Starting phenix.real_space_refine on Sun Jul 5 00:12:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jns_36450/07_2026/8jns_36450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jns_36450/07_2026/8jns_36450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jns_36450/07_2026/8jns_36450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jns_36450/07_2026/8jns_36450.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jns_36450/07_2026/8jns_36450.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jns_36450/07_2026/8jns_36450.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jns_36450/07_2026/8jns_36450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jns_36450/07_2026/8jns_36450.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 174 5.16 5 C 15336 2.51 5 N 4041 2.21 5 O 4593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24168 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "C" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "D" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 375} Chain breaks: 2 Chain: "E" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 375} Chain breaks: 2 Chain: "F" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 375} Chain breaks: 2 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "H" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "I" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.00, per 1000 atoms: 0.21 Number of scatterers: 24168 At special positions: 0 Unit cell: (168.96, 171.6, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 174 16.00 P 18 15.00 Mg 6 11.99 O 4593 8.00 N 4041 7.00 C 15336 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 13 sheets defined 61.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.562A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.758A pdb=" N ALA A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 49 through 65 removed outlier: 3.559A pdb=" N ARG A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.726A pdb=" N ASP A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.522A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 4.022A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.978A pdb=" N ILE A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.648A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.886A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 removed outlier: 3.738A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 399 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 458 through 466 removed outlier: 4.193A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 removed outlier: 3.767A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU A 535 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.562A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 32 removed outlier: 3.757A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.559A pdb=" N ARG B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.620A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.597A pdb=" N ARG B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 164 through 173 removed outlier: 3.523A pdb=" N ILE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.022A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.684A pdb=" N ARG B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 4.102A pdb=" N ILE B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.649A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 removed outlier: 4.886A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 344 through 355 Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.890A pdb=" N ALA B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 397 removed outlier: 3.775A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.501A pdb=" N PHE B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 486 removed outlier: 3.767A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 481 " --> pdb=" O ILE B 477 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU B 535 " --> pdb=" O PHE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.563A pdb=" N LEU C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.757A pdb=" N ALA C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 46 Processing helix chain 'C' and resid 49 through 65 removed outlier: 3.558A pdb=" N ARG C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 65 " --> pdb=" O TYR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 78 removed outlier: 3.531A pdb=" N TYR C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA C 84 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 86 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 94 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE C 95 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 111 through 122 removed outlier: 3.597A pdb=" N ARG C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.522A pdb=" N ILE C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 Processing helix chain 'C' and resid 198 through 212 removed outlier: 4.022A pdb=" N PHE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 254 through 264 removed outlier: 4.118A pdb=" N ILE C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE C 277 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 305 removed outlier: 3.648A pdb=" N TYR C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 327 removed outlier: 4.886A pdb=" N VAL C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 344 through 355 Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 373 through 384 removed outlier: 3.892A pdb=" N ALA C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG C 380 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 399 removed outlier: 3.738A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 393 " --> pdb=" O ASP C 389 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 428 through 440 Processing helix chain 'C' and resid 457 through 466 Processing helix chain 'C' and resid 469 through 485 removed outlier: 3.767A pdb=" N ALA C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU C 535 " --> pdb=" O PHE C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.597A pdb=" N ARG D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 Processing helix chain 'D' and resid 164 through 173 Processing helix chain 'D' and resid 198 through 212 removed outlier: 4.021A pdb=" N PHE D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 240 Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.946A pdb=" N ILE D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE D 277 " --> pdb=" O ASP D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 