0.8388 (t80) REVERT: C 489 ASP cc_start: 0.8847 (m-30) cc_final: 0.7934 (m-30) REVERT: C 492 ARG cc_start: 0.8996 (ptt180) cc_final: 0.7743 (ptp90) REVERT: C 515 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8102 (mp0) REVERT: C 528 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.9073 (tpp) REVERT: C 577 MET cc_start: 0.9215 (tmm) cc_final: 0.7876 (tmm) REVERT: C 603 MET cc_start: 0.9320 (ttp) cc_final: 0.8890 (tmm) REVERT: D 35 GLU cc_start: 0.9586 (tt0) cc_final: 0.9207 (mt-10) REVERT: D 61 LEU cc_start: 0.9536 (mt) cc_final: 0.9304 (mt) REVERT: D 85 ILE cc_start: 0.9845 (mm) cc_final: 0.9587 (tp) REVERT: D 114 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9094 (tp) REVERT: D 184 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8620 (mm-30) REVERT: D 345 MET cc_start: 0.9076 (tpp) cc_final: 0.8270 (tmm) REVERT: D 363 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8302 (tpp80) REVERT: D 364 ASP cc_start: 0.9318 (m-30) cc_final: 0.8991 (m-30) REVERT: D 371 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8979 (ttpp) REVERT: D 378 MET cc_start: 0.8772 (pmm) cc_final: 0.8451 (pmm) REVERT: D 442 MET cc_start: 0.9238 (tpp) cc_final: 0.8856 (ttm) REVERT: D 491 MET cc_start: 0.8831 (tpt) cc_final: 0.8374 (tmm) REVERT: D 497 MET cc_start: 0.9363 (ttp) cc_final: 0.8687 (tmm) REVERT: D 577 MET cc_start: 0.9097 (tmm) cc_final: 0.8591 (tmm) REVERT: D 603 MET cc_start: 0.9343 (ttp) cc_final: 0.8860 (tmm) REVERT: D 625 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9329 (tm) REVERT: E 8 GLN cc_start: 0.9020 (mt0) cc_final: 0.8786 (mt0) REVERT: E 14 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9310 (tm-30) REVERT: E 30 LYS cc_start: 0.9429 (ttmp) cc_final: 0.9202 (tttt) REVERT: E 36 MET cc_start: 0.9240 (ttt) cc_final: 0.8878 (tpp) REVERT: E 37 ARG cc_start: 0.8942 (ptt90) cc_final: 0.8698 (ptt90) REVERT: E 71 MET cc_start: 0.9556 (ttt) cc_final: 0.9286 (ttt) REVERT: E 72 MET cc_start: 0.8884 (mmp) cc_final: 0.8353 (mmm) REVERT: E 77 LYS cc_start: 0.6032 (mmmt) cc_final: 0.5828 (tppt) REVERT: E 116 LEU cc_start: 0.8795 (mt) cc_final: 0.8569 (tp) REVERT: E 145 MET cc_start: 0.8067 (mmm) cc_final: 0.7651 (mmm) REVERT: E 148 LYS cc_start: 0.6649 (pmtt) cc_final: 0.5679 (mmtm) outliers start: 82 outliers final: 43 residues processed: 345 average time/residue: 0.3022 time to fit residues: 166.0560 Evaluate side-chains 319 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 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 189 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain 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 421 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 464 ASN 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 311 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 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 575 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 28 optimal weight: 7.9990 chunk 218 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 42 optimal weight: 0.0040 chunk 175 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** 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 = 0.3127 r_free = 0.3127 target = 0.069218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.052628 restraints weight = 82831.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.054519 restraints weight = 44765.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.055831 restraints weight = 29728.099| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4622 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= 0.114 Angle : 0.756 15.259 29370 Z= 0.360 Chirality : 0.041 0.190 3323 Planarity : 0.003 0.038 3736 Dihedral : 5.470 53.275 2900 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.25 % Favored : 90.60 % Rotamer: Outliers : 3.32 % Allowed : 17.07 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2628 helix: 1.16 (0.14), residues: 1450 sheet: -3.43 (0.49), residues: 76 loop : -2.42 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 495 HIS 0.007 0.001 HIS E 107 PHE 0.019 0.001 PHE B 472 TYR 0.017 0.001 TYR A 432 ARG 0.005 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 848) hydrogen bonds : angle 3.75980 ( 2439) covalent geometry : bond 0.00251 (21666) covalent geometry : angle 0.75558 (29370) *********************** 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 412 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 336 time to evaluate : 2.271 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: 0.9309 (pp) REVERT: A 96 MET cc_start: 0.9272 (mpp) cc_final: 0.8998 (mpp) REVERT: A 128 GLN cc_start: 0.8964 (tt0) cc_final: 0.8099 (tm-30) REVERT: A 209 LYS cc_start: 0.9094 (mttp) cc_final: 0.8813 (mmtt) REVERT: A 311 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8177 (p) REVERT: A 315 GLU cc_start: 0.9083 (mp0) cc_final: 0.8750 (mp0) REVERT: A 410 MET cc_start: 0.8178 (mpp) cc_final: 0.7888 (mpp) REVERT: A 414 ARG cc_start: 0.9109 (tpp80) cc_final: 0.8626 (tpt90) REVERT: A 437 LEU cc_start: 0.9547 (mp) cc_final: 0.8972 (mm) REVERT: A 440 MET cc_start: 0.9238 (tmm) cc_final: 0.8951 (ppp) REVERT: A 474 MET cc_start: 0.9236 (ppp) cc_final: 0.8849 (ppp) REVERT: A 491 MET cc_start: 0.8833 (ttm) cc_final: 0.8274 (tmm) REVERT: A 497 MET cc_start: 0.9392 (ttp) cc_final: 0.9063 (ttp) REVERT: A 528 MET cc_start: 0.9219 (tpt) cc_final: 0.8757 (tpp) REVERT: A 535 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8674 (tt0) REVERT: A 557 ILE cc_start: 0.9635 (mt) cc_final: 0.9431 (tp) REVERT: A 603 MET cc_start: 0.9455 (ttp) cc_final: 0.8988 (tmm) REVERT: A 634 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8609 (mp0) REVERT: B 57 ASP cc_start: 0.9165 (m-30) cc_final: 0.8711 (m-30) REVERT: B 168 SER cc_start: 0.9771 (m) cc_final: 0.9533 (p) REVERT: B 241 LEU cc_start: 0.9302 (mt) cc_final: 0.9092 (mp) REVERT: B 260 MET cc_start: 0.9467 (tpp) cc_final: 0.9245 (tpp) REVERT: B 294 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8651 (pt0) REVERT: B 302 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.8303 (tpp-160) REVERT: B 345 MET cc_start: 0.8970 (mmm) cc_final: 0.8510 (tmm) REVERT: B 386 LEU cc_start: 0.9771 (tp) cc_final: 0.9409 (mm) REVERT: B 389 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: B 408 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: B 464 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.8889 (t0) REVERT: B 474 MET cc_start: 0.9242 (ptm) cc_final: 0.8554 (ttp) REVERT: B 485 MET cc_start: 0.9426 (tpp) cc_final: 0.8533 (tpp) REVERT: B 515 GLU cc_start: 0.8983 (tp30) cc_final: 0.8411 (mp0) REVERT: B 578 MET cc_start: 0.9440 (mmm) cc_final: 0.9043 (mmm) REVERT: B 584 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8732 (mmt90) REVERT: B 641 ARG cc_start: 0.9219 (mtt180) cc_final: 0.8703 (tpt170) REVERT: C 99 MET cc_start: 0.9665 (mmt) cc_final: 0.9266 (mmm) REVERT: C 114 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8507 (tp) REVERT: C 284 ASP cc_start: 0.8875 (t70) cc_final: 0.8555 (t0) REVERT: C 345 MET cc_start: 0.8593 (mmt) cc_final: 0.8377 (tpp) REVERT: C 410 MET cc_start: 0.8307 (mtp) cc_final: 0.7621 (ttp) REVERT: C 432 TYR cc_start: 0.8531 (t80) cc_final: 0.8238 (t80) REVERT: C 485 MET cc_start: 0.8862 (tpp) cc_final: 0.8464 (ttm) REVERT: C 489 ASP cc_start: 0.8612 (m-30) cc_final: 0.8018 (m-30) REVERT: C 515 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8397 (mm-30) REVERT: C 535 GLU cc_start: 0.8890 (mp0) cc_final: 0.8629 (mp0) REVERT: C 577 MET cc_start: 0.9102 (tmm) cc_final: 0.8415 (tmm) REVERT: C 584 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8614 (tpp80) REVERT: C 603 MET cc_start: 0.9235 (ttp) cc_final: 0.8809 (tmm) REVERT: C 608 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9182 (tt) REVERT: D 35 GLU cc_start: 0.9550 (tt0) cc_final: 0.9147 (mt-10) REVERT: D 61 LEU cc_start: 0.9530 (mt) cc_final: 0.9296 (mt) REVERT: D 85 ILE cc_start: 0.9812 (mm) cc_final: 0.9502 (tp) REVERT: D 99 MET cc_start: 0.9484 (mmt) cc_final: 0.9026 (mmm) REVERT: D 345 MET cc_start: 0.9059 (tpp) cc_final: 0.8234 (tmm) REVERT: D 363 ARG cc_start: 0.8814 (tpp80) cc_final: 0.8272 (tpp80) REVERT: D 364 ASP cc_start: 0.9348 (m-30) cc_final: 0.9022 (m-30) REVERT: D 371 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9126 (ttpp) REVERT: D 378 MET cc_start: 0.8768 (pmm) cc_final: 0.8438 (pmm) REVERT: D 432 TYR cc_start: 0.9099 (t80) cc_final: 0.8804 (t80) REVERT: D 491 MET cc_start: 0.8686 (tpt) cc_final: 0.8312 (tmm) REVERT: D 497 MET cc_start: 0.9375 (ttp) cc_final: 0.8727 (tmm) REVERT: D 535 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8760 (mt-10) REVERT: D 577 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8767 (tmm) REVERT: D 603 MET cc_start: 0.9330 (ttp) cc_final: 0.8826 (tmm) REVERT: E 8 GLN cc_start: 0.9002 (mt0) cc_final: 0.8762 (mt0) REVERT: E 14 GLU cc_start: 0.9618 (mm-30) cc_final: 0.9325 (tm-30) REVERT: E 30 LYS cc_start: 0.9463 (ttmp) cc_final: 0.9208 (tttt) REVERT: E 36 MET cc_start: 0.9260 (ttt) cc_final: 0.8846 (tpp) REVERT: E 37 ARG cc_start: 0.8904 (ptt90) cc_final: 0.8648 (ptt-90) REVERT: E 71 MET cc_start: 0.9565 (ttt) cc_final: 0.9264 (ttt) REVERT: E 72 MET cc_start: 0.8855 (mmp) cc_final: 0.8193 (mmm) REVERT: E 145 MET cc_start: 0.8164 (mmm) cc_final: 0.7828 (mmm) REVERT: E 148 LYS cc_start: 0.6550 (pmtt) cc_final: 0.5596 (mmtm) outliers start: 76 outliers final: 38 residues processed: 387 average time/residue: 0.2973 time to fit residues: 183.1108 Evaluate side-chains 324 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 426 HIS 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 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 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 144 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 204 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 464 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.053236 restraints weight = 83000.