Starting phenix.real_space_refine on Sun Sep 29 03:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2f_8961/09_2024/6e2f_8961.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2f_8961/09_2024/6e2f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2f_8961/09_2024/6e2f_8961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2f_8961/09_2024/6e2f_8961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2f_8961/09_2024/6e2f_8961.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2f_8961/09_2024/6e2f_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-5461/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: 12.26, per 1000 atoms: 0.58 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: 5.17 Conformation dependent library (CDL) restraints added in 2.8 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: 2.53 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: 5.77 Time building geometry restraints manager: 5.96 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: 0.770 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: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 45.500 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.260 ------------------------------------------------------------------------------- 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= 0.625 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 *********************** 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 fitting. rotamer outliers: 32 poor density : 461 time to evaluate : 2.274 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: 0.3379 time to fit residues: 254.1707 Evaluate side-chains 303 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 293 time to evaluate : 2.370 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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= 0.226 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 *********************** 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 fitting. rotamer outliers: 86 poor density : 374 time to evaluate : 2.609 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: 0.9624 (mt) cc_final: 0.9286 (pp) REVERT: A 128 GLN cc_start: 0.9214 (tt0) cc_final: 0.7855 (tm-30) REVERT: A 209 LYS cc_start: 0.9161 (mttp) cc_final: 0.8919 (mmtt) REVERT: A 315 GLU cc_start: 0.8785 (mp0) cc_final: 0.8470 (mp0) REVERT: A 414 ARG cc_start: 0.9093 (tpp80) cc_final: 0.8634 (tpt90) REVERT: A 435 MET cc_start: 0.9496 (mmm) cc_final: 0.9284 (mmm) REVERT: A 437 LEU cc_start: 0.9526 (mp) cc_final: 0.8872 (mm) REVERT: A 440 MET cc_start: 0.8940 (tmm) cc_final: 0.8633 (ppp) REVERT: A 474 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8918 (ppp) REVERT: A 485 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8940 (ttm) REVERT: A 489 ASP cc_start: 0.8654 (m-30) cc_final: 0.8397 (t70) REVERT: A 515 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8542 (tp30) REVERT: A 528 MET cc_start: 0.9375 (tpt) cc_final: 0.8858 (tpp) REVERT: A 542 ASP cc_start: 0.7161 (t0) cc_final: 0.6852 (m-30) REVERT: A 557 ILE cc_start: 0.9714 (mt) cc_final: 0.9413 (tp) REVERT: A 577 MET cc_start: 0.9365 (tmt) cc_final: 0.8618 (tmm) REVERT: A 578 MET cc_start: 0.9521 (OUTLIER) cc_final: 0.9266 (tpp) REVERT: A 603 MET cc_start: 0.9445 (ttp) cc_final: 0.8881 (tmm) REVERT: B 38 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9442 (tp) REVERT: B 57 ASP cc_start: 0.9182 (m-30) cc_final: 0.8697 (m-30) REVERT: B 110 MET cc_start: 0.8803 (mtm) cc_final: 0.8585 (mtm) REVERT: B 168 SER cc_start: 0.9785 (m) cc_final: 0.9499 (p) REVERT: B 260 MET cc_start: 0.9634 (tpp) cc_final: 0.9168 (tpp) REVERT: B 345 MET cc_start: 0.8975 (mmm) cc_final: 0.8620 (tmm) REVERT: B 464 ASN cc_start: 0.9370 (OUTLIER) cc_final: 0.8749 (t0) REVERT: B 489 ASP cc_start: 0.8507 (t0) cc_final: 0.8042 (t0) REVERT: B 542 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: B 591 GLU cc_start: 0.9196 (pt0) cc_final: 0.8706 (pm20) REVERT: B 637 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8480 (tm-30) REVERT: B 641 ARG cc_start: 0.9111 (mtt180) cc_final: 0.8815 (mmp80) REVERT: C 35 GLU cc_start: 0.9345 (tt0) cc_final: 0.9053 (pp20) REVERT: C 38 LEU cc_start: 0.9635 (mt) cc_final: 0.9270 (tt) REVERT: C 99 MET cc_start: 0.9528 (mmt) cc_final: 0.9098 (mmm) REVERT: C 110 MET cc_start: 0.8148 (mtp) cc_final: 0.7885 (mtm) REVERT: C 130 MET cc_start: 0.8189 (mmt) cc_final: 0.7923 (mmm) REVERT: C 284 ASP cc_start: 0.8883 (t70) cc_final: 0.8591 (t70) REVERT: C 315 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8800 (mp0) REVERT: C 410 MET cc_start: 0.7973 (mtp) cc_final: 0.7402 (ttp) REVERT: C 434 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.9120 (t80) REVERT: C 489 ASP cc_start: 0.8966 (m-30) cc_final: 0.8580 (m-30) REVERT: C 528 MET cc_start: 0.9336 (ttm) cc_final: 0.9047 (tpp) REVERT: C 532 SER cc_start: 0.9819 (t) cc_final: 0.9377 (p) REVERT: C 569 LEU cc_start: 0.9392 (tp) cc_final: 0.9173 (tt) REVERT: C 577 MET cc_start: 0.9343 (tmm) cc_final: 0.8314 (tmm) REVERT: C 591 GLU cc_start: 0.8890 (pt0) cc_final: 0.8615 (pm20) REVERT: C 603 MET cc_start: 0.9295 (ttp) cc_final: 0.8937 (tmm) REVERT: D 35 GLU cc_start: 0.9523 (tt0) cc_final: 0.9088 (mt-10) REVERT: D 61 LEU cc_start: 0.9615 (mt) cc_final: 0.9372 (mt) REVERT: D 85 ILE cc_start: 0.9846 (mm) cc_final: 0.9580 (tp) REVERT: D 99 MET cc_start: 0.9480 (mmt) cc_final: 0.8789 (mmm) REVERT: D 289 GLU cc_start: 0.8078 (mp0) cc_final: 0.7870 (pm20) REVERT: D 364 ASP cc_start: 0.9362 (m-30) cc_final: 0.8901 (m-30) REVERT: D 483 GLN cc_start: 0.8985 (tt0) cc_final: 0.8673 (tm-30) REVERT: D 491 MET cc_start: 0.9073 (tpt) cc_final: 0.8649 (tmm) REVERT: D 577 MET cc_start: 0.9181 (tmt) cc_final: 0.8653 (tmt) REVERT: D 588 GLU cc_start: 0.9305 (tt0) cc_final: 0.9098 (tt0) REVERT: D 603 MET cc_start: 0.9261 (ttp) cc_final: 0.8851 (tmm) REVERT: D 625 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9280 (tm) REVERT: E 8 GLN cc_start: 0.8946 (mt0) cc_final: 0.8683 (mt0) REVERT: E 14 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9283 (tm-30) REVERT: E 18 LEU cc_start: 0.9285 (tt) cc_final: 0.9070 (pp) REVERT: E 30 LYS cc_start: 0.9406 (ttmp) cc_final: 0.9179 (tttt) REVERT: E 36 MET cc_start: 0.9242 (ttt) cc_final: 0.8887 (tpp) REVERT: E 37 ARG cc_start: 0.9051 (ptt90) cc_final: 0.8785 (ptt-90) REVERT: E 49 GLN cc_start: 0.9093 (pt0) cc_final: 0.8792 (pm20) REVERT: E 71 MET cc_start: 0.9577 (ttt) cc_final: 0.9114 (ttt) REVERT: E 72 MET cc_start: 0.8799 (mmp) cc_final: 0.8189 (mmm) REVERT: E 116 LEU cc_start: 0.9096 (mt) cc_final: 0.8689 (tp) REVERT: E 143 GLN cc_start: 0.6752 (mt0) cc_final: 0.6277 (tm-30) REVERT: E 144 MET cc_start: 0.7861 (mmp) cc_final: 0.7172 (mtt) REVERT: E 148 LYS cc_start: 0.6829 (pmtt) cc_final: 0.5944 (mmtm) outliers start: 86 outliers final: 27 residues processed: 438 average time/residue: 0.2916 time to fit residues: 202.2177 Evaluate side-chains 312 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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 434 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 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 131 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 190 optimal weight: 5.