305 removed outlier: 3.649A pdb=" N TYR D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 327 Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 344 through 355 Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 396 removed outlier: 3.738A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 428 through 440 Processing helix chain 'D' and resid 458 through 466 removed outlier: 3.592A pdb=" N PHE D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 485 removed outlier: 3.767A pdb=" N ALA D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 485 " --> pdb=" O GLU D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU D 535 " --> pdb=" O PHE D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 122 removed outlier: 3.636A pdb=" N ARG E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 Processing helix chain 'E' and resid 164 through 176 removed outlier: 3.522A pdb=" N ILE E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 212 removed outlier: 4.038A pdb=" N PHE E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 240 Processing helix chain 'E' and resid 254 through 264 removed outlier: 4.063A pdb=" N ILE E 258 " --> pdb=" O GLN E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE E 277 " --> pdb=" O ASP E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 305 removed outlier: 3.648A pdb=" N TYR E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 327 Processing helix chain 'E' and resid 329 through 340 Processing helix chain 'E' and resid 344 through 355 Processing helix chain 'E' and resid 358 through 363 Processing helix chain 'E' and resid 373 through 384 removed outlier: 3.892A pdb=" N ALA E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 397 removed outlier: 3.531A pdb=" N VAL E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 428 through 440 Processing helix chain 'E' and resid 457 through 468 Processing helix chain 'E' and resid 469 through 484 removed outlier: 3.768A pdb=" N ALA E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG E 483 " --> pdb=" O ILE E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.852A pdb=" N LEU E 535 " --> pdb=" O PHE E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER E 542 " --> pdb=" O LYS E 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.597A pdb=" N ARG F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 146 Processing helix chain 'F' and resid 164 through 173 removed outlier: 3.522A pdb=" N ILE F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 212 removed outlier: 3.959A pdb=" N PHE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 254 through 265 removed outlier: 4.066A pdb=" N ILE F 258 " --> pdb=" O GLN F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 281 removed outlier: 3.915A pdb=" N ILE F 277 " --> pdb=" O ASP F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 305 removed outlier: 3.648A pdb=" N TYR F 299 " --> pdb=" O ILE F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 327 removed outlier: 4.886A pdb=" N VAL F 318 " --> pdb=" O LYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 338 Processing helix chain 'F' and resid 344 through 355 Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA F 377 " --> pdb=" O SER F 373 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 396 removed outlier: 3.711A pdb=" N SER F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 428 through 440 Processing helix chain 'F' and resid 457 through 468 Processing helix chain 'F' and resid 469 through 485 removed outlier: 3.768A pdb=" N ALA F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU F 535 " --> pdb=" O PHE F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER F 542 " --> pdb=" O LYS F 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU G 10 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS G 19 " --> pdb=" O THR G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 removed outlier: 3.774A pdb=" N ALA G 26 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 46 Processing helix chain 'G' and resid 49 through 65 removed outlier: 3.552A pdb=" N ARG G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN G 64 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA G 65 " --> pdb=" O TYR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 78 Processing helix chain 'G' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G 94 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU H 10 " --> pdb=" O GLU H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS H 19 " --> pdb=" O THR H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 33 removed outlier: 3.774A pdb=" N ALA H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 46 Processing helix chain 'H' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG H 53 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN H 64 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA H 65 " --> pdb=" O TYR H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 Processing helix chain 'H' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE H 86 " --> pdb=" O HIS H 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU I 10 " --> pdb=" O GLU I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 33 removed outlier: 3.773A pdb=" N ALA I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR I 28 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 46 Processing helix chain 'I' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA I 65 " --> pdb=" O TYR I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 Processing helix chain 'I' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE I 86 " --> pdb=" O HIS I 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA I 94 " --> pdb=" O TYR I 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 7.086A pdb=" N THR A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU A 269 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE A 247 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR A 271 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 249 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 153 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 270 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 155 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 272 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 157 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 removed outlier: 6.872A pdb=" N THR B 245 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU B 269 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR B 271 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 