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.055167 restraints weight = 44885.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.056503 restraints weight = 29776.697| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4903 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= 0.115 Angle : 0.782 15.939 29370 Z= 0.368 Chirality : 0.042 0.199 3323 Planarity : 0.003 0.036 3736 Dihedral : 5.374 53.683 2900 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.90 % Favored : 90.98 % Rotamer: Outliers : 2.53 % Allowed : 19.17 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2628 helix: 1.30 (0.14), residues: 1443 sheet: -3.16 (0.53), residues: 76 loop : -2.38 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 613 HIS 0.008 0.001 HIS E 107 PHE 0.018 0.001 PHE B 472 TYR 0.032 0.001 TYR C 324 ARG 0.005 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 848) hydrogen bonds : angle 3.72782 ( 2439) covalent geometry : bond 0.00256 (21666) covalent geometry : angle 0.78186 (29370) *********************** 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 364 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 306 time to evaluate : 2.325 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: 0.9315 (pp) REVERT: A 96 MET cc_start: 0.9292 (mpp) cc_final: 0.8980 (mpp) REVERT: A 114 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8736 (tp) REVERT: A 128 GLN cc_start: 0.8964 (tt0) cc_final: 0.8045 (tm-30) REVERT: A 209 LYS cc_start: 0.9089 (mttp) cc_final: 0.8754 (mmtt) REVERT: A 216 TYR cc_start: 0.9460 (t80) cc_final: 0.9259 (t80) REVERT: A 255 MET cc_start: 0.9550 (mmt) cc_final: 0.9199 (mmm) REVERT: A 311 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 315 GLU cc_start: 0.9064 (mp0) cc_final: 0.8749 (mp0) REVERT: A 410 MET cc_start: 0.8215 (mpp) cc_final: 0.7891 (mpp) REVERT: A 414 ARG cc_start: 0.9082 (tpp80) cc_final: 0.8624 (tpt90) REVERT: A 437 LEU cc_start: 0.9567 (mp) cc_final: 0.8957 (mm) REVERT: A 440 MET cc_start: 0.9228 (tmm) cc_final: 0.8945 (ppp) REVERT: A 474 MET cc_start: 0.9190 (ppp) cc_final: 0.8905 (ppp) REVERT: A 491 MET cc_start: 0.8784 (ttm) cc_final: 0.8237 (tmm) REVERT: A 497 MET cc_start: 0.9404 (ttp) cc_final: 0.9081 (ttp) REVERT: A 528 MET cc_start: 0.9236 (tpt) cc_final: 0.8896 (tpp) REVERT: A 554 MET cc_start: 0.8452 (tpp) cc_final: 0.7856 (tpp) REVERT: A 557 ILE cc_start: 0.9585 (mt) cc_final: 0.9353 (tp) REVERT: A 577 MET cc_start: 0.9397 (ttp) cc_final: 0.9102 (tmm) REVERT: A 603 MET cc_start: 0.9455 (ttp) cc_final: 0.8938 (tmm) REVERT: A 634 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8730 (mp0) REVERT: B 57 ASP cc_start: 0.9111 (m-30) cc_final: 0.8657 (m-30) REVERT: B 168 SER cc_start: 0.9779 (m) cc_final: 0.9539 (p) REVERT: B 241 LEU cc_start: 0.9314 (mt) cc_final: 0.9100 (mp) REVERT: B 294 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8636 (pt0) REVERT: B 302 ARG cc_start: 0.8597 (tpp-160) cc_final: 0.8344 (tpp-160) REVERT: B 345 MET cc_start: 0.8814 (mmm) cc_final: 0.8479 (tmm) REVERT: B 386 LEU cc_start: 0.9704 (tp) cc_final: 0.9375 (mm) REVERT: B 389 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: B 464 ASN cc_start: 0.9256 (t0) cc_final: 0.8958 (t0) REVERT: B 474 MET cc_start: 0.9210 (ptm) cc_final: 0.8622 (ttp) REVERT: B 515 GLU cc_start: 0.9015 (tp30) cc_final: 0.8317 (mp0) REVERT: B 578 MET cc_start: 0.9384 (mmm) cc_final: 0.8957 (mmm) REVERT: B 584 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8732 (mmt90) REVERT: B 641 ARG cc_start: 0.9269 (mtt180) cc_final: 0.8739 (tpt170) REVERT: C 90 ASP cc_start: 0.9052 (t0) cc_final: 0.8776 (p0) REVERT: C 99 MET cc_start: 0.9692 (mmt) cc_final: 0.9279 (mmm) REVERT: C 284 ASP cc_start: 0.8862 (t70) cc_final: 0.8532 (t0) REVERT: C 331 MET cc_start: 0.8626 (mmt) cc_final: 0.8419 (mmp) REVERT: C 345 MET cc_start: 0.8649 (mmt) cc_final: 0.8378 (tpp) REVERT: C 400 LEU cc_start: 0.9430 (mt) cc_final: 0.8911 (pp) REVERT: C 410 MET cc_start: 0.8277 (mtp) cc_final: 0.7527 (ttp) REVERT: C 432 TYR cc_start: 0.8481 (t80) cc_final: 0.8172 (t80) REVERT: C 489 ASP cc_start: 0.8551 (m-30) cc_final: 0.8048 (m-30) REVERT: C 491 MET cc_start: 0.8492 (ttt) cc_final: 0.8052 (tmm) REVERT: C 515 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8358 (mm-30) REVERT: C 535 GLU cc_start: 0.8854 (mp0) cc_final: 0.8589 (mp0) REVERT: C 577 MET cc_start: 0.8968 (tmm) cc_final: 0.8183 (tmm) REVERT: C 603 MET cc_start: 0.9220 (ttp) cc_final: 0.8783 (tmm) REVERT: D 35 GLU cc_start: 0.9559 (tt0) cc_final: 0.9154 (mt-10) REVERT: D 61 LEU cc_start: 0.9528 (mt) cc_final: 0.9295 (mt) REVERT: D 85 ILE cc_start: 0.9789 (mm) cc_final: 0.9494 (tp) REVERT: D 99 MET cc_start: 0.9488 (mmt) cc_final: 0.9058 (mmm) REVERT: D 181 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9455 (tm) REVERT: D 345 MET cc_start: 0.9058 (tpp) cc_final: 0.8268 (tmm) REVERT: D 363 ARG cc_start: 0.8853 (tpp80) cc_final: 0.8390 (mmp80) REVERT: D 371 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9142 (ttpp) REVERT: D 378 MET cc_start: 0.8753 (pmm) cc_final: 0.8426 (pmm) REVERT: D 497 MET cc_start: 0.9381 (ttp) cc_final: 0.8735 (tmm) REVERT: D 535 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8719 (mt-10) REVERT: D 577 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8762 (tmm) REVERT: D 603 MET cc_start: 0.9319 (ttp) cc_final: 0.8680 (tmm) REVERT: D 608 LEU cc_start: 0.9601 (tt) cc_final: 0.9344 (tt) REVERT: E 8 GLN cc_start: 0.8983 (mt0) cc_final: 0.8741 (mt0) REVERT: E 14 GLU cc_start: 0.9599 (mm-30) cc_final: 0.9345 (tm-30) REVERT: E 30 LYS cc_start: 0.9454 (ttmp) cc_final: 0.9227 (tttt) REVERT: E 36 MET cc_start: 0.9223 (ttt) cc_final: 0.8781 (tpp) REVERT: E 51 MET cc_start: 0.8081 (mmt) cc_final: 0.7812 (tpt) REVERT: E 71 MET cc_start: 0.9565 (ttt) cc_final: 0.9267 (ttt) REVERT: E 72 MET cc_start: 0.8833 (mmp) cc_final: 0.8282 (mmm) REVERT: E 148 LYS cc_start: 0.6524 (pmtt) cc_final: 0.5612 (mmtm) outliers start: 58 outliers final: 37 residues processed: 347 average time/residue: 0.2971 time to fit residues: 164.3432 Evaluate side-chains 327 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 136 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 235 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 206 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 464 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS C 572 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.053499 restraints weight = 82975.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.055429 restraints weight = 44999.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.056755 restraints weight = 29943.495| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21666 Z= 0.119 Angle : 0.797 15.672 29370 Z= 0.373 Chirality : 0.041 0.186 3323 Planarity : 0.003 0.035 3736 Dihedral : 5.281 54.138 2900 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.13 % Favored : 90.79 % Rotamer: Outliers : 3.06 % Allowed : 19.26 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2628 helix: 1.35 (0.14), residues: 1451 sheet: -3.11 (0.54), residues: 76 loop : -2.33 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 613 HIS 0.009 0.001 HIS E 107 PHE 0.016 0.001 PHE B 472 TYR 0.027 0.001 TYR C 324 ARG 0.008 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 848) hydrogen bonds : angle 3.68951 ( 2439) covalent geometry : bond 0.00273 (21666) covalent geometry : angle 0.79665 (29370) *********************** 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 374 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 304 time to evaluate : 2.456 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: 0.9576 (mt) cc_final: 0.9318 (pp) REVERT: A 96 MET cc_start: 0.9296 (mpp) cc_final: 0.9055 (mpp) REVERT: A 99 MET cc_start: 0.9525 (mmm) cc_final: 0.9032 (mpp) REVERT: A 114 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8764 (tp) REVERT: A 128 GLN cc_start: 0.8970 (tt0) cc_final: 0.8064 (tm-30) REVERT: A 209 LYS cc_start: 0.9056 (mttp) cc_final: 0.8745 (mmtt) REVERT: A 255 MET cc_start: 0.9517 (mmt) cc_final: 0.9196 (mmm) REVERT: A 311 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8135 (p) REVERT: A 315 GLU cc_start: 0.9052 (mp0) cc_final: 0.8722 (mp0) REVERT: A 410 MET cc_start: 0.8236 (mpp) cc_final: 0.7926 (mpp) REVERT: A 414 ARG cc_start: 0.9076 (tpp80) cc_final: 0.8615 (tpt90) REVERT: A 437 LEU cc_start: 0.9578 (mp) cc_final: 0.8972 (mm) REVERT: A 440 MET cc_start: 0.9241 (tmm) cc_final: 0.8949 (ppp) REVERT: A 454 MET cc_start: 0.9210 (tpp) cc_final: 0.9009 (tpp) REVERT: A 474 MET cc_start: 0.9145 (ppp) cc_final: 0.8928 (ppp) REVERT: A 497 MET cc_start: 0.9402 (ttp) cc_final: 0.9070 (ttp) REVERT: A 528 MET cc_start: 0.9231 (tpt) cc_final: 0.8893 (tpp) REVERT: A 554 MET cc_start: 0.8520 (tpp) cc_final: 0.7930 (tpp) REVERT: A 557 ILE cc_start: 0.9587 (mt) cc_final: 0.9357 (tp) REVERT: A 577 MET cc_start: 0.9379 (ttp) cc_final: 0.9129 (tmm) REVERT: A 603 MET cc_start: 0.9444 (ttp) cc_final: 0.8945 (tmm) REVERT: B 57 ASP cc_start: 0.9124 (m-30) cc_final: 0.8639 (m-30) REVERT: B 130 MET cc_start: 0.8185 (mmm) cc_final: 0.7940 (mmm) REVERT: B 168 SER cc_start: 0.9757 (m) cc_final: 0.9523 (p) REVERT: B 260 