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- 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 464 ASN A 572 ASN B 73 HIS B 217 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 HIS D 37 ASN D 91 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21666 Z= 0.316 Angle : 0.847 14.069 29370 Z= 0.422 Chirality : 0.044 0.223 3323 Planarity : 0.004 0.036 3736 Dihedral : 6.513 59.185 2912 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.82 % Favored : 90.03 % Rotamer: Outliers : 4.32 % Allowed : 14.24 % Favored : 81.44 % 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: -1.80 (0.16), residues: 2628 helix: 0.07 (0.13), residues: 1444 sheet: -3.84 (0.40), residues: 84 loop : -2.75 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 613 HIS 0.010 0.001 HIS A 582 PHE 0.027 0.002 PHE E 68 TYR 0.016 0.002 TYR C 324 ARG 0.008 0.001 ARG A 302 *********************** 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 387 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 288 time to evaluate : 2.370 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: 0.9631 (mt) cc_final: 0.9306 (pp) REVERT: A 128 GLN cc_start: 0.9197 (tt0) cc_final: 0.7800 (tm-30) REVERT: A 209 LYS cc_start: 0.9169 (mttp) cc_final: 0.8870 (mmtt) REVERT: A 311 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 315 GLU cc_start: 0.8965 (mp0) cc_final: 0.8677 (mp0) REVERT: A 410 MET cc_start: 0.8246 (mpp) cc_final: 0.7857 (mpp) REVERT: A 414 ARG cc_start: 0.9071 (tpp80) cc_final: 0.8591 (tpt90) REVERT: A 435 MET cc_start: 0.9507 (mmm) cc_final: 0.9302 (mmp) REVERT: A 437 LEU cc_start: 0.9592 (mp) cc_final: 0.8931 (mm) REVERT: A 440 MET cc_start: 0.9064 (tmm) cc_final: 0.8813 (ppp) REVERT: A 454 MET cc_start: 0.9528 (mmm) cc_final: 0.9242 (mmm) REVERT: A 474 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8927 (ppp) REVERT: A 485 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8851 (ttm) REVERT: A 515 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8107 (mp0) REVERT: A 528 MET cc_start: 0.9305 (tpt) cc_final: 0.8860 (tpp) REVERT: A 535 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8783 (tt0) REVERT: A 554 MET cc_start: 0.8879 (tpp) cc_final: 0.8597 (tpp) REVERT: A 557 ILE cc_start: 0.9763 (mt) cc_final: 0.9506 (tp) REVERT: A 603 MET cc_start: 0.9463 (ttp) cc_final: 0.8885 (tmm) REVERT: B 38 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9477 (tp) REVERT: B 57 ASP cc_start: 0.9197 (m-30) cc_final: 0.8699 (m-30) REVERT: B 110 MET cc_start: 0.8681 (mtm) cc_final: 0.8469 (mtm) REVERT: B 130 MET cc_start: 0.8549 (mmm) cc_final: 0.8042 (mmm) REVERT: B 168 SER cc_start: 0.9827 (m) cc_final: 0.9576 (p) REVERT: B 302 ARG cc_start: 0.8229 (tpt170) cc_final: 0.7938 (tpp-160) REVERT: B 345 MET cc_start: 0.9056 (mmm) cc_final: 0.8681 (tmm) REVERT: B 377 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7923 (m-10) REVERT: B 489 ASP cc_start: 0.8273 (t0) cc_final: 0.7004 (t0) REVERT: B 528 MET cc_start: 0.9185 (tpp) cc_final: 0.8805 (tpp) REVERT: B 542 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: B 577 MET cc_start: 0.9179 (tmt) cc_final: 0.8446 (tmt) REVERT: B 591 GLU cc_start: 0.9176 (pt0) cc_final: 0.8792 (pm20) REVERT: B 637 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8409 (tm-30) REVERT: B 641 ARG cc_start: 0.9172 (mtt180) cc_final: 0.8868 (mmp80) REVERT: C 38 LEU cc_start: 0.9689 (mt) cc_final: 0.9349 (tt) REVERT: C 99 MET cc_start: 0.9560 (mmt) cc_final: 0.9147 (mmm) REVERT: C 284 ASP cc_start: 0.8886 (t70) cc_final: 0.8588 (t0) REVERT: C 315 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8865 (mp0) REVERT: C 410 MET cc_start: 0.8381 (mtp) cc_final: 0.7875 (ttp) REVERT: C 432 TYR cc_start: 0.8932 (t80) cc_final: 0.8683 (t80) REVERT: C 489 ASP cc_start: 0.8960 (m-30) cc_final: 0.8174 (m-30) REVERT: C 528 MET cc_start: 0.9351 (ttm) cc_final: 0.9050 (tpp) REVERT: C 577 MET cc_start: 0.9292 (tmm) cc_final: 0.8137 (tmm) REVERT: C 591 GLU cc_start: 0.8852 (pt0) cc_final: 0.8638 (pm20) REVERT: C 603 MET cc_start: 0.9377 (ttp) cc_final: 0.8920 (tmm) REVERT: D 35 GLU cc_start: 0.9570 (tt0) cc_final: 0.9189 (mt-10) REVERT: D 61 LEU cc_start: 0.9586 (mt) cc_final: 0.9352 (mt) REVERT: D 85 ILE cc_start: 0.9864 (mm) cc_final: 0.9641 (tp) REVERT: D 99 MET cc_start: 0.9473 (mmt) cc_final: 0.8978 (mmm) REVERT: D 345 MET cc_start: 0.9228 (mmm) cc_final: 0.8233 (tmm) REVERT: D 363 ARG cc_start: 0.8644 (tpp80) cc_final: 0.8108 (tpp80) REVERT: D 364 ASP cc_start: 0.9248 (m-30) cc_final: 0.8915 (m-30) REVERT: D 378 MET cc_start: 0.8838 (pmm) cc_final: 0.8576 (pmm) REVERT: D 491 MET cc_start: 0.9092 (tpt) cc_final: 0.8546 (tmm) REVERT: D 577 MET cc_start: 0.9206 (tmt) cc_final: 0.8957 (tmm) REVERT: D 603 MET cc_start: 0.9367 (ttp) cc_final: 0.8873 (tmm) REVERT: D 625 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9335 (tm) REVERT: E 8 GLN cc_start: 0.9030 (mt0) cc_final: 0.8804 (mt0) REVERT: E 14 GLU cc_start: 0.9595 (mm-30) cc_final: 0.9354 (tm-30) REVERT: E 30 LYS cc_start: 0.9467 (ttmp) cc_final: 0.9244 (tttt) REVERT: E 36 MET cc_start: 0.9269 (ttt) cc_final: 0.8844 (tpp) REVERT: E 69 LEU cc_start: 0.9749 (mt) cc_final: 0.9541 (mt) REVERT: E 71 MET cc_start: 0.9570 (ttt) cc_final: 0.9231 (ttt) REVERT: E 72 MET cc_start: 0.8771 (mmp) cc_final: 0.8363 (mmm) REVERT: E 143 GLN cc_start: 0.6460 (mt0) cc_final: 0.5975 (tm-30) REVERT: E 144 MET cc_start: 0.7722 (mmp) cc_final: 0.7506 (tpp) REVERT: E 145 MET cc_start: 0.8292 (mmm) cc_final: 0.7968 (mmm) REVERT: E 148 LYS cc_start: 0.6793 (pmtt) cc_final: 0.5834 (mmtm) outliers start: 99 outliers final: 45 residues processed: 365 average time/residue: 0.2961 time to fit residues: 170.5948 Evaluate side-chains 321 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 268 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain A residue 631 LEU 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 133 VAL 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 377 TYR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 455 SER 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 342 CYS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 575 ILE 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 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 234 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 225 optimal weight: 0.0570 chunk 67 optimal weight: 3.