249 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE B 153 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 270 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 155 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR B 272 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 157 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE B 154 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE B 288 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 156 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 290 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N HIS B 158 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 191 removed outlier: 7.063A pdb=" N THR C 245 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU C 269 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE C 247 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR C 271 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE C 249 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE C 153 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 270 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 155 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR C 272 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 157 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 186 through 191 removed outlier: 7.063A pdb=" N THR C 245 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU C 269 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE C 247 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR C 271 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE C 249 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE C 153 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 270 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 155 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR C 272 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 157 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 290 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N HIS C 158 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AA8, first strand: chain 'D' and resid 186 through 191 removed outlier: 4.780A pdb=" N ARG D 267 " --> pdb=" O THR D 245 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE D 153 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL D 270 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU D 155 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR D 272 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU D 157 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE D 154 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE D 288 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE D 156 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 290 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS D 158 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AB1, first strand: chain 'E' and resid 186 through 191 removed outlier: 6.851A pdb=" N THR E 245 " --> pdb=" O ARG E 267 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU E 269 " --> pdb=" O THR E 245 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE E 247 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR E 271 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE E 249 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE E 153 " --> pdb=" O CYS E 268 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL E 270 " --> pdb=" O PHE E 153 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU E 155 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR E 272 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 157 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE E 154 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE E 288 " --> pdb=" O PHE E 154 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE E 156 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL E 290 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N HIS E 158 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AB3, first strand: chain 'F' and resid 186 through 191 removed outlier: 4.819A pdb=" N ARG F 267 " --> pdb=" O THR F 245 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE F 153 " --> pdb=" O CYS F 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL F 270 " --> pdb=" O PHE F 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU F 155 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR F 272 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU F 157 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE F 154 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE F 288 " --> pdb=" O PHE F 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE F 156 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL F 290 " --> pdb=" O PHE F 156 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N HIS F 158 " --> pdb=" O VAL F 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 405 through 406 1066 hydrogen bonds defined for protein. 3000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7711 1.34 - 1.47: 4970 1.47 - 1.59: 11631 1.59 - 1.72: 18 1.72 - 1.85: 276 Bond restraints: 24606 Sorted by residual: bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.23e+01 bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.12e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.10e+01 bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.06e+01 bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.05e+01 ... (remaining 24601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 32893 5.15 - 10.30: 358 10.30 - 15.46: 25 15.46 - 20.61: 0 20.61 - 25.76: 6 Bond angle restraints: 33282 Sorted by residual: angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 114.11 25.76 1.00e+00 1.00e+00 6.64e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 114.13 25.74 1.00e+00 1.00e+00 6.63e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.15 25.72 1.00e+00 1.00e+00 6.61e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 114.16 25.71 1.00e+00 1.00e+00 6.61e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 114.17 25.70 1.00e+00 1.00e+00 6.61e+02 ... (remaining 33277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 12884 16.90 - 33.79: 1407 33.79 - 50.69: 495 50.69 - 67.59: 213 67.59 - 84.48: 34 Dihedral angle restraints: 15033 sinusoidal: 6231 harmonic: 8802 Sorted by residual: dihedral pdb=" CA ASP F 216 " pdb=" C ASP F 216 " pdb=" N LEU F 217 " pdb=" CA LEU F 217 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ASP C 216 " pdb=" C ASP C 216 " pdb=" N LEU C 217 " pdb=" CA LEU C 217 