MET cc_start: 0.9548 (tpp) cc_final: 0.9348 (tpp) REVERT: B 290 GLN cc_start: 0.7384 (tm-30) cc_final: 0.7049 (tm-30) REVERT: B 294 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8639 (pt0) REVERT: B 302 ARG cc_start: 0.8611 (tpp-160) cc_final: 0.8329 (tpp-160) REVERT: B 345 MET cc_start: 0.8830 (mmm) cc_final: 0.8562 (tmm) REVERT: B 386 LEU cc_start: 0.9718 (tp) cc_final: 0.9398 (mm) REVERT: B 408 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: B 464 ASN cc_start: 0.9217 (t0) cc_final: 0.8989 (t0) REVERT: B 474 MET cc_start: 0.9226 (ptm) cc_final: 0.8634 (ttp) REVERT: B 515 GLU cc_start: 0.8995 (tp30) cc_final: 0.8190 (mp0) REVERT: B 584 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8757 (mmt90) REVERT: B 641 ARG cc_start: 0.9270 (mtt180) cc_final: 0.8728 (tpt170) REVERT: C 99 MET cc_start: 0.9694 (mmt) cc_final: 0.9269 (mmm) REVERT: C 114 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8589 (tp) REVERT: C 284 ASP cc_start: 0.8830 (t70) cc_final: 0.8514 (t70) REVERT: C 306 GLN cc_start: 0.9477 (tp-100) cc_final: 0.8964 (tp40) REVERT: C 331 MET cc_start: 0.8595 (mmt) cc_final: 0.8358 (mmp) REVERT: C 345 MET cc_start: 0.8597 (mmt) cc_final: 0.8321 (tpp) REVERT: C 400 LEU cc_start: 0.9431 (mt) cc_final: 0.8917 (pp) REVERT: C 410 MET cc_start: 0.8313 (mtp) cc_final: 0.7587 (ttp) REVERT: C 432 TYR cc_start: 0.8476 (t80) cc_final: 0.8196 (t80) REVERT: C 489 ASP cc_start: 0.8713 (m-30) cc_final: 0.8170 (m-30) REVERT: C 491 MET cc_start: 0.8495 (ttt) cc_final: 0.7975 (tmm) REVERT: C 515 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8630 (mm-30) REVERT: C 535 GLU cc_start: 0.8838 (mp0) cc_final: 0.8397 (mp0) REVERT: C 577 MET cc_start: 0.9004 (tmm) cc_final: 0.8239 (tmm) REVERT: C 603 MET cc_start: 0.9266 (ttp) cc_final: 0.8807 (tmm) REVERT: D 35 GLU cc_start: 0.9565 (tt0) cc_final: 0.9150 (mt-10) REVERT: D 61 LEU cc_start: 0.9530 (mt) cc_final: 0.9295 (mt) REVERT: D 85 ILE cc_start: 0.9794 (mm) cc_final: 0.9513 (tp) REVERT: D 99 MET cc_start: 0.9503 (mmt) cc_final: 0.9096 (mmm) REVERT: D 181 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9478 (tm) REVERT: D 183 ILE cc_start: 0.9710 (tp) cc_final: 0.9395 (pt) REVERT: D 345 MET cc_start: 0.9025 (tpp) cc_final: 0.8252 (tmm) REVERT: D 363 ARG cc_start: 0.8918 (tpp80) cc_final: 0.8639 (mmp80) REVERT: D 378 MET cc_start: 0.8757 (pmm) cc_final: 0.8436 (pmm) REVERT: D 497 MET cc_start: 0.9362 (ttp) cc_final: 0.8678 (tmm) REVERT: D 535 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8712 (mt-10) REVERT: D 577 MET cc_start: 0.9068 (tmm) cc_final: 0.8763 (tmm) REVERT: D 603 MET cc_start: 0.9292 (ttp) cc_final: 0.8647 (tmm) REVERT: D 608 LEU cc_start: 0.9589 (tt) cc_final: 0.9326 (tt) REVERT: D 625 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9354 (mm) REVERT: E 8 GLN cc_start: 0.8956 (mt0) cc_final: 0.8713 (mt0) REVERT: E 36 MET cc_start: 0.9195 (ttt) cc_final: 0.8771 (tpp) REVERT: E 51 MET cc_start: 0.8103 (mmt) cc_final: 0.7896 (tpt) REVERT: E 99 TYR cc_start: 0.6368 (m-80) cc_final: 0.6151 (m-80) REVERT: E 148 LYS cc_start: 0.6475 (pmtt) cc_final: 0.5606 (mmtm) outliers start: 70 outliers final: 42 residues processed: 352 average time/residue: 0.2916 time to fit residues: 165.1860 Evaluate side-chains 335 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 480 ILE 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 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 408 PHE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 444 LEU 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 215 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 572 ASN Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 216 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 572 ASN ** D 37 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 = 0.3110 r_free = 0.3110 target = 0.067648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.051162 restraints weight = 84132.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.053033 restraints weight = 45482.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.054322 restraints weight = 30269.147| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21666 Z= 0.177 Angle : 0.833 15.890 29370 Z= 0.395 Chirality : 0.043 0.210 3323 Planarity : 0.004 0.033 3736 Dihedral : 5.380 55.473 2900 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.28 % Favored : 90.56 % Rotamer: Outliers : 2.93 % Allowed : 19.21 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2628 helix: 1.41 (0.14), residues: 1453 sheet: -3.15 (0.55), residues: 76 loop : -2.31 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 613 HIS 0.016 0.001 HIS B 426 PHE 0.015 0.001 PHE D 162 TYR 0.024 0.001 TYR C 324 ARG 0.009 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 848) hydrogen