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 208 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 165 HIS C 230 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3931 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= 0.183 Angle : 0.774 15.220 29370 Z= 0.375 Chirality : 0.042 0.203 3323 Planarity : 0.004 0.094 3736 Dihedral : 6.003 55.021 2904 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.36 % Favored : 90.49 % Rotamer: Outliers : 3.80 % Allowed : 15.94 % Favored : 80.26 % 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: -1.23 (0.17), residues: 2628 helix: 0.63 (0.14), residues: 1448 sheet: -3.94 (0.42), residues: 76 loop : -2.66 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 613 HIS 0.006 0.001 HIS A 582 PHE 0.020 0.001 PHE A 493 TYR 0.024 0.001 TYR C 324 ARG 0.004 0.000 ARG C 323 *********************** 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 396 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 309 time to evaluate : 2.643 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: 0.9609 (mt) cc_final: 0.9289 (pp) REVERT: A 96 MET cc_start: 0.9192 (mpp) cc_final: 0.8976 (mpp) REVERT: A 128 GLN cc_start: 0.9043 (tt0) cc_final: 0.7780 (tm-30) REVERT: A 209 LYS cc_start: 0.9099 (mttp) cc_final: 0.8830 (mmtt) REVERT: A 215 MET cc_start: 0.9017 (ttm) cc_final: 0.8731 (ttm) REVERT: A 311 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8300 (p) REVERT: A 315 GLU cc_start: 0.9039 (mp0) cc_final: 0.8695 (mp0) REVERT: A 410 MET cc_start: 0.8262 (mpp) cc_final: 0.7955 (mpp) REVERT: A 414 ARG cc_start: 0.9067 (tpp80) cc_final: 0.8621 (tpt90) REVERT: A 437 LEU cc_start: 0.9573 (mp) cc_final: 0.8914 (mm) REVERT: A 440 MET cc_start: 0.9073 (tmm) cc_final: 0.8809 (ppp) REVERT: A 528 MET cc_start: 0.9266 (tpt) cc_final: 0.8838 (tpp) REVERT: A 535 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8783 (tt0) REVERT: A 557 ILE cc_start: 0.9727 (mt) cc_final: 0.9449 (tp) REVERT: A 570 MET cc_start: 0.9164 (mmm) cc_final: 0.8828 (mmm) REVERT: A 577 MET cc_start: 0.9311 (tmt) cc_final: 0.9041 (tmm) REVERT: A 603 MET cc_start: 0.9437 (ttp) cc_final: 0.8889 (tmm) REVERT: A 604 LEU cc_start: 0.9655 (tt) cc_final: 0.9413 (tt) REVERT: B 57 ASP cc_start: 0.9144 (m-30) cc_final: 0.8658 (m-30) REVERT: B 130 MET cc_start: 0.8475 (mmm) cc_final: 0.8010 (mmm) REVERT: B 168 SER cc_start: 0.9794 (m) cc_final: 0.9532 (p) REVERT: B 260 MET cc_start: 0.9507 (tpp) cc_final: 0.9220 (tpp) REVERT: B 345 MET cc_start: 0.8984 (mmm) cc_final: 0.8565 (tmm) REVERT: B 386 LEU cc_start: 0.9769 (tp) cc_final: 0.9451 (mm) REVERT: B 408 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: B 440 MET cc_start: 0.9310 (tpp) cc_final: 0.9016 (tpp) REVERT: B 464 ASN cc_start: 0.9371 (OUTLIER) cc_final: 0.8786 (t0) REVERT: B 489 ASP cc_start: 0.8508 (t0) cc_final: 0.7315 (t0) REVERT: B 528 MET cc_start: 0.9154 (tpp) cc_final: 0.8706 (tpp) REVERT: B 577 MET cc_start: 0.9143 (tmt) cc_final: 0.8533 (tmt) REVERT: B 637 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8454 (tm-30) REVERT: B 641 ARG cc_start: 0.9177 (mtt180) cc_final: 0.8872 (mmp80) REVERT: C 38 LEU cc_start: 0.9681 (mt) cc_final: 0.9288 (tt) REVERT: C 90 ASP cc_start: 0.8836 (t0) cc_final: 0.8634 (p0) REVERT: C 99 MET cc_start: 0.9588 (mmt) cc_final: 0.9193 (mmm) REVERT: C 284 ASP cc_start: 0.8909 (t70) cc_final: 0.8624 (t0) REVERT: C 410 MET cc_start: 0.8400 (mtp) cc_final: 0.7648 (ttp) REVERT: C 432 TYR cc_start: 0.8789 (t80) cc_final: 0.8544 (t80) REVERT: C 454 MET cc_start: 0.9572 (mmm) cc_final: 0.9156 (tpp) REVERT: C 485 MET cc_start: 0.9083 (ttm) cc_final: 0.8862 (ttm) REVERT: C 489 ASP cc_start: 0.8879 (m-30) cc_final: 0.8322 (m-30) REVERT: C 515 GLU cc_start: 0.8840 (mm-30) cc_final: 0.7944 (mp0) REVERT: C 554 MET cc_start: 0.9096 (tpp) cc_final: 0.8751 (tpp) REVERT: C 577 MET cc_start: 0.9302 (tmm) cc_final: 0.8325 (tmm) REVERT: C 603 MET cc_start: 0.9323 (ttp) cc_final: 0.8910 (tmm) REVERT: D 35 GLU cc_start: 0.9558 (tt0) cc_final: 0.9220 (mt-10) REVERT: D 61 LEU cc_start: 0.9554 (mt) cc_final: 0.9325 (mt) REVERT: D 85 ILE cc_start: 0.9854 (mm) cc_final: 0.9576 (tp) REVERT: D 345 MET cc_start: 0.9204 (mmm) cc_final: 0.8571 (tmm) REVERT: D 363 ARG cc_start: 0.8631 (tpp80) cc_final: 0.8110 (tpp80) REVERT: D 364 ASP cc_start: 0.9207 (m-30) cc_final: 0.8859 (m-30) REVERT: D 371 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8989 (ttpp) REVERT: D 378 MET cc_start: 0.8770 (pmm) cc_final: 0.8477 (pmm) REVERT: D 491 MET cc_start: 0.9001 (tpt) cc_final: 0.8518 (tmm) REVERT: D 603 MET cc_start: 0.9351 (ttp) cc_final: 0.8908 (tmm) REVERT: D 625 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9346 (tm) REVERT: E 8 GLN cc_start: 0.9038 (mt0) cc_final: 0.8796 (mt0) REVERT: E 14 GLU cc_start: 0.9633 (mm-30) cc_final: 0.9314 (tm-30) REVERT: E 30 LYS cc_start: 0.9443 (ttmp) cc_final: 0.9185 (tttt) REVERT: E 36 MET cc_start: 0.9258 (ttt) cc_final: 0.8879 (tpp) REVERT: E 37 ARG cc_start: 0.9016 (ptt90) cc_final: 0.8813 (ptt-90) REVERT: E 69 LEU cc_start: 0.9752 (mt) cc_final: 0.9524 (mt) REVERT: E 148 LYS cc_start: 0.6773 (pmtt) cc_final: 0.5913 (mmtm) outliers start: 87 outliers final: 37 residues processed: 370 average time/residue: 0.2981 time to fit residues: 175.0745 Evaluate side-chains 312 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 270 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 133 VAL 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 408 PHE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 464 ASN 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 400 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 613 TRP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 chunk 174 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4230 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= 0.194 Angle : 0.779 15.559 29370 Z= 0.373 Chirality : 0.042 0.199 3323 Planarity : 0.003 0.038 3736 Dihedral : 5.829 55.197 2904 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.51 % Favored : 90.33 % Rotamer: Outliers : 3.32 % Allowed : 17.47 % Favored : 79.21 % 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: -0.90 (0.17), residues: 2628 helix: 0.91 (0.14), residues: 1460 sheet: -3.68 (0.46), residues: 76 loop : -2.56 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 613 HIS 0.008 0.001 HIS E 107 PHE 0.017 0.001 PHE B 472 TYR 0.013 0.001 TYR C 324 ARG 0.007 0.000 ARG C 323 *********************** 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 363 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 287 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9609 (mt) cc_final: 0.9291 (pp) REVERT: A 96 MET cc_start: 0.9191 (mpp) cc_final: 0.8909 (mpp) REVERT: A 128 GLN cc_start: 0.9008 (tt0) cc_final: 0.8083 (tm-30) REVERT: A 209 LYS cc_start: 0.9091 (mttp) cc_final: 0.8822 (mmtt) REVERT: A 215 MET cc_start: 0.8993 (ttm) cc_final: 0.8730 (ttm) REVERT: A 311 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8262 (p) REVERT: A 315 GLU cc_start: 0.9045 (mp0) cc_final: 0.8714 (mp0) REVERT: A 410 MET cc_start: 0.8246 (mpp) cc_final: 0.7928 (mpp) REVERT: A 414 ARG cc_start: 0.9070 (tpp80) cc_final: 0.8703 (tpt170) REVERT: A 434 PHE cc_start: 0.9103 (t80) cc_final: 0.8891 (t80) REVERT: A 437 LEU cc_start: 0.9596 (mp) cc_final: 0.8952 (mm) REVERT: A 440 MET cc_start: 0.9144 (tmm) cc_final: 0.8851 (ppp) REVERT: A 474 MET cc_start: 0.9085 (ppp) cc_final: 0.8588 (ppp) REVERT: A 485 MET cc_start: 0.9206 (ttm) cc_final: 0.8838 (ttm) REVERT: A 491 MET cc_start: 0.8931 (ttm) cc_final: 0.8539 (tmm) REVERT: A 528 MET cc_start: 0.9257 (tpt) cc_final: 0.8838 (tpp) REVERT: A 557 ILE cc_start: 0.9758 (mt) cc_final: 0.9501 (tp) REVERT: A 603 MET cc_start: 0.9437 (ttp) cc_final: 0.8912 (tmm) REVERT: B 57 ASP cc_start: 0.9167 (m-30) cc_final: 0.8684 (m-30) REVERT: B 168 SER cc_start: 0.9804 (m) cc_final: 0.9556 (p) REVERT: B 260 MET cc_start: 0.9503 (tpp) cc_final: 0.9188 (tpp) REVERT: B 294 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8746 (mt-10) REVERT: B 302 ARG cc_start: 0.8479 (tpp-160) cc_final: 0.8168 (tpp-160) REVERT: B 345 MET cc_start: 0.8905 (mmm) cc_final: 0.8584 (tmm) REVERT: B 389 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: B 408 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: B 464 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.8819 (t0) REVERT: B 489 ASP cc_start: 0.8503 (t0) cc_final: 0.7391 (t0) REVERT: B 528 MET cc_start: 0.9104 (tpp) cc_final: 0.8638 (tpp) REVERT: B 577 MET cc_start: 0.9157 (tmt) cc_final: 0.8514 (tmt) REVERT: B 637 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8511 (tm-30) REVERT: B 641 ARG cc_start: 0.9182 (mtt180) cc_final: 0.8729 (tpt170) REVERT: C 38 LEU cc_start: 0.9671 (mt) cc_final: 0.9281 (tt) REVERT: C 99 MET cc_start: 0.9596 (mmt) cc_final: 0.9198 (mmm) REVERT: C 114 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8502 (tp) REVERT: C 284 ASP cc_start: 0.8901 (t70) cc_final: 0.8634 (t0) REVERT: C 345 MET cc_start: 0.8727 (mmt) cc_final: 0.8384 (tpp) REVERT: C 410 MET cc_start: 0.8375 (mtp) cc_final: 0.7577 (ttp) REVERT: C 432 TYR cc_start: 0.8784 (t80) cc_final: 0.8384 (t80) REVERT: C 454 MET cc_start: 0.9568 (mmm) cc_final: 0.9205 (tpt) REVERT: C 489 ASP cc_start: 0.8874 (m-30) cc_final: 0.7844 (m-30) REVERT: C 492 ARG cc_start: 0.9084 (ptt180) cc_final: 0.7829 (ptp90) REVERT: C 515 GLU cc_start: 0.8774 (mm-30) cc_final: 0.7882 (mp0) REVERT: C 577 MET cc_start: 0.9269 (tmm) cc_final: 0.8049 (tmm) REVERT: C 603 MET cc_start: 0.9305 (ttp) cc_final: 0.8876 (tmm) REVERT: D 35 GLU cc_start: 0.9555 (tt0) cc_final: 0.9196 (mt-10) REVERT: D 61 LEU cc_start: 0.9555 (mt) cc_final: 0.9333 (mt) REVERT: D 85 ILE cc_start: 0.9849 (mm) cc_final: 0.9579 (tp) REVERT: D 99 MET cc_start: 0.9444 (mmt) cc_final: 0.8844 (mmm) REVERT: D 345 MET cc_start: 0.9188 (mmm) cc_final: 0.8251 (tmm) REVERT: D 363 ARG cc_start: 0.8705 (tpp80) cc_final: 0.8184 (tpp80) REVERT: D 364 ASP cc_start: 0.9233 (m-30) cc_final: 0.8866 (m-30) REVERT: D 371 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9155 (ttpp) REVERT: D 378 MET cc_start: 0.8767 (pmm) cc_final: 0.8458 (pmm) REVERT: D 442 MET cc_start: 0.9258 (tpp) cc_final: 0.8930 (ttm) REVERT: D 491 MET cc_start: 0.8985 (tpt) cc_final: 0.8559 (tmm) REVERT: D 492 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (ptt180) REVERT: D 497 MET cc_start: 0.9333 (ttp) cc_final: 0.8732 (tmm) REVERT: D 603 MET cc_start: 0.9363 (ttp) cc_final: 0.8902 (tmm) REVERT: D 625 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9308 (tm) REVERT: E 8 GLN cc_start: 0.9015 (mt0) cc_final: 0.8775 (mt0) REVERT: E 14 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9315 (tm-30) REVERT: E 30 LYS cc_start: 0.9461 (ttmp) cc_final: 0.9224 (tttt) REVERT: E 36 MET cc_start: 0.9260 (ttt) cc_final: 0.8856 (tpp) REVERT: E 37 ARG cc_start: 0.9009 (ptt90) cc_final: 0.8731 (ptt90) REVERT: E 51 MET cc_start: 0.8329 (mmt) cc_final: 0.7958 (tpp) REVERT: E 68 PHE cc_start: 0.9003 (t80) cc_final: 0.8693 (t80) REVERT: E 69 LEU cc_start: 0.9759 (mt) cc_final: 0.9532 (mt) REVERT: E 71 MET cc_start: 0.9296 (ttt) cc_final: 0.8894 (ppp) REVERT: E 106 ARG cc_start: 0.8772 (mmp80) cc_final: 0.8535 (mmp80) REVERT: E 148 LYS cc_start: 0.6762 (pmtt) cc_final: 0.5833 (mmtm) outliers start: 76 outliers final: 40 residues processed: 344 average time/residue: 0.3044 time to fit residues: 164.6396 Evaluate side-chains 314 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 266 time to evaluate : 2.396 ------------------------------------------------------------------------------- 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 377 TYR 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 551 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 189 ILE Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 389 GLU 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 464 ASN 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 372 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 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 112 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 84 optimal weight: 0.0060 chunk 227 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 252 optimal weight: 20.0000 chunk 209 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 overall best weight: 0.5974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS E 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21666 Z= 0.165 Angle : 0.770 15.236 29370 Z= 0.364 Chirality : 0.041 0.297 3323 Planarity : 0.003 0.039 3736 Dihedral : 5.658 52.170 2904 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.17 % Favored : 90.68 % Rotamer: Outliers : 2.71 % Allowed : 17.64 % Favored : 79.65 % 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: -0.62 (0.17), residues: 2628 helix: 1.13 (0.14), residues: 1449 sheet: -3.41 (0.49), residues: 76 loop : -2.41 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 495 HIS 0.004 0.001 HIS D 582 PHE 0.019 0.001 PHE B 472 TYR 0.033 0.001 TYR A 324 ARG 0.005 0.000 ARG E 106 *********************** 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 382 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 320 time to evaluate : 2.362 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: 0.9600 (mt) cc_final: 0.9281 (pp) REVERT: A 96 MET cc_start: 0.9254 (mpp) cc_final: 0.8951 (mpp) REVERT: A 128 GLN cc_start: 0.8929 (tt0) cc_final: 0.8009 (tm-30) REVERT: A 209 LYS cc_start: 0.9025 (mttp) cc_final: 0.8760 (mmtt) REVERT: A 215 MET cc_start: 0.8947 (ttm) cc_final: 0.8724 (ttm) REVERT: A 311 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8204 (p) REVERT: A 315 GLU cc_start: 0.9033 (mp0) cc_final: 0.8695 (mp0) REVERT: A 410 MET cc_start: 0.8232 (mpp) cc_final: 0.7947 (mpp) REVERT: A 414 ARG cc_start: 0.9066 (tpp80) cc_final: 0.8629 (tpt90) REVERT: A 434 PHE cc_start: 0.9062 (t80) cc_final: 0.8860 (t80) REVERT: A 437 LEU cc_start: 0.9583 (mp) cc_final: 0.8954 (mt) REVERT: A 440 MET cc_start: 0.9170 (tmm) cc_final: 0.8959 (ppp) REVERT: A 474 MET cc_start: 0.8920 (ppp) cc_final: 0.8674 (ppp) REVERT: A 489 ASP cc_start: 0.8447 (t0) cc_final: 0.7990 (t70) REVERT: A 491 MET cc_start: 0.8823 (ttm) cc_final: 0.8417 (tmm) REVERT: A 528 MET cc_start: 0.9228 (tpt) cc_final: 0.8799 (tpp) REVERT: A 554 MET cc_start: 0.8384 (tpp) cc_final: 0.7941 (tpp) REVERT: A 557 ILE cc_start: 0.9651 (mt) cc_final: 0.9392 (tp) REVERT: A 577 MET cc_start: 0.9215 (tmm) cc_final: 0.8978 (tmm) REVERT: A 603 MET cc_start: 0.9432 (ttp) cc_final: 0.8922 (tmm) REVERT: B 57 ASP cc_start: 0.9144 (m-30) cc_final: 0.8699 (m-30) REVERT: B 130 MET cc_start: 0.8377 (mmm) cc_final: 0.8017 (mmm) REVERT: B 168 SER cc_start: 0.9773 (m) cc_final: 0.9533 (p) REVERT: B 193 ASP cc_start: 0.9319 (p0) cc_final: 0.9072 (p0) REVERT: B 260 MET cc_start: 0.9472 (tpp) cc_final: 0.9172 (tpp) REVERT: B 294 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8584 (pt0) REVERT: B 345 MET cc_start: 0.8873 (mmm) cc_final: 0.8527 (tmm) REVERT: B 386 LEU cc_start: 0.9739 (tp) cc_final: 0.9375 (mm) REVERT: B 390 LEU cc_start: 0.9730 (OUTLIER) cc_final: 0.9497 (mm) REVERT: B 408 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: B 464 ASN cc_start: 0.9324 (OUTLIER) cc_final: 0.8855 (t0) REVERT: B 474 MET cc_start: 0.9096 (ptm) cc_final: 0.8516 (ttp) REVERT: B 485 MET cc_start: 0.9591 (tpp) cc_final: 0.8317 (tpp) REVERT: B 489 ASP cc_start: 0.8450 (t0) cc_final: 0.7846 (t0) REVERT: B 515 GLU cc_start: 0.8621 (tp30) cc_final: 0.8124 (mp0) REVERT: B 578 MET cc_start: 0.9308 (ttm) cc_final: 0.9033 (mmm) REVERT: B 584 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8873 (mmt90) REVERT: B 641 ARG cc_start: 0.9205 (mtt180) cc_final: 0.8722 (tpt170) REVERT: C 38 LEU cc_start: 0.9641 (mt) cc_final: 0.9309 (tp) REVERT: C 90 ASP cc_start: 0.8827 (t0) cc_final: 0.8579 (p0) REVERT: C 99 MET cc_start: 0.9617 (mmt) cc_final: 0.9225 (mmm) REVERT: C 114 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8594 (tp) REVERT: C 284 ASP cc_start: 0.8890 (t70) cc_final: 0.8623 (t0) REVERT: C 345 MET cc_start: 0.8654 (mmt) cc_final: 0.8369 (tpp) REVERT: C 400 LEU cc_start: 0.9365 (mt) cc_final: 0.8926 (pp) REVERT: C 410 MET cc_start: 0.8353 (mtp) cc_final: 0.7556 (ttp) REVERT: C 432 TYR cc_start: 0.8657 (t80) cc_final: 0.8291 (t80) REVERT: C 454 MET cc_start: 0.9489 (mmm) cc_final: 0.9156 (tpp) REVERT: C 485 MET cc_start: 0.9529 (tpp) cc_final: 0.8662 (tpp) REVERT: C 489 ASP cc_start: 0.8740 (m-30) cc_final: 0.7603 (m-30) REVERT: C 491 MET cc_start: 0.8527 (ttt) cc_final: 0.8293 (tmm) REVERT: C 492 ARG cc_start: 0.9027 (ptt180) cc_final: 0.7796 (ptp90) REVERT: C 515 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8155 (mm-30) REVERT: C 577 MET cc_start: 0.9143 (tmm) cc_final: 0.7804 (tmm) REVERT: C 603 MET cc_start: 0.9241 (ttp) cc_final: 0.8833 (tmm) REVERT: C 608 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9226 (tt) REVERT: D 35 GLU cc_start: 0.9542 (tt0) cc_final: 0.9178 (mt-10) REVERT: D 37 ASN cc_start: 0.9438 (OUTLIER) cc_final: 0.9217 (t160) REVERT: D 61 LEU cc_start: 0.9555 (mt) cc_final: 0.9324 (mt) REVERT: D 85 ILE cc_start: 0.9828 (mm) cc_final: 0.9528 (tp) REVERT: D 99 MET cc_start: 0.9446 (mmt) cc_final: 0.9011 (mmm) REVERT: D 331 MET cc_start: 0.7770 (mmt) cc_final: 0.7418 (mmp) REVERT: D 345 MET cc_start: 0.9190 (mmm) cc_final: 0.8400 (tmm) REVERT: D 363 ARG cc_start: 0.8725 (tpp80) cc_final: 0.8300 (mmp80) REVERT: D 371 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9236 (ttpp) REVERT: D 378 MET cc_start: 0.8766 (pmm) cc_final: 0.8450 (pmm) REVERT: D 432 TYR cc_start: 0.9213 (t80) cc_final: 0.8879 (t80) REVERT: D 474 MET cc_start: 0.8458 (pmm) cc_final: 0.8152 (ppp) REVERT: D 491 MET cc_start: 0.8812 (tpt) cc_final: 0.8460 (tmm) REVERT: D 497 MET cc_start: 0.9341 (ttp) cc_final: 0.8785 (tmm) REVERT: D 535 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8734 (mt-10) REVERT: D 603 MET cc_start: 0.9326 (ttp) cc_final: 0.8880 (tmm) REVERT: D 608 LEU cc_start: 0.9630 (tt) cc_final: 0.9374 (tt) REVERT: E 8 GLN cc_start: 0.8960 (mt0) cc_final: 0.8725 (mt0) REVERT: E 14 GLU cc_start: 0.9602 (mm-30) cc_final: 0.9400 (tm-30) REVERT: E 30 LYS cc_start: 0.9489 (ttmp) cc_final: 0.9215 (tttt) REVERT: E 36 MET cc_start: 0.9234 (ttt) cc_final: 0.8898 (tpp) REVERT: E 37 ARG cc_start: 0.8954 (ptt90) cc_final: 0.8697 (ptt-90) REVERT: E 51 MET cc_start: 0.8420 (mmt) cc_final: 0.8033 (tpp) REVERT: E 71 MET cc_start: 0.9262 (ttt) cc_final: 0.8957 (tmm) REVERT: E 112 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6291 (mm) REVERT: E 145 MET cc_start: 0.7983 (mmm) cc_final: 0.7728 (mmm) REVERT: E 148 LYS cc_start: 0.6638 (pmtt) cc_final: 0.5716 (mmtm) outliers start: 62 outliers final: 33 residues processed: 365 average time/residue: 0.2968 time to fit residues: 171.6784 Evaluate side-chains 322 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 279 time to evaluate : 2.414 ------------------------------------------------------------------------------- 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 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 390 LEU 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 464 ASN Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 37 ASN 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 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 625 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 143 optimal weight: 0.0570 chunk 184 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN B 464 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4888 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= 0.162 Angle : 0.784 14.741 29370 Z= 0.369 Chirality : 0.041 0.188 3323 Planarity : 0.003 0.038 3736 Dihedral : 5.390 52.930 2900 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.28 % Favored : 90.60 % Rotamer: Outliers : 3.01 % Allowed : 18.43 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (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: -0.49 (0.17), residues: 2628 helix: 1.27 (0.14), residues: 1447 sheet: -3.19 (0.53), residues: 76 loop : -2.40 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 613 HIS 0.005 0.001 HIS B 426 PHE 0.018 0.001 PHE B 472 TYR 0.020 0.001 TYR A 324 ARG 0.005 0.000 ARG A 302 *********************** 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 375 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 306 time to evaluate : 2.461 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: 0.9593 (mt) cc_final: 0.9308 (pp) REVERT: A 96 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8972 (mpp) REVERT: A 114 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8957 (tp) REVERT: A 128 GLN cc_start: 0.9001 (tt0) cc_final: 0.8004 (tm-30) REVERT: A 209 LYS cc_start: 0.8955 (mttp) cc_final: 0.8689 (mmtt) REVERT: A 311 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 315 GLU cc_start: 0.9021 (mp0) cc_final: 0.8699 (mp0) REVERT: A 410 MET cc_start: 0.8250 (mpp) cc_final: 0.7953 (mpp) REVERT: A 414 ARG cc_start: 0.9038 (tpp80) cc_final: 0.8617 (tpt90) REVERT: A 437 LEU cc_start: 0.9610 (mp) cc_final: 0.8947 (mm) REVERT: A 440 MET cc_start: 0.9175 (tmm) cc_final: 0.8950 (ppp) REVERT: A 491 MET cc_start: 0.8833 (ttm) cc_final: 0.8365 (tmm) REVERT: A 515 GLU cc_start: 0.8847 (tp30) cc_final: 0.8428 (mp0) REVERT: A 528 MET cc_start: 0.9233 (tpt) cc_final: 0.8771 (tpp) REVERT: A 535 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8576 (tt0) REVERT: A 554 MET cc_start: 0.8318 (tpp) cc_final: 0.7876 (tpp) REVERT: A 557 ILE cc_start: 0.9640 (mt) cc_final: 0.9395 (tp) REVERT: A 603 MET cc_start: 0.9430 (ttp) cc_final: 0.8985 (tmm) REVERT: B 57 ASP cc_start: 0.9091 (m-30) cc_final: 0.8625 (m-30) REVERT: B 130 MET cc_start: 0.8408 (mmm) cc_final: 0.7998 (mmm) REVERT: B 168 SER cc_start: 0.9780 (m) cc_final: 0.9552 (p) REVERT: B 193 ASP cc_start: 0.9329 (p0) cc_final: 0.9094 (p0) REVERT: B 294 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8581 (pt0) REVERT: B 302 ARG cc_start: 0.8510 (tpp-160) cc_final: 0.8259 (tpp-160) REVERT: B 345 MET cc_start: 0.8846 (mmm) cc_final: 0.8502 (tmm) REVERT: B 386 LEU cc_start: 0.9724 (tp) cc_final: 0.9368 (mm) REVERT: B 390 LEU cc_start: 0.9732 (OUTLIER) cc_final: 0.9493 (mm) REVERT: B 408 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: B 464 ASN cc_start: 0.9193 (t0) cc_final: 0.8926 (t0) REVERT: B 474 MET cc_start: 0.9043 (ptm) cc_final: 0.8527 (ttp) REVERT: B 485 MET cc_start: 0.9561 (tpp) cc_final: 0.8273 (tpp) REVERT: B 489 ASP cc_start: 0.8485 (t0) cc_final: 0.7888 (t0) REVERT: B 515 GLU cc_start: 0.8654 (tp30) cc_final: 0.8299 (mp0) REVERT: B 578 MET cc_start: 0.9281 (ttm) cc_final: 0.9044 (mmm) REVERT: B 584 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8885 (mmt90) REVERT: B 641 ARG cc_start: 0.9230 (mtt180) cc_final: 0.8750 (tpt170) REVERT: C 67 TYR cc_start: 0.8454 (t80) cc_final: 0.8074 (t80) REVERT: C 90 ASP cc_start: 0.8830 (t0) cc_final: 