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ASP D 216 " pdb=" C ASP D 216 " pdb=" N LEU D 217 " pdb=" CA LEU D 217 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 15030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2558 0.070 - 0.140: 953 0.140 - 0.210: 235 0.210 - 0.280: 57 0.280 - 0.350: 16 Chirality restraints: 3819 Sorted by residual: chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA PHE B 532 " pdb=" N PHE B 532 " pdb=" C PHE B 532 " pdb=" CB PHE B 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA PHE E 532 " pdb=" N PHE E 532 " pdb=" C PHE E 532 " pdb=" CB PHE E 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 3816 not shown) Planarity restraints: 4233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 116 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C ASP E 116 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP E 116 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG E 117 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 220 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO F 221 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 220 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 221 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.032 5.00e-02 4.00e+02 ... (remaining 4230 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 6 2.09 - 2.79: 6391 2.79 - 3.50: 34751 3.50 - 4.20: 59519 4.20 - 4.90: 100478 Nonbonded interactions: 201145 Sorted by model distance: nonbonded pdb=" CD GLU A 97 " pdb=" CD1 LEU H 51 " model vdw 1.390 3.690 nonbonded pdb=" CD GLU B 97 " pdb=" CD1 LEU I 51 " model vdw 1.745 3.690 nonbonded pdb=" OE1 GLU A 97 " pdb=" CD1 LEU H 51 " model vdw 1.773 3.460 nonbonded pdb=" CD GLU C 97 " pdb=" CD1 LEU G 51 " model vdw 1.799 3.690 nonbonded pdb=" CG GLU A 97 " pdb=" CD1 LEU H 51 " model vdw 1.969 3.860 ... (remaining 201140 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.210 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 0.096 24606 Z= 0.614 Angle : 1.516 25.759 33282 Z= 1.048 Chirality : 0.078 0.350 3819 Planarity : 0.005 0.059 4233 Dihedral : 17.904 84.482 9267 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 39.59 Ramachandran Plot: Outliers : 0.82 % Allowed : 12.81 % Favored : 86.37 % Rotamer: Outliers : 17.81 % Allowed : 13.94 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.88 (0.13), residues: 2943 helix: -3.31 (0.09), residues: 1650 sheet: -2.70 (0.34), residues: 195 loop : -2.90 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 112 TYR 0.022 0.004 TYR A 371 PHE 0.018 0.003 PHE F 532 TRP 0.023 0.004 TRP B 189 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00955 / 0.61 (24606) covalent geometry : angle 1.51588 / 1.05 (33282) hydrogen bonds : bond 0.25127 / 16.58 ( 1061) hydrogen bonds : angle 9.05686 / 6.28 ( 3000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 484 poor density : 354 time to evaluate : 1.151 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: 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: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7888 (ttt90) REVERT: A 47 MET cc_start: 0.8044 (mmm) cc_final: 0.6338 (mmm) REVERT: A 58 LEU cc_start: 0.9049 (mt) cc_final: 0.8559 (pp) REVERT: A 173 LEU cc_start: 0.8974 (mt) cc_final: 0.8760 (pp) REVERT: A 180 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8101 (mm) REVERT: A 255 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: A 290 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8643 (p) REVERT: A 332 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 434 LEU cc_start: 0.9225 (mt) cc_final: 0.8976 (mt) REVERT: B 8 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7950 (tpt170) REVERT: B 216 ASP cc_start: 0.8988 (m-30) cc_final: 0.8115 (t0) REVERT: B 307 MET cc_start: 0.8125 (tpp) cc_final: 0.7869 (tpp) REVERT: B 369 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7987 (t80) REVERT: B 459 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8886 (mm) REVERT: C 47 MET cc_start: 0.8417 (mmm) cc_final: 0.8179 (mmm) REVERT: C 49 THR cc_start: 0.9057 (m) cc_final: 0.8631 (p) REVERT: C 58 LEU cc_start: 0.9132 (mt) cc_final: 0.8735 (pp) REVERT: C 290 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9006 (p) REVERT: C 296 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8391 (p0) REVERT: C 348 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8915 (tmm) REVERT: C 355 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9278 (mm) REVERT: C 363 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8721 (p) REVERT: C 437 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8960 (tp) REVERT: D 175 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8382 (ttpp) REVERT: D 226 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8948 (p) REVERT: D 290 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9214 (t) REVERT: D 296 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8576 (p0) REVERT: D 355 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9226 (tp) REVERT: D 369 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7891 (t80) REVERT: F 113 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6132 (mp10) REVERT: F 144 LEU cc_start: 0.9412 (mt) cc_final: 0.9170 (mt) REVERT: F 207 ILE cc_start: 0.9599 (mt) cc_final: 0.9340 (mt) REVERT: F 277 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8910 (pt) REVERT: F 334 MET cc_start: 0.9429 (tpt) cc_final: 0.9188 (tpp) REVERT: F 344 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8396 (p) REVERT: F 369 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7642 (t80) REVERT: F 381 CYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8584 (t) REVERT: F 437 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9377 (mt) REVERT: H 88 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8841 (mm-30) REVERT: I 45 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.6563 (p) REVERT: I 68 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7378 (tt) REVERT: I 76 ASN cc_start: 0.8256 (m-40) cc_final: 0.7594 (p0) outliers start: 484 outliers final: 101 residues processed: 759 average time/residue: 0.1636 time to fit residues: 192.7122 Evaluate side-chains 338 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 209 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS A 34 ASN A 123 ASN A 237 ASN A 262 GLN A 283 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 536 HIS B 34 ASN B 40 HIS B 219 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN C 19 HIS C 34 ASN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 GLN D 123 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN D 262 GLN D 283 GLN E 123 ASN E 244 ASN E 283 GLN E 482 GLN F 123 ASN F 244 ASN F 458 HIS G 34 ASN H 14 HIS H 19 HIS I 34 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.043077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.031792 restraints weight = 231335.