bonds : angle 3.92937 ( 2439) covalent geometry : bond 0.00397 (21666) covalent geometry : angle 0.83293 (29370) *********************** 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 345 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 278 time to evaluate : 2.329 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: 0.9589 (mt) cc_final: 0.9327 (pp) REVERT: A 96 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8940 (mpp) REVERT: A 114 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8808 (tp) REVERT: A 128 GLN cc_start: 0.9147 (tt0) cc_final: 0.8171 (tm-30) REVERT: A 209 LYS cc_start: 0.9070 (mttp) cc_final: 0.8770 (mmtt) REVERT: A 311 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8267 (p) REVERT: A 315 GLU cc_start: 0.9053 (mp0) cc_final: 0.8762 (mp0) REVERT: A 410 MET cc_start: 0.8313 (mpp) cc_final: 0.7991 (mpp) REVERT: A 414 ARG cc_start: 0.9058 (tpp80) cc_final: 0.8685 (tpt170) REVERT: A 437 LEU cc_start: 0.9626 (mp) cc_final: 0.9013 (mm) REVERT: A 440 MET cc_start: 0.9201 (tmm) cc_final: 0.8963 (ppp) REVERT: A 454 MET cc_start: 0.9177 (tpp) cc_final: 0.8976 (tpp) REVERT: A 474 MET cc_start: 0.9009 (ppp) cc_final: 0.8745 (ppp) REVERT: A 491 MET cc_start: 0.8756 (ttm) cc_final: 0.8244 (tmm) REVERT: A 497 MET cc_start: 0.9369 (ttp) cc_final: 0.9023 (ttp) REVERT: A 528 MET cc_start: 0.9317 (tpt) cc_final: 0.8983 (tpp) REVERT: A 535 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8679 (tt0) REVERT: A 554 MET cc_start: 0.8685 (tpp) cc_final: 0.8165 (tpp) REVERT: A 557 ILE cc_start: 0.9703 (mt) cc_final: 0.9491 (tp) REVERT: A 577 MET cc_start: 0.9510 (ttp) cc_final: 0.8900 (tmm) REVERT: A 603 MET cc_start: 0.9448 (ttp) cc_final: 0.9021 (tmm) REVERT: B 57 ASP cc_start: 0.9129 (m-30) cc_final: 0.8654 (m-30) REVERT: B 130 MET cc_start: 0.8193 (mmm) cc_final: 0.7967 (mmm) REVERT: B 168 SER cc_start: 0.9775 (m) cc_final: 0.9528 (p) REVERT: B 290 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7089 (tm-30) REVERT: B 294 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8667 (pt0) REVERT: B 345 MET cc_start: 0.8922 (mmm) cc_final: 0.8575 (tmm) REVERT: B 389 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: B 408 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: B 464 ASN cc_start: 0.9249 (t0) cc_final: 0.9007 (t0) REVERT: B 474 MET cc_start: 0.9116 (ptm) cc_final: 0.8615 (ttp) REVERT: B 515 GLU cc_start: 0.8949 (tp30) cc_final: 0.8302 (mp0) REVERT: B 570 MET cc_start: 0.9601 (tpt) cc_final: 0.9368 (mmm) REVERT: B 584 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8930 (mmt90) REVERT: B 641 ARG cc_start: 0.9276 (mtt180) cc_final: 0.8763 (tpt170) REVERT: C 99 MET cc_start: 0.9648 (mmt) cc_final: 0.9270 (mmm) REVERT: C 114 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8741 (tp) REVERT: C 284 ASP cc_start: 0.8833 (t70) cc_final: 0.8517 (t0) REVERT: C 331 MET cc_start: 0.8685 (mmt) cc_final: 0.8458 (mmp) REVERT: C 345 MET cc_start: 0.8735 (mmt) cc_final: 0.8462 (tpp) REVERT: C 410 MET cc_start: 0.8415 (mtp) cc_final: 0.7748 (ttp) REVERT: C 426 HIS cc_start: 0.6451 (OUTLIER) cc_final: 0.5889 (t-90) REVERT: C 432 TYR cc_start: 0.8709 (t80) cc_final: 0.8382 (t80) REVERT: C 454 MET cc_start: 0.9465 (tpt) cc_final: 0.9231 (tpt) REVERT: C 489 ASP cc_start: 0.8707 (m-30) cc_final: 0.8110 (m-30) REVERT: C 491 MET cc_start: 0.8538 (ttt) cc_final: 0.8125 (tmm) REVERT: C 515 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8474 (mm-30) REVERT: C 603 MET cc_start: 0.9351 (ttp) cc_final: 0.8879 (tmm) REVERT: D 35 GLU cc_start: 0.9582 (tt0) cc_final: 0.9162 (mt-10) REVERT: D 61 LEU cc_start: 0.9555 (mt) cc_final: 0.9335 (mt) REVERT: D 85 ILE cc_start: 0.9842 (mm) cc_final: 0.9584 (tp) REVERT: D 99 MET cc_start: 0.9482 (mmt) cc_final: 0.9053 (mmm) REVERT: D 181 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9508 (tm) REVERT: D 345 MET cc_start: 0.9107 (tpp) cc_final: 0.8307 (tmm) REVERT: D 363 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8580 (mmp80) REVERT: D 371 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9218 (ttpp) REVERT: D 378 MET cc_start: 0.8753 (pmm) cc_final: 0.8436 (pmm) REVERT: D 410 MET cc_start: 0.8801 (mmp) cc_final: 0.8466 (mtt) REVERT: D 497 MET cc_start: 0.9388 (ttp) cc_final: 0.8693 (tmm) REVERT: D 535 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8734 (mt-10) REVERT: D 603 MET cc_start: 0.9388 (ttp) cc_final: 0.8718 (tmm) REVERT: D 608 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9380 (tt) REVERT: E 36 MET cc_start: 0.9172 (ttt) cc_final: 0.8755 (tpp) REVERT: E 51 MET cc_start: 0.8205 (mmt) cc_final: 0.7981 (tpt) REVERT: E 71 MET cc_start: 0.9491 (ttt) cc_final: 0.9094 (tmm) REVERT: E 148 LYS cc_start: 0.6551 (pmtt) cc_final: 0.5605 (mmtm) outliers start: 67 outliers final: 43 