0.8610 (p0) REVERT: C 99 MET cc_start: 0.9625 (mmt) cc_final: 0.9231 (mmm) REVERT: C 114 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8568 (tp) REVERT: C 284 ASP cc_start: 0.8852 (t70) cc_final: 0.8579 (t0) REVERT: C 306 GLN cc_start: 0.9453 (tp-100) cc_final: 0.8883 (tp40) REVERT: C 331 MET cc_start: 0.8621 (mmt) cc_final: 0.8410 (mmp) REVERT: C 345 MET cc_start: 0.8712 (mmt) cc_final: 0.8403 (tpp) REVERT: C 400 LEU cc_start: 0.9356 (mt) cc_final: 0.8884 (pp) REVERT: C 410 MET cc_start: 0.8339 (mtp) cc_final: 0.7564 (ttp) REVERT: C 432 TYR cc_start: 0.8594 (t80) cc_final: 0.8209 (t80) REVERT: C 489 ASP cc_start: 0.8683 (m-30) cc_final: 0.8129 (m-30) REVERT: C 491 MET cc_start: 0.8508 (ttt) cc_final: 0.8176 (tmm) REVERT: C 515 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8113 (mm-30) REVERT: C 542 ASP cc_start: 0.7775 (t70) cc_final: 0.7566 (t0) REVERT: C 577 MET cc_start: 0.9084 (tmm) cc_final: 0.8286 (tmm) REVERT: C 584 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8701 (tpp80) REVERT: C 603 MET cc_start: 0.9246 (ttp) cc_final: 0.8830 (tmm) REVERT: D 35 GLU cc_start: 0.9551 (tt0) cc_final: 0.9177 (mt-10) REVERT: D 61 LEU cc_start: 0.9553 (mt) cc_final: 0.9328 (mt) REVERT: D 85 ILE cc_start: 0.9811 (mm) cc_final: 0.9543 (tp) REVERT: D 99 MET cc_start: 0.9465 (mmt) cc_final: 0.9080 (mmm) REVERT: D 331 MET cc_start: 0.7713 (mmt) cc_final: 0.7388 (mmp) REVERT: D 345 MET cc_start: 0.9176 (mmm) cc_final: 0.8389 (tmm) REVERT: D 371 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9284 (ttpp) REVERT: D 378 MET cc_start: 0.8769 (pmm) cc_final: 0.8443 (pmm) REVERT: D 491 MET cc_start: 0.8751 (tpt) cc_final: 0.8439 (tmm) REVERT: D 497 MET cc_start: 0.9374 (ttp) cc_final: 0.8771 (tmm) REVERT: D 535 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8707 (mt-10) REVERT: D 577 MET cc_start: 0.9083 (tmm) cc_final: 0.8316 (tmm) REVERT: D 603 MET cc_start: 0.9332 (ttp) cc_final: 0.8890 (tmm) REVERT: D 608 LEU cc_start: 0.9608 (tt) cc_final: 0.9365 (tt) REVERT: E 8 GLN cc_start: 0.8806 (mt0) cc_final: 0.8606 (mt0) REVERT: E 36 MET cc_start: 0.9219 (ttt) cc_final: 0.8770 (tpp) REVERT: E 51 MET cc_start: 0.8446 (mmt) cc_final: 0.8082 (mmt) REVERT: E 71 MET cc_start: 0.9277 (ttt) cc_final: 0.9045 (tmm) REVERT: E 99 TYR cc_start: 0.6410 (m-80) cc_final: 0.6187 (m-80) REVERT: E 112 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6339 (mm) REVERT: E 145 MET cc_start: 0.7953 (mmm) cc_final: 0.7500 (mmm) REVERT: E 148 LYS cc_start: 0.6523 (pmtt) cc_final: 0.5567 (mmtm) outliers start: 69 outliers final: 39 residues processed: 355 average time/residue: 0.2981 time to fit residues: 166.9910 Evaluate side-chains 335 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 286 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 377 TYR 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 608 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 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 452 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 189 ILE 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 490 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 112 LEU 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 155 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 0.0980 chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 217 ASN A 258 HIS ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 158 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21666 Z= 0.313 Angle : 0.841 17.268 29370 Z= 0.406 Chirality : 0.043 0.193 3323 Planarity : 0.004 0.036 3736 Dihedral : 5.517 54.429 2900 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.51 % Favored : 90.33 % Rotamer: Outliers : 2.93 % Allowed : 18.86 % Favored : 78.21 % 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: -0.41 (0.17), residues: 2628 helix: 1.34 (0.14), residues: 1453 sheet: -3.31 (0.54), residues: 76 loop : -2.38 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 613 HIS 0.009 0.002 HIS C 426 PHE 0.023 0.001 PHE E 12 TYR 0.016 0.002 TYR A 324 ARG 0.008 0.000 ARG A 302 *********************** 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 333 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 266 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9613 (mt) cc_final: 0.9337 (pp) REVERT: A 96 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8967 (mpp) REVERT: A 128 GLN cc_start: 0.9129 (tt0) cc_final: 0.8106 (tm-30) REVERT: A 209 LYS cc_start: 0.9078 (mttp) cc_final: 0.8774 (mmtt) REVERT: A 311 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8307 (p) REVERT: A 315 GLU cc_start: 0.9069 (mp0) cc_final: 0.8726 (mp0) REVERT: A 410 MET cc_start: 0.8265 (mpp) cc_final: 0.7969 (mpp) REVERT: A 414 ARG cc_start: 0.9035 (tpp80) cc_final: 0.8674 (tpt170) REVERT: A 474 MET cc_start: 0.8916 (ppp) cc_final: 0.8691 (tmm) REVERT: A 491 MET cc_start: 0.8875 (ttm) cc_final: 0.8440 (tmm) REVERT: A 528 MET cc_start: 0.9288 (tpt) cc_final: 0.8855 (tpp) REVERT: A 535 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8758 (tt0) REVERT: A 557 ILE cc_start: 0.9745 (mt) cc_final: 0.9540 (tp) REVERT: A 603 MET cc_start: 0.9462 (ttp) cc_final: 0.9038 (tmm) REVERT: B 57 ASP cc_start: 0.9158 (m-30) cc_final: 0.8683 (m-30) REVERT: B 130 MET cc_start: 0.8391 (mmm) cc_final: 0.8071 (mmm) REVERT: B 168 SER cc_start: 0.9791 (m) cc_final: 0.9548 (p) REVERT: B 290 GLN cc_start: 0.7544 (tm-30) cc_final: 0.6509 (pp30) REVERT: B 294 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8617 (mp0) REVERT: B 345 MET cc_start: 0.8980 (mmm) cc_final: 0.8587 (tmm) REVERT: B 377 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: B 408 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: B 464 ASN cc_start: 0.9259 (t0) cc_final: 0.8979 (t0) REVERT: B 474 MET cc_start: 0.9086 (ptm) cc_final: 0.8627 (ttp) REVERT: B 485 MET cc_start: 0.9575 (tpp) cc_final: 0.8354 (tpp) REVERT: B 489 ASP cc_start: 0.8549 (t0) cc_final: 0.8076 (t0) REVERT: B 515 GLU cc_start: 0.8905 (tp30) cc_final: 0.8399 (mp0) REVERT: B 578 MET cc_start: 0.9352 (ttm) cc_final: 0.9084 (mmm) REVERT: B 584 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.9032 (mmt90) REVERT: B 641 ARG cc_start: 0.9261 (mtt180) cc_final: 0.8760 (tpt170) REVERT: C 38 LEU cc_start: 0.9686 (mt) cc_final: 0.9341 (tt) REVERT: C 67 TYR cc_start: 0.8487 (t80) cc_final: 0.8133 (t80) REVERT: C 99 MET cc_start: 0.9644 (mmt) cc_final: 0.9297 (mmm) REVERT: C 114 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8635 (tp) REVERT: C 284 ASP cc_start: 0.8868 (t70) cc_final: 0.8559 (t0) REVERT: C 331 MET cc_start: 0.8689 (mmt) cc_final: 0.8470 (mmp) REVERT: C 345 MET cc_start: 0.8817 (mmt) cc_final: 0.8505 (tpp) REVERT: C 410 MET cc_start: 0.8447 (mtp) cc_final: 0.7756 (ttp) REVERT: C 432 TYR cc_start: 0.8850 (t80) cc_final: 0.8556 (t80) REVERT: C 454 MET cc_start: 0.9307 (tpp) cc_final: 0.9025 (tpp) REVERT: C 489 ASP cc_start: 0.8712 (m-30) cc_final: 0.7607 (m-30) REVERT: C 491 MET cc_start: 0.8569 (ttt) cc_final: 0.8311 (tmm) REVERT: C 492 ARG cc_start: 0.8842 (ptt180) cc_final: 0.7801 (ptp90) REVERT: C 515 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8006 (mp0) REVERT: C 577 MET cc_start: 0.9124 (tmm) cc_final: 0.7571 (tmm) REVERT: C 603 MET cc_start: 0.9369 (ttp) cc_final: 0.8907 (tmm) REVERT: D 35 GLU cc_start: 