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.032653 restraints weight = 153916.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.033277 restraints weight = 112917.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.033736 restraints weight = 88816.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034081 restraints weight = 73847.649| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24606 Z= 0.151 Angle : 0.756 9.641 33282 Z= 0.381 Chirality : 0.044 0.211 3819 Planarity : 0.006 0.076 4233 Dihedral : 6.361 71.555 3225 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.26 % Allowed : 3.83 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.14), residues: 2943 helix: -1.34 (0.11), residues: 1716 sheet: -2.64 (0.30), residues: 213 loop : -2.03 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 8 TYR 0.018 0.002 TYR B 90 PHE 0.018 0.002 PHE I 74 TRP 0.037 0.005 TRP F 189 HIS 0.007 0.001 HIS G 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (24606) covalent geometry : angle 0.75628 / 0.38 (33282) hydrogen bonds : bond 0.04545 / 2.99 ( 1061) hydrogen bonds : angle 5.07666 / 3.57 ( 3000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 257 time to evaluate : 0.899 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7530 (mm) cc_final: 0.7309 (mt) REVERT: A 114 MET cc_start: 0.9183 (mmp) cc_final: 0.8947 (mmm) REVERT: A 157 LEU cc_start: 0.9347 (tp) cc_final: 0.8988 (tp) REVERT: A 334 MET cc_start: 0.8552 (mmm) cc_final: 0.8155 (mmm) REVERT: B 140 VAL cc_start: 0.9313 (t) cc_final: 0.9081 (t) REVERT: B 335 MET cc_start: 0.9379 (mtp) cc_final: 0.8736 (ttm) REVERT: B 462 MET cc_start: 0.9113 (mtp) cc_final: 0.8885 (ttm) REVERT: C 307 MET cc_start: 0.7169 (mmt) cc_final: 0.6727 (mmt) REVERT: C 399 MET cc_start: 0.9081 (mmm) cc_final: 0.8745 (mpp) REVERT: C 462 MET cc_start: 0.9402 (mtp) cc_final: 0.8931 (ttp) REVERT: D 334 MET cc_start: 0.9374 (tpp) cc_final: 0.9153 (tpp) REVERT: E 128 MET cc_start: 0.8561 (tpp) cc_final: 0.7892 (tpp) REVERT: E 334 MET cc_start: 0.9122 (mtt) cc_final: 0.8868 (mtp) REVERT: E 376 MET cc_start: 0.9455 (mtm) cc_final: 0.9163 (ptp) REVERT: F 144 LEU cc_start: 0.9491 (mt) cc_final: 0.9285 (tp) REVERT: F 207 ILE cc_start: 0.9491 (mt) cc_final: 0.9266 (mt) REVERT: F 234 MET cc_start: 0.8736 (mtm) cc_final: 0.8374 (mtm) REVERT: F 348 MET cc_start: 0.8830 (ttm) cc_final: 0.8342 (mtm) REVERT: F 462 MET cc_start: 0.9006 (mtp) cc_final: 0.8706 (tmm) REVERT: G 47 MET cc_start: 0.5971 (mmm) cc_final: 0.4810 (mmm) REVERT: G 75 PHE cc_start: 0.9460 (m-10) cc_final: 0.9236 (m-80) REVERT: H 31 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6517 (mp0) REVERT: H 73 ASP cc_start: 0.9390 (t70) cc_final: 0.9027 (p0) outliers start: 7 outliers final: 0 residues processed: 264 average time/residue: 0.1625 time to fit residues: 68.7413 Evaluate side-chains 184 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 248 optimal weight: 0.9990 chunk 180 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 227 optimal weight: 0.0470 chunk 12 optimal weight: 7.9990 chunk 251 optimal weight: 0.4980 chunk 150 optimal weight: 10.0000 chunk 294 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.042949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.032524 restraints weight = 232175.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033327 restraints weight = 154522.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.033898 restraints weight = 115190.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.034313 restraints weight = 92790.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.034606 restraints weight = 78938.658| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24606 Z= 0.129 Angle : 0.618 9.202 33282 Z= 0.310 Chirality : 0.040 0.180 3819 Planarity : 0.005 0.061 4233 Dihedral : 5.568 60.162 3225 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 2943 helix: -0.17 (0.13), residues: 1716 sheet: -2.12 (0.31), residues: 213 loop : -1.37 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 16 TYR 0.019 0.002 TYR B 90 PHE 0.020 0.002 PHE H 75 TRP 0.026 0.003 TRP C 189 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (24606) covalent geometry : angle 0.61812 / 0.31 (33282) hydrogen bonds : bond 0.03430 / 2.24 ( 1061) hydrogen bonds : angle 4.41253 / 3.12 ( 3000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.994 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: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7711 (mm) cc_final: 0.7466 (mt) REVERT: A 48 SER cc_start: 0.9331 (m) cc_final: 0.9122 (p) REVERT: A 128 MET cc_start: 0.7725 (mmp) cc_final: 0.7094 (tpp) REVERT: A 399 MET cc_start: 0.8412 (tpp) cc_final: 0.8002 (tmm) REVERT: B 216 ASP cc_start: 0.7813 (t0) cc_final: 0.7493 (t0) REVERT: B 335 MET cc_start: 0.9528 (mtp) cc_final: 0.9279 (mtp) REVERT: B 533 MET cc_start: 0.8837 (ppp) cc_final: 0.8102 (ppp) REVERT: C 1 MET cc_start: 0.9196 (mmp) cc_final: 0.8878 (mmm) REVERT: C 462 MET cc_start: 0.9554 (mtp) cc_final: 0.9262 (ttp) REVERT: D 144 LEU cc_start: 0.9766 (mt) cc_final: 0.9552 (mt) REVERT: D 307 MET cc_start: 0.7627 (mmt) cc_final: 0.7230 (mmp) REVERT: D 334 MET cc_start: 0.9501 (tpp) cc_final: 0.9290 (tpp) REVERT: D 348 MET cc_start: 0.9536 (ptm) cc_final: 0.9177 (ptm) REVERT: E 128 MET cc_start: 0.8639 (tpp) cc_final: 0.7630 (tmm) REVERT: E 225 HIS cc_start: 0.7492 (p90) cc_final: 0.7140 (p-80) REVERT: E 307 MET cc_start: 0.7665 (tpp) cc_final: 0.7392 (tpp) REVERT: E 334 MET cc_start: 0.9217 (mtt) cc_final: 0.8800 (mtt) REVERT: E 376 MET cc_start: 0.9482 (mtm) cc_final: 0.9089 (ptp) REVERT: E 533 MET cc_start: 0.8519 (ppp) cc_final: 0.7637 (mmp) REVERT: F 147 MET cc_start: 0.8950 (mmt) cc_final: 0.8699 (mmp) REVERT: F 207 ILE cc_start: 0.9569 (mt) cc_final: 0.9357 (mt) REVERT: F 216 ASP cc_start: 0.8790 (m-30) cc_final: 0.8560 (t0) REVERT: F 234 MET cc_start: 0.8756 (mtm) cc_final: 0.8382 (mtp) REVERT: F 348 MET cc_start: 0.8819 (ttm) cc_final: 0.8243 (ttt) REVERT: F 462 MET cc_start: 0.9140 (mtp) cc_final: 0.8839 (tmm) REVERT: G 88 GLU cc_start: 0.8700 (pt0) cc_final: 0.8112 (mm-30) REVERT: H 31 GLU cc_start: 0.6343 (mt-10) cc_final: 0.6118 (mm-30) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1612 time to fit residues: 56.3509 Evaluate side-chains 171 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 237 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 268 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 162 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.041394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.031246 restraints weight = 239100.