residues processed: 327 average time/residue: 0.3012 time to fit residues: 157.6698 Evaluate side-chains 320 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 266 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 114 LEU 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 348 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 480 ILE 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 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 444 LEU 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 181 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 479 THR 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 105 LEU Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 129 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 234 optimal weight: 0.0980 chunk 123 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 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 = 0.3145 r_free = 0.3145 target = 0.070171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.053581 restraints weight = 82791.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.055509 restraints weight = 45015.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.056835 restraints weight = 30015.256| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5256 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= 0.121 Angle : 0.823 16.726 29370 Z= 0.380 Chirality : 0.042 0.217 3323 Planarity : 0.003 0.035 3736 Dihedral : 5.165 37.466 2898 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.79 % Favored : 91.13 % Rotamer: Outliers : 2.10 % Allowed : 20.13 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2628 helix: 1.38 (0.14), residues: 1461 sheet: -2.92 (0.56), residues: 76 loop : -2.25 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 462 HIS 0.014 0.001 HIS B 426 PHE 0.015 0.001 PHE B 256 TYR 0.024 0.001 TYR C 324 ARG 0.010 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 848) hydrogen bonds : angle 3.70792 ( 2439) covalent geometry : bond 0.00268 (21666) covalent geometry : angle 0.82330 (29370) ********************** 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 348 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 300 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9568 (mt) cc_final: 0.9326 (pp) REVERT: A 96 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.9028 (mpp) REVERT: A 99 MET cc_start: 0.9515 (mmm) cc_final: 0.9023 (mpp) REVERT: A 114 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8756 (tp) REVERT: A 128 GLN cc_start: 0.8993 (tt0) cc_final: 0.8110 (tm-30) REVERT: A 209 LYS cc_start: 0.8988 (mttp) cc_final: 0.8642 (mmtt) REVERT: A 255 MET cc_start: 0.9498 (mmt) cc_final: 0.9198 (mmm) REVERT: A 302 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7901 (ttp80) REVERT: A 311 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8178 (p) REVERT: A 315 GLU cc_start: 0.9078 (mp0) cc_final: 0.8728 (mp0) REVERT: A 410 MET cc_start: 0.8257 (mpp) cc_final: 0.7939 (mpp) REVERT: A 414 ARG cc_start: 0.9110 (tpp80) cc_final: 0.8640 (tpt90) REVERT: A 437 LEU cc_start: 0.9561 (mp) cc_final: 0.8990 (mt) REVERT: A 440 MET cc_start: 0.9264 (tmm) cc_final: 0.8951 (ppp) REVERT: A 497 MET cc_start: 0.9396 (ttp) cc_final: 0.9056 (ttp) REVERT: A 528 MET cc_start: 0.9251 (tpt) cc_final: 0.8890 (tpp) REVERT: A 535 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8743 (mt-10) REVERT: A 554 MET cc_start: 0.8539 (tpp) cc_final: 0.8015 (tpp) REVERT: A 557 ILE cc_start: 0.9623 (mt) cc_final: 0.9421 (tp) REVERT: A 577 MET cc_start: 0.9427 (ttp) cc_final: 0.9213 (tmm) REVERT: A 603 MET cc_start: 0.9433 (ttp) cc_final: 0.8938 (tmm) REVERT: B 57 ASP cc_start: 0.9102 (m-30) cc_final: 0.8649 (m-30) REVERT: B 130 MET cc_start: 0.8055 (mmm) cc_final: 0.7819 (mmm) REVERT: B 168 SER cc_start: 0.9733 (m) cc_final: 0.9502 (p) REVERT: B 241 LEU cc_start: 0.9256 (mt) cc_final: 0.9051 (mp) REVERT: B 255 MET cc_start: 0.9808 (mmp) cc_final: 0.9316 (mmm) REVERT: B 260 MET cc_start: 0.9437 (tpp) cc_final: 0.9138 (tpp) REVERT: B 282 GLU cc_start: 0.8879 (mp0) cc_final: 0.8481 (mp0) REVERT: B 294 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8680 (pt0) REVERT: B 345 MET cc_start: 0.8814 (mmm) cc_final: 0.8439 (tmm) REVERT: B 386 LEU cc_start: 0.9733 (tp) cc_final: 0.9355 (mm) REVERT: B 408 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: B 464 ASN cc_start: 0.9234 (t0) cc_final: 0.8976 (t0) REVERT: B 474 MET cc_start: 0.9184 (ptm) cc_final: 0.8661 (ttp) REVERT: B 489 ASP cc_start: 0.7608 (t0) cc_final: 0.7269 (t70) REVERT: B 515 GLU cc_start: 0.8996 (tp30) cc_final: 0.8174 (mp0) REVERT: B 528 MET cc_start: 0.8665 (tpp) cc_final: 0.8280 (mmt) REVERT: B 577 MET cc_start: 0.8946 (tmm) cc_final: 0.8521 (tmm) REVERT: B 584 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8734 (mmt90) REVERT: B 641 ARG cc_start: 0.9277 (mtt180) cc_final: 0.8757 (tpt170) REVERT: C 99 MET cc_start: 0.9696 (mmt) cc_final: 0.9292 (mmm) REVERT: C 114 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8655 (tp) REVERT: C 284 ASP cc_start: 0.8828 (t70) cc_final: 0.8522 (t70) REVERT: C 306 GLN cc_start: 0.9476 (tp-100) cc_final: 0.9005 (tp40) REVERT: C 331 MET cc_start: 0.8646 (mmt) cc_final: 0.8426 (mmp) REVERT: C 345 MET cc_start: 0.8608 (mmt) cc_final: 0.8349 (tpp) REVERT: C 410 MET cc_start: 0.8367 (mtp) cc_final: 0.7680 (ttp) REVERT: C 426 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5566 (t-90) REVERT: C 432 TYR cc_start: 0.8485 (t80) cc_final: 0.8204 (t80) REVERT: C 454 MET cc_start: 0.9444 (tpt) cc_final: 0.9096 (tpt) REVERT: C 489 ASP cc_start: 0.8700 (m-30) cc_final: 0.8178 (m-30) REVERT: C 491 MET cc_start: 0.8493 (ttt) cc_final: 0.7992 (tmm) REVERT: C 515 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8371 (mm-30) REVERT: C 542 ASP cc_start: 0.7605 (t70) cc_final: 0.7404 (t0) REVERT: C 577 MET cc_start: 0.9005 (tmm) cc_final: 0.8157 (tmm) REVERT: C 603 MET cc_start: 0.9243 (ttp) cc_final: 0.8807 (tmm) REVERT: D 35 GLU cc_start: 0.9562 (tt0) cc_final: 0.9160 (mp0) REVERT: D 61 LEU cc_start: 0.9558 (mt) cc_final: 0.9323 (mt) REVERT: D 78 MET cc_start: 0.8759 (pmm) cc_final: 0.8493 (pmm) REVERT: D 85 ILE cc_start: 0.9790 (mm) cc_final: 0.9525 (tp) REVERT: D 99 MET cc_start: 0.9502 (mmt) cc_final: 0.9102 (mmm) REVERT: D 181 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9490 (tm) REVERT: D 345 MET cc_start: 0.9006 (tpp) cc_final: 0.8255 (tmm) REVERT: D 363 ARG cc_start: 0.8959 (tpp80) cc_final: 0.8622 (mmp80) REVERT: D 371 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9172 (ttpp) REVERT: D 378 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8424 (pmm) REVERT: D 410 MET cc_start: 0.8771 (mmp) cc_final: 0.8385 (mtt) REVERT: D 497 MET cc_start: 0.9354 (ttp) cc_final: 0.8686 (tmm) REVERT: D 535 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8738 (mt-10) REVERT: D 603 MET cc_start: 0.9318 (ttp) cc_final: 0.8658 (tmm) REVERT: D 608 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9362 (tt) REVERT: E 8 GLN cc_start: 0.8941 (mt0) cc_final: 0.8689 (mt0) REVERT: E 36 MET cc_start: 0.9150 (ttt) cc_final: 0.8768 (tpp) REVERT: E 51 MET cc_start: 0.8109 (mmt) cc_final: 0.7898 (tpt) REVERT: E 71 MET cc_start: 0.9454 (ttt) cc_final: 0.9120 (tmm) REVERT: E 112 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6269 (mm) REVERT: E 148 LYS cc_start: 0.6711 (pmtt) cc_final: 0.5786 (mmtm) outliers start: 48 outliers final: 32 residues processed: 332 average time/residue: 0.3079 time to fit residues: 163.4355 Evaluate side-chains 325 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 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 444 LEU 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 215 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 572 ASN Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 479 THR 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 105 LEU Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 176 optimal weight: 0.0570 chunk 242 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 1 optimal weight: 0.0060 chunk 34 optimal weight: 0.0000 chunk 77 optimal weight: 0.3980 overall best weight: 0.2318 ------------------------------------------------------------------------------- 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 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3172 r_free = 0.3172 target = 0.071443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.054883 restraints weight = 82997.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.056848 restraints weight = 45105.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.058184 restraints weight = 30027.814| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5479 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= 0.121 Angle : 0.825 16.646 29370 Z= 0.380 Chirality : 0.041 0.182 3323 Planarity : 0.003 0.035 3736 Dihedral : 5.029 38.425 2898 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.10 % Allowed : 20.22 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2628 helix: 1.35 (0.14), residues: 1459 sheet: -2.71 (0.57), residues: 76 loop : -2.25 (0.20), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 613 HIS 0.009 0.001 HIS E 107 PHE 0.026 0.001 PHE B 472 TYR 0.020 0.001 TYR C 324 ARG 0.009 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 848) hydrogen bonds : angle 3.64236 ( 2439) covalent geometry : bond 0.00263 (21666) covalent geometry : angle 0.82536 (29370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6722.45 seconds wall clock time: 118 minutes 55.85 seconds (7135.85 seconds total)