0.9599 (tt0) cc_final: 0.9196 (mt-10) REVERT: D 61 LEU cc_start: 0.9560 (mt) cc_final: 0.9342 (mt) REVERT: D 78 MET cc_start: 0.8954 (pmm) cc_final: 0.8727 (pmm) REVERT: D 85 ILE cc_start: 0.9850 (mm) cc_final: 0.9607 (tp) REVERT: D 99 MET cc_start: 0.9463 (mmt) cc_final: 0.9029 (mmm) REVERT: D 181 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9444 (tm) REVERT: D 345 MET cc_start: 0.9174 (mmm) cc_final: 0.8286 (tmm) REVERT: D 371 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9263 (ttpp) REVERT: D 378 MET cc_start: 0.8795 (pmm) cc_final: 0.8466 (pmm) REVERT: D 442 MET cc_start: 0.9300 (tpp) cc_final: 0.8906 (ttm) REVERT: D 491 MET cc_start: 0.8846 (tpt) cc_final: 0.8442 (tmm) REVERT: D 497 MET cc_start: 0.9440 (ttp) cc_final: 0.8769 (tmm) REVERT: D 603 MET cc_start: 0.9405 (ttp) cc_final: 0.9183 (tmm) REVERT: D 608 LEU cc_start: 0.9652 (tt) cc_final: 0.9416 (tt) REVERT: E 36 MET cc_start: 0.9220 (ttt) cc_final: 0.8771 (tpp) REVERT: E 51 MET cc_start: 0.8444 (mmt) cc_final: 0.8168 (mmt) REVERT: E 71 MET cc_start: 0.9308 (ttt) cc_final: 0.9099 (tmm) REVERT: E 145 MET cc_start: 0.8000 (mmm) cc_final: 0.7612 (mmm) REVERT: E 148 LYS cc_start: 0.6493 (pmtt) cc_final: 0.5500 (mmtm) outliers start: 67 outliers final: 46 residues processed: 315 average time/residue: 0.2945 time to fit residues: 147.6409 Evaluate side-chains 313 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 259 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 401 LEU 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 536 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain 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 311 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 465 VAL 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 181 LEU 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 404 VAL Chi-restraints excluded: chain D residue 479 THR 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 112 LEU Chi-restraints excluded: chain E residue 136 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 464 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 426 HIS ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5010 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= 0.180 Angle : 0.821 17.056 29370 Z= 0.383 Chirality : 0.042 0.198 3323 Planarity : 0.003 0.035 3736 Dihedral : 5.299 37.778 2898 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.17 % Favored : 90.72 % Rotamer: Outliers : 2.62 % Allowed : 19.56 % Favored : 77.82 % 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: -0.28 (0.18), residues: 2628 helix: 1.42 (0.14), residues: 1452 sheet: -3.09 (0.56), residues: 76 loop : -2.30 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 613 HIS 0.022 0.001 HIS B 426 PHE 0.019 0.001 PHE E 12 TYR 0.017 0.001 TYR A 432 ARG 0.009 0.000 ARG A 302 *********************** 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 348 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 288 time to evaluate : 2.494 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: 0.9594 (mt) cc_final: 0.9321 (pp) REVERT: A 96 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.9008 (mpp) REVERT: A 99 MET cc_start: 0.9408 (mmm) cc_final: 0.8975 (mpp) REVERT: A 128 GLN cc_start: 0.9072 (tt0) cc_final: 0.8032 (tm-30) REVERT: A 209 LYS cc_start: 0.8968 (mttp) cc_final: 0.8677 (mmtt) REVERT: A 255 MET cc_start: 0.9485 (mmt) cc_final: 0.9143 (mmm) REVERT: A 311 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8277 (p) REVERT: A 315 GLU cc_start: 0.9045 (mp0) cc_final: 0.8777 (mp0) REVERT: A 410 MET cc_start: 0.8250 (mpp) cc_final: 0.7964 (mpp) REVERT: A 414 ARG cc_start: 0.9037 (tpp80) cc_final: 0.8612 (tpt90) REVERT: A 440 MET cc_start: 0.9038 (ppp) cc_final: 0.8835 (ppp) REVERT: A 491 MET cc_start: 0.8810 (ttm) cc_final: 0.8365 (tmm) REVERT: A 528 MET cc_start: 0.9244 (tpt) cc_final: 0.8898 (tpp) REVERT: A 535 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8699 (tt0) REVERT: A 554 MET cc_start: 0.8502 (tpp) cc_final: 0.7767 (tpp) REVERT: A 557 ILE cc_start: 0.9682 (mt) cc_final: 0.9461 (tp) REVERT: A 603 MET cc_start: 0.9447 (ttp) cc_final: 0.8981 (tmm) REVERT: B 57 ASP cc_start: 0.9089 (m-30) cc_final: 0.8582 (m-30) REVERT: B 130 MET cc_start: 0.8264 (mmm) cc_final: 0.7999 (mmm) REVERT: B 168 SER cc_start: 0.9777 (m) cc_final: 0.9529 (p) REVERT: B 282 GLU cc_start: 0.8842 (mp0) cc_final: 0.8464 (mp0) REVERT: B 290 GLN cc_start: 0.7245 (tm-30) cc_final: 0.6668 (tm-30) REVERT: B 294 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8549 (pt0) REVERT: B 345 MET cc_start: 0.8851 (mmm) cc_final: 0.8494 (tmm) REVERT: B 386 LEU cc_start: 0.9745 (tp) cc_final: 0.9373 (mm) REVERT: B 408 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: B 464 ASN cc_start: 0.9203 (t0) cc_final: 0.8957 (t0) REVERT: B 474 MET cc_start: 0.9026 (ptm) cc_final: 0.8574 (ttp) REVERT: B 485 MET cc_start: 0.9586 (tpp) cc_final: 0.9370 (tpp) REVERT: B 584 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8951 (mmt90) REVERT: B 641 ARG cc_start: 0.9258 (mtt180) cc_final: 0.8748 (tpt170) REVERT: C 38 LEU cc_start: 0.9661 (mt) cc_final: 0.9320 (tp) REVERT: C 99 MET cc_start: 0.9623 (mmt) cc_final: 0.9284 (mmm) REVERT: C 114 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8618 (tp) REVERT: C 284 ASP cc_start: 0.8822 (t70) cc_final: 0.8520 (t0) REVERT: C 331 MET cc_start: 0.8712 (mmt) cc_final: 0.8467 (mmp) REVERT: C 410 MET cc_start: 0.8358 (mtp) cc_final: 0.7594 (ttp) REVERT: C 432 TYR cc_start: 0.8630 (t80) cc_final: 0.8228 (t80) REVERT: C 454 MET cc_start: 0.9339 (tpp) cc_final: 0.9120 (tpp) REVERT: C 489 ASP cc_start: 0.8735 (m-30) cc_final: 0.7975 (m-30) REVERT: C 491 MET cc_start: 0.8500 (ttt) cc_final: 0.8225 (tmm) REVERT: C 515 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8246 (mm-30) REVERT: C 577 MET cc_start: 0.9162 (tmm) cc_final: 0.8263 (tmm) REVERT: C 603 MET cc_start: 0.9295 (ttp) cc_final: 0.8883 (tmm) REVERT: D 35 GLU cc_start: 0.9575 (tt0) cc_final: 0.9165 (mt-10) REVERT: D 61 LEU cc_start: 0.9577 (mt) cc_final: 0.9343 (mt) REVERT: D 78 MET cc_start: 0.8973 (pmm) cc_final: 0.8677 (pmm) REVERT: D 85 ILE cc_start: 0.9825 (mm) cc_final: 0.9563 (tp) REVERT: D 99 MET cc_start: 0.9453 (mmt) cc_final: 0.9045 (mmm) REVERT: D 181 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9471 (tm) REVERT: D 331 MET cc_start: 0.7740 (mmt) cc_final: 0.7397 (mmp) REVERT: D 345 MET cc_start: 0.9222 (mmm) cc_final: 0.8400 (tmm) REVERT: D 371 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9304 (ttpp) REVERT: D 378 MET cc_start: 0.8787 (pmm) cc_final: 0.8469 (pmm) REVERT: D 491 MET cc_start: 0.8809 (tpt) cc_final: 0.8456 (tmm) REVERT: D 497 MET cc_start: 0.9401 (ttp) cc_final: 0.8778 (tmm) REVERT: D 603 MET cc_start: 0.9379 (ttp) cc_final: 0.8722 (tmm) REVERT: D 608 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9407 (tt) REVERT: E 36 MET cc_start: 0.9196 (ttt) cc_final: 0.8734 (tpp) REVERT: E 51 MET cc_start: 0.8440 (mmt) cc_final: 0.8160 (mmt) REVERT: E 145 MET cc_start: 0.7986 (mmm) cc_final: 0.7574 (mmm) REVERT: E 148 LYS cc_start: 0.6512 (pmtt) cc_final: 0.5595 (mmtm) outliers start: 60 outliers final: 40 residues processed: 329 average time/residue: 0.3034 time to fit residues: 158.9033 Evaluate side-chains 326 