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.032044 restraints weight = 156069.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.032609 restraints weight = 115449.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033034 restraints weight = 92127.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.033339 restraints weight = 77919.149| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24606 Z= 0.118 Angle : 0.599 10.466 33282 Z= 0.294 Chirality : 0.039 0.165 3819 Planarity : 0.005 0.062 4233 Dihedral : 5.308 58.033 3225 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 2943 helix: 0.39 (0.13), residues: 1710 sheet: -1.85 (0.30), residues: 219 loop : -1.11 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 380 TYR 0.018 0.001 TYR B 90 PHE 0.019 0.001 PHE H 74 TRP 0.025 0.003 TRP F 410 HIS 0.005 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (24606) covalent geometry : angle 0.59887 / 0.29 (33282) hydrogen bonds : bond 0.02953 / 1.92 ( 1061) hydrogen bonds : angle 4.10260 / 2.89 ( 3000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7633 (mm) cc_final: 0.7367 (mt) REVERT: A 128 MET cc_start: 0.8053 (mmp) cc_final: 0.7499 (tpp) REVERT: A 157 LEU cc_start: 0.9430 (tp) cc_final: 0.9117 (tp) REVERT: A 234 MET cc_start: 0.8993 (mtm) cc_final: 0.8639 (mtm) REVERT: A 334 MET cc_start: 0.8515 (mmm) cc_final: 0.8243 (mmm) REVERT: A 399 MET cc_start: 0.8454 (tpp) cc_final: 0.8091 (tmm) REVERT: B 335 MET cc_start: 0.9518 (mtp) cc_final: 0.9318 (mtp) REVERT: B 462 MET cc_start: 0.9168 (ttm) cc_final: 0.8957 (ttm) REVERT: B 533 MET cc_start: 0.9018 (ppp) cc_final: 0.8356 (ppp) REVERT: C 128 MET cc_start: 0.9212 (mtp) cc_final: 0.7960 (tmm) REVERT: D 234 MET cc_start: 0.9223 (mtm) cc_final: 0.8600 (mtm) REVERT: D 307 MET cc_start: 0.7791 (mmt) cc_final: 0.7413 (mmp) REVERT: D 334 MET cc_start: 0.9528 (tpp) cc_final: 0.9286 (tpp) REVERT: E 128 MET cc_start: 0.8769 (tpp) cc_final: 0.7855 (tmm) REVERT: E 225 HIS cc_start: 0.7359 (p90) cc_final: 0.7032 (p-80) REVERT: E 334 MET cc_start: 0.9310 (mtt) cc_final: 0.9060 (mtt) REVERT: E 376 MET cc_start: 0.9428 (mtm) cc_final: 0.9183 (ptp) REVERT: F 207 ILE cc_start: 0.9583 (mt) cc_final: 0.9359 (mt) REVERT: F 309 MET cc_start: 0.8451 (ppp) cc_final: 0.7737 (ppp) REVERT: F 462 MET cc_start: 0.9122 (mtp) cc_final: 0.8859 (tmm) REVERT: G 47 MET cc_start: 0.6165 (mmm) cc_final: 0.5110 (tmm) REVERT: G 88 GLU cc_start: 0.8717 (pt0) cc_final: 0.7988 (mm-30) REVERT: H 19 HIS cc_start: 0.9295 (m90) cc_final: 0.9086 (m-70) REVERT: I 46 LYS cc_start: 0.9116 (pptt) cc_final: 0.8797 (pttm) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.1504 time to fit residues: 51.5542 Evaluate side-chains 166 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 8 optimal weight: 9.9990 chunk 187 optimal weight: 0.2980 chunk 129 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 153 optimal weight: 0.0970 chunk 176 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 ASN A 244 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 262 GLN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.040603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.030588 restraints weight = 242618.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.031364 restraints weight = 157975.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.031914 restraints weight = 116336.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.032316 restraints weight = 92741.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.032603 restraints weight = 78432.168| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24606 Z= 0.113 Angle : 0.596 10.290 33282 Z= 0.289 Chirality : 0.038 0.154 3819 Planarity : 0.004 0.057 4233 Dihedral : 5.185 53.250 3225 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2943 helix: 0.64 (0.13), residues: 1740 sheet: -1.60 (0.31), residues: 219 loop : -1.07 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 433 TYR 0.014 0.001 TYR A 77 PHE 0.019 0.001 PHE H 74 TRP 0.022 0.002 TRP F 410 HIS 0.004 0.001 HIS I 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (24606) covalent geometry : angle 0.59557 / 0.29 (33282) hydrogen bonds : bond 0.02764 / 1.81 ( 1061) hydrogen bonds : angle 3.98629 / 2.81 ( 3000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.994 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 30 LEU cc_start: 0.7926 (mm) cc_final: 0.7691 (mt) REVERT: A 128 MET cc_start: 0.8138 (mmp) cc_final: 0.7291 (mmm) REVERT: A 157 LEU cc_start: 0.9434 (tp) cc_final: 0.9099 (tp) REVERT: A 317 ASP cc_start: 0.9451 (t70) cc_final: 0.9037 (m-30) REVERT: A 399 MET cc_start: 0.8478 (tpp) cc_final: 0.8188 (tmm) REVERT: B 207 ILE cc_start: 0.9787 (mt) cc_final: 0.9564 (mt) REVERT: B 216 ASP cc_start: 0.8107 (t0) cc_final: 0.7853 (t0) REVERT: B 460 ILE cc_start: 0.9582 (tp) cc_final: 0.9256 (pt) REVERT: B 462 MET cc_start: 0.9269 (ttm) cc_final: 0.9039 (ttm) REVERT: C 128 MET cc_start: 0.9226 (mtp) cc_final: 0.8572 (ptp) REVERT: C 144 LEU cc_start: 0.9820 (mm) cc_final: 0.9577 (mt) REVERT: C 334 MET cc_start: 0.9552 (tpt) cc_final: 0.9241 (tpt) REVERT: C 376 MET cc_start: 0.9490 (mpp) cc_final: 0.9123 (ptp) REVERT: D 147 MET cc_start: 0.8640 (mmp) cc_final: 0.8389 (mmt) REVERT: D 234 MET cc_start: 0.9330 (mtm) cc_final: 0.8867 (mtp) REVERT: D 307 MET cc_start: 0.7630 (mmt) cc_final: 0.7366 (mmp) REVERT: D 334 MET cc_start: 0.9546 (tpp) cc_final: 0.9326 (tpp) REVERT: D 348 MET cc_start: 0.9497 (ptm) cc_final: 0.9129 (ptm) REVERT: D 376 MET cc_start: 0.9283 (ptp) cc_final: 0.9059 (ptp) REVERT: E 128 MET cc_start: 0.8805 (tpp) cc_final: 0.7814 (tmm) REVERT: E 225 HIS cc_start: 0.7490 (p90) cc_final: 0.7109 (p-80) REVERT: E 334 MET cc_start: 0.9336 (mtt) cc_final: 0.8998 (mtt) REVERT: F 207 ILE cc_start: 0.9602 (mt) cc_final: 0.9374 (mt) REVERT: F 234 MET cc_start: 0.9307 (mtm) cc_final: 0.8962 (mtm) REVERT: F 309 MET cc_start: 0.8803 (ppp) cc_final: 0.8390 (ppp) REVERT: F 348 MET cc_start: 0.8730 (ttm) cc_final: 0.8176 (ttt) REVERT: F 399 MET cc_start: 0.9242 (mmt) cc_final: 0.9016 (mpp) REVERT: F 462 MET cc_start: 0.9230 (mtp) cc_final: 0.8959 (tmm) REVERT: G 88 GLU cc_start: 0.8770 (pt0) cc_final: 0.8072 (mm-30) REVERT: H 19 HIS cc_start: 0.9244 (m90) cc_final: 0.9011 (m-70) REVERT: I 46 LYS cc_start: 0.9067 (pptt) cc_final: 0.8609 (pttm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1399 time to fit residues: 46.2588 Evaluate side-chains 172 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 263 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 265 optimal weight: 0.0970 chunk 296 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 288 optimal weight: 0.0670 chunk 115 optimal weight: 5.9990 overall best weight: 0.8318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN D 536 HIS F 262 GLN G 19 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.039485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.028490 restraints weight = 252149.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.029291 restraints weight = 163834.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.029862 restraints weight = 120039.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.030273 restraints weight = 95156.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.030583 restraints weight = 79743.960| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.6939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 24606 Z= 0.096 Angle : 0.585 11.353 33282 Z= 0.279 Chirality : 0.038 0.175 3819 Planarity : 0.004 0.054 4233 Dihedral : 5.072 51.074 3225 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2943 helix: 0.86 (0.13), residues: 1728 sheet: -1.43 (0.33), residues: 213 loop : -0.85 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 53 TYR 0.017 0.001 TYR D 135 PHE 0.018 0.001 PHE H 74 TRP 0.019 0.002 TRP F 410 HIS 0.008 0.001 HIS G 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (24606) covalent geometry : angle 0.58524 / 0.28 (33282) hydrogen bonds : bond 0.02626 / 1.72 ( 1061) hydrogen bonds : angle 3.87880 / 2.73 ( 3000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.819 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 128 MET cc_start: 0.8204 (mmp) cc_final: 0.7350 (mmm) REVERT: A 157 LEU cc_start: 0.9525 (tp) cc_final: 0.9207 (tt) REVERT: A 234 MET cc_start: 0.9258 (mtm) cc_final: 0.8995 (ptp) REVERT: A 317 ASP cc_start: 0.9442 (t70) cc_final: 0.9029 (m-30) REVERT: A 334 MET cc_start: 0.8393 (mmm) cc_final: 0.8167 (mmm) REVERT: A 399 MET cc_start: 0.8375 (tpp) cc_final: 0.8117 (mmm) REVERT: A 462 MET cc_start: 0.9286 (mpp) cc_final: 0.8774 (ttm) REVERT: B 216 ASP cc_start: 0.8163 (t0) cc_final: 0.7877 (t0) REVERT: B 348 MET cc_start: 0.8752 (ppp) cc_final: 0.8525 (ppp) REVERT: B 462 MET cc_start: 0.9329 (ttm) cc_final: 0.9116 (ttm) REVERT: B 533 MET cc_start: 0.9072 (ptm) cc_final: 0.8521 (ptm) REVERT: C 1 MET cc_start: 0.8857 (mmm) cc_final: 0.7413 (ppp) REVERT: C 128 MET cc_start: 0.9217 (mtp) cc_final: 0.8898 (ptp) REVERT: C 334 MET cc_start: 0.9559 (tpt) cc_final: 0.9245 (tpt) REVERT: D 135 TYR cc_start: 0.8304 (t80) cc_final: 0.7984 (t80) REVERT: D 147 MET cc_start: 0.8625 (mmp) cc_final: 0.8392 (mmt) REVERT: D 234 MET cc_start: 0.9422 (mtm) cc_final: 0.8983 (mtp) REVERT: D 334 MET cc_start: 0.9500 (tpp) cc_final: 0.9263 (tpp) REVERT: D 348 MET cc_start: 0.9496 (ptm) cc_final: 0.9127 (ptm) REVERT: D 376 MET cc_start: 0.9290 (ptp) cc_final: 0.9053 (ptp) REVERT: E 128 MET cc_start: 0.8819 (tpp) cc_final: 0.7886 (tmm) REVERT: E 225 HIS cc_start: 0.7732 (p90) cc_final: 0.7366 (p-80) REVERT: E 334 MET cc_start: 0.9308 (mtt) cc_final: 0.8948 (mtt) REVERT: F 207 ILE cc_start: 0.9596 (mt) cc_final: 0.9381 (mt) REVERT: F 234 MET cc_start: 0.9329 (mtm) cc_final: 0.8957 (mtm) REVERT: F 348 MET cc_start: 0.8757 (ttm) cc_final: 0.8175 (ttt) REVERT: F 462 MET cc_start: 0.9208 (mtp) cc_final: 0.8922 (tmm) REVERT: F 533 MET cc_start: 0.9146 (ppp) cc_final: 0.8919 (ppp) REVERT: G 88 GLU cc_start: 0.8718 (pt0) cc_final: 0.8103 (mm-30) REVERT: H 19 HIS cc_start: 0.9204 (m90) cc_final: 0.8998 (m-70) REVERT: H 73 ASP cc_start: 0.9600 (t70) cc_final: 0.9318 (p0) REVERT: I 47 MET cc_start: 0.5753 (ttp) cc_final: 0.4996 (tmm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1440 time to fit residues: 46.6041 Evaluate side-chains 170 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 40 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 HIS F 458 HIS G 56 ASN I 40 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.034955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.025166 restraints weight = 277212.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.025890 restraints weight = 168204.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.026403 restraints weight = 118864.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.026767 restraints weight = 92118.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.027019 restraints weight = 76427.298| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.8040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 24606 Z= 0.287 Angle : 0.809 11.117 33282 Z= 0.402 Chirality : 0.042 0.176 3819 Planarity : 0.006 0.072 4233 Dihedral : 5.720 53.171 3225 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 2943 helix: 0.12 (0.12), residues: 1752 sheet: -1.71 (0.32), residues: 243 loop : -0.94 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 8 TYR 0.021 0.002 TYR F 540 PHE 0.024 0.003 PHE C 454 TRP 0.035 0.003 TRP F 410 HIS 0.008 0.002 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.29 (24606) covalent geometry : angle 0.80892 / 0.40 (33282) hydrogen bonds : bond 0.03928 / 2.59 ( 1061) hydrogen bonds : angle 4.66611 / 3.27 ( 3000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.742 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 128 MET cc_start: 0.8658 (mmp) cc_final: 0.8221 (mtt) REVERT: A 234 MET cc_start: 0.9457 (mtm) cc_final: 0.9122 (mtp) REVERT: A 334 MET cc_start: 0.8683 (mmm) cc_final: 0.8466 (mmm) REVERT: A 399 MET cc_start: 0.8995 (tpp) cc_final: 0.8669 (tmm) REVERT: A 462 MET cc_start: 0.9338 (mpp) cc_final: 0.8889 (mpp) REVERT: B 114 MET cc_start: 0.9281 (mmp) cc_final: 0.9029 (mmm) REVERT: B 216 ASP cc_start: 0.8161 (t0) cc_final: 0.7926 (t0) REVERT: B 307 MET cc_start: 0.8540 (mmp) cc_final: 0.8103 (mmm) REVERT: B 348 MET cc_start: 0.8746 (ppp) cc_final: 0.8485 (ppp) REVERT: B 462 MET cc_start: 0.9296 (ttm) cc_final: 0.8967 (ttm) REVERT: B 533 MET cc_start: 0.9404 (ptm) cc_final: 0.8959 (ptp) REVERT: C 19 HIS cc_start: 0.9582 (t70) cc_final: 0.9283 (m90) REVERT: C 147 MET cc_start: 0.9132 (mmt) cc_final: 0.8812 (mpp) REVERT: C 334 MET cc_start: 0.9473 (tpt) cc_final: 0.9216 (tpt) REVERT: C 374 LEU cc_start: 0.9395 (tp) cc_final: 0.9165 (tp) REVERT: D 135 TYR cc_start: 0.8475 (t80) cc_final: 