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 278 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 429 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 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 408 PHE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 536 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 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 465 VAL 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 181 LEU Chi-restraints excluded: chain D residue 189 ILE 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 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 112 LEU Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 247 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 260 optimal weight: 30.0000 chunk 239 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21666 Z= 0.200 Angle : 0.823 17.081 29370 Z= 0.384 Chirality : 0.042 0.202 3323 Planarity : 0.003 0.034 3736 Dihedral : 5.266 38.258 2898 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.36 % Favored : 90.49 % Rotamer: Outliers : 2.18 % Allowed : 20.17 % Favored : 77.64 % 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: -0.24 (0.18), residues: 2628 helix: 1.43 (0.14), residues: 1457 sheet: -3.01 (0.56), residues: 76 loop : -2.26 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 613 HIS 0.013 0.001 HIS B 426 PHE 0.033 0.001 PHE B 493 TYR 0.014 0.001 TYR A 324 ARG 0.010 0.000 ARG A 302 ********************** 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 333 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 283 time to evaluate : 2.570 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: 0.9594 (mt) cc_final: 0.9323 (pp) REVERT: A 96 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.9010 (mpp) REVERT: A 99 MET cc_start: 0.9388 (mmm) cc_final: 0.8948 (mpp) REVERT: A 128 GLN cc_start: 0.9095 (tt0) cc_final: 0.8090 (tm-30) REVERT: A 209 LYS cc_start: 0.8964 (mttp) cc_final: 0.8677 (mmtt) REVERT: A 311 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8278 (p) REVERT: A 315 GLU cc_start: 0.9058 (mp0) cc_final: 0.8783 (mp0) REVERT: A 410 MET cc_start: 0.8300 (mpp) cc_final: 0.8003 (mpp) REVERT: A 414 ARG cc_start: 0.9035 (tpp80) cc_final: 0.8610 (tpt90) REVERT: A 528 MET cc_start: 0.9250 (tpt) cc_final: 0.8904 (tpp) REVERT: A 535 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8644 (tt0) REVERT: A 554 MET cc_start: 0.8520 (tpp) cc_final: 0.7800 (tpp) REVERT: A 557 ILE cc_start: 0.9683 (mt) cc_final: 0.9464 (tp) REVERT: A 603 MET cc_start: 0.9452 (ttp) cc_final: 0.9040 (tmm) REVERT: B 57 ASP cc_start: 0.9077 (m-30) cc_final: 0.8568 (m-30) REVERT: B 130 MET cc_start: 0.8222 (mmm) cc_final: 0.7877 (mmm) REVERT: B 168 SER cc_start: 0.9758 (m) cc_final: 0.9524 (p) REVERT: B 345 MET cc_start: 0.8857 (mmm) cc_final: 0.8516 (tmm) REVERT: B 386 LEU cc_start: 0.9731 (tp) cc_final: 0.9342 (mm) REVERT: B 408 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: B 464 ASN cc_start: 0.9200 (t0) cc_final: 0.8949 (t0) REVERT: B 474 MET cc_start: 0.9028 (ptm) cc_final: 0.8622 (ttp) REVERT: B 584 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8954 (mmt90) REVERT: B 641 ARG cc_start: 0.9286 (mtt180) cc_final: 0.8758 (tpt170) REVERT: C 99 MET cc_start: 0.9628 (mmt) cc_final: 0.9283 (mmm) REVERT: C 114 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8589 (tp) REVERT: C 284 ASP cc_start: 0.8812 (t70) cc_final: 0.8515 (t0) REVERT: C 331 MET cc_start: 0.8694 (mmt) cc_final: 0.8456 (mmp) REVERT: C 410 MET cc_start: 0.8357 (mtp) cc_final: 0.7700 (ttp) REVERT: C 432 TYR cc_start: 0.8680 (t80) cc_final: 0.8268 (t80) REVERT: C 454 MET cc_start: 0.9328 (tpp) cc_final: 0.9100 (tpp) REVERT: C 489 ASP cc_start: 0.8706 (m-30) cc_final: 0.8016 (m-30) REVERT: C 491 MET cc_start: 0.8483 (ttt) cc_final: 0.8157 (tmm) REVERT: C 515 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8252 (mm-30) REVERT: C 577 MET cc_start: 0.9105 (tmm) cc_final: 0.8212 (tmm) REVERT: C 603 MET cc_start: 0.9306 (ttp) cc_final: 0.8898 (tmm) REVERT: D 35 GLU cc_start: 0.9577 (tt0) cc_final: 0.9210 (mp0) REVERT: D 61 LEU cc_start: 0.9573 (mt) cc_final: 0.9333 (mt) REVERT: D 78 MET cc_start: 0.8895 (pmm) cc_final: 0.8642 (pmm) REVERT: D 85 ILE cc_start: 0.9827 (mm) cc_final: 0.9572 (tp) REVERT: D 99 MET cc_start: 0.9439 (mmt) cc_final: 0.9027 (mmm) REVERT: D 181 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9474 (tm) REVERT: D 331 MET cc_start: 0.7773 (mmt) cc_final: 0.7447 (mmp) REVERT: D 345 MET cc_start: 0.9194 (mmm) cc_final: 0.8395 (tmm) REVERT: D 364 ASP cc_start: 0.9137 (m-30) cc_final: 0.8589 (p0) REVERT: D 371 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9311 (ttpp) REVERT: D 378 MET cc_start: 0.8785 (pmm) cc_final: 0.8466 (pmm) REVERT: D 497 MET cc_start: 0.9408 (ttp) cc_final: 0.8777 (tmm) REVERT: D 577 MET cc_start: 0.9151 (tmm) cc_final: 0.8382 (tmm) REVERT: D 603 MET cc_start: 0.9380 (ttp) cc_final: 0.9176 (tmm) REVERT: D 608 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9406 (tt) REVERT: E 36 MET cc_start: 0.9180 (ttt) cc_final: 0.8717 (tpp) REVERT: E 51 MET cc_start: 0.8427 (mmt) cc_final: 0.8175 (mmt) REVERT: E 145 MET cc_start: 0.7977 (mmm) cc_final: 0.7582 (mmm) REVERT: E 148 LYS cc_start: 0.6464 (pmtt) cc_final: 0.5514 (mmtm) outliers start: 50 outliers final: 37 residues processed: 316 average time/residue: 0.2936 time to fit residues: 148.0084 Evaluate side-chains 313 residues out of total 2290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 268 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 429 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 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 497 MET Chi-restraints excluded: chain B residue 536 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 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain 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 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 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 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 30 optimal weight: 0.0770 chunk 57 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 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** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.068217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051689 restraints weight = 84887.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.053563 restraints weight = 46088.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.054873 restraints weight = 30704.030| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21666 Z= 0.215 Angle : 0.838 17.287 29370 Z= 0.392 Chirality : 0.042 0.187 3323 Planarity : 0.004 0.034 3736 Dihedral : 5.237 37.854 2898 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.55 % Favored : 90.30 % Rotamer: Outliers : 2.62 % Allowed : 20.00 % Favored : 77.38 % 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: -0.20 (0.18), residues: 2628 helix: 1.48 (0.14), residues: 1459 sheet: -3.03 (0.55), residues: 76 loop : -2.28 (0.20), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 613 HIS 0.005 0.001 HIS B 582 PHE 0.032 0.001 PHE B 493 TYR 0.036 0.001 TYR A 324 ARG 0.010 0.000 ARG A 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4065.89 seconds wall clock time: 73 minutes 19.73 seconds (4399.73 seconds total)