0.8197 (t80) REVERT: D 147 MET cc_start: 0.8854 (mmp) cc_final: 0.8615 (mpp) REVERT: D 234 MET cc_start: 0.9460 (mtm) cc_final: 0.8999 (mtp) REVERT: D 348 MET cc_start: 0.9564 (ptm) cc_final: 0.9153 (ptm) REVERT: E 128 MET cc_start: 0.8940 (tpp) cc_final: 0.8575 (tpp) REVERT: E 225 HIS cc_start: 0.7659 (p90) cc_final: 0.7268 (p-80) REVERT: E 307 MET cc_start: 0.8556 (tpp) cc_final: 0.8318 (tpp) REVERT: E 334 MET cc_start: 0.9249 (mtt) cc_final: 0.8903 (mtt) REVERT: E 348 MET cc_start: 0.9599 (mtp) cc_final: 0.9395 (mtt) REVERT: F 210 MET cc_start: 0.9078 (tpp) cc_final: 0.8857 (tpp) REVERT: F 348 MET cc_start: 0.8832 (ttm) cc_final: 0.8544 (ttp) REVERT: F 399 MET cc_start: 0.8907 (mpp) cc_final: 0.8629 (mpp) REVERT: F 462 MET cc_start: 0.9262 (mtp) cc_final: 0.8949 (tmm) REVERT: H 19 HIS cc_start: 0.9159 (m90) cc_final: 0.8904 (m-70) REVERT: H 73 ASP cc_start: 0.9536 (t70) cc_final: 0.9277 (p0) REVERT: I 47 MET cc_start: 0.7215 (ttp) cc_final: 0.6518 (ttp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1364 time to fit residues: 40.8648 Evaluate side-chains 143 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 chunk 253 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 238 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 536 HIS D 536 HIS E 237 ASN E 475 ASN F 536 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.036557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.026318 restraints weight = 270575.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.027036 restraints weight = 164296.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.027531 restraints weight = 116737.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.027861 restraints weight = 91143.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.028100 restraints weight = 76452.131| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.8152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 24606 Z= 0.106 Angle : 0.620 10.036 33282 Z= 0.300 Chirality : 0.040 0.218 3819 Planarity : 0.004 0.052 4233 Dihedral : 5.275 57.028 3225 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2943 helix: 0.70 (0.13), residues: 1743 sheet: -1.47 (0.35), residues: 213 loop : -0.84 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 8 TYR 0.015 0.001 TYR A 77 PHE 0.021 0.001 PHE D 532 TRP 0.019 0.002 TRP F 410 HIS 0.006 0.001 HIS D 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (24606) covalent geometry : angle 0.62048 / 0.30 (33282) hydrogen bonds : bond 0.02801 / 1.82 ( 1061) hydrogen bonds : angle 4.08440 / 2.89 ( 3000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8622 (mmp) cc_final: 0.8188 (mtt) REVERT: A 147 MET cc_start: 0.9017 (mpp) cc_final: 0.8754 (mpp) REVERT: A 157 LEU cc_start: 0.9459 (tp) cc_final: 0.9185 (tp) REVERT: A 234 MET cc_start: 0.9519 (mtm) cc_final: 0.9045 (mtm) REVERT: A 317 ASP cc_start: 0.9482 (t70) cc_final: 0.9106 (m-30) REVERT: A 334 MET cc_start: 0.8675 (mmm) cc_final: 0.8467 (mmm) REVERT: A 399 MET cc_start: 0.8659 (tpp) cc_final: 0.8341 (tmm) REVERT: A 462 MET cc_start: 0.9324 (mpp) cc_final: 0.8990 (mpp) REVERT: B 147 MET cc_start: 0.9157 (mmm) cc_final: 0.8790 (mmm) REVERT: B 210 MET cc_start: 0.9628 (tpt) cc_final: 0.9186 (tpp) REVERT: B 216 ASP cc_start: 0.8252 (t0) cc_final: 0.7970 (t0) REVERT: B 335 MET cc_start: 0.9432 (mtt) cc_final: 0.9221 (mtp) REVERT: B 376 MET cc_start: 0.9598 (ptp) cc_final: 0.9330 (pmm) REVERT: B 443 LEU cc_start: 0.9304 (mt) cc_final: 0.9104 (mt) REVERT: B 533 MET cc_start: 0.9368 (ptm) cc_final: 0.8807 (ptm) REVERT: C 19 HIS cc_start: 0.9621 (t70) cc_final: 0.9293 (m90) REVERT: D 135 TYR cc_start: 0.8477 (t80) cc_final: 0.8221 (t80) REVERT: D 234 MET cc_start: 0.9552 (mtm) cc_final: 0.9137 (mtp) REVERT: D 348 MET cc_start: 0.9551 (ptm) cc_final: 0.9121 (ptm) REVERT: E 147 MET cc_start: 0.8819 (mtm) cc_final: 0.8552 (ptp) REVERT: E 225 HIS cc_start: 0.8043 (p90) cc_final: 0.7693 (p-80) REVERT: E 307 MET cc_start: 0.8349 (tpp) cc_final: 0.8022 (tpp) REVERT: E 334 MET cc_start: 0.9318 (mtt) cc_final: 0.9005 (mtt) REVERT: E 348 MET cc_start: 0.9592 (mtp) cc_final: 0.9388 (mtt) REVERT: E 376 MET cc_start: 0.9531 (mpp) cc_final: 0.9232 (mpp) REVERT: F 348 MET cc_start: 0.8627 (ttm) cc_final: 0.8180 (ttt) REVERT: F 462 MET cc_start: 0.9220 (mtp) cc_final: 0.8872 (tmm) REVERT: H 73 ASP cc_start: 0.9551 (t70) cc_final: 0.9334 (p0) REVERT: I 47 MET cc_start: 0.7145 (ttp) cc_final: 0.6590 (ttp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1452 time to fit residues: 45.8266 Evaluate side-chains 154 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 6 optimal weight: 20.0000 chunk 292 optimal weight: 2.9990 chunk 277 optimal weight: 50.0000 chunk 147 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN H 19 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.034477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.024736 restraints weight = 277399.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.025455 restraints weight = 166601.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.025963 restraints weight = 117711.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.026299 restraints weight = 91185.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.026561 restraints weight = 75916.551| |-----------------------------------------------------------------------------| r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.8618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24606 Z= 0.224 Angle : 0.710 11.143 33282 Z= 0.351 Chirality : 0.040 0.175 3819 Planarity : 0.005 0.053 4233 Dihedral : 5.436 55.601 3225 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2943 helix: 0.48 (0.13), residues: 1725 sheet: -1.49 (0.35), residues: 219 loop : -0.96 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 8 TYR 0.013 0.002 TYR B 540 PHE 0.020 0.002 PHE D 532 TRP 0.029 0.002 TRP F 410 HIS 0.007 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (24606) covalent geometry : angle 0.71035 / 0.35 (33282) hydrogen bonds : bond 0.03329 / 2.18 ( 1061) hydrogen bonds : angle 4.46515 / 3.14 ( 3000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.865 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 128 MET cc_start: 0.8621 (mmp) cc_final: 0.8325 (mtm) REVERT: A 147 MET cc_start: 0.9183 (mpp) cc_final: 0.8964 (mpp) REVERT: A 234 MET cc_start: 0.9529 (mtm) cc_final: 0.9049 (mtm) REVERT: A 317 ASP cc_start: 0.9546 (t70) cc_final: 0.9242 (m-30) REVERT: A 334 MET cc_start: 0.8777 (mmm) cc_final: 0.8525 (mmm) REVERT: A 399 MET cc_start: 0.8868 (tpp) cc_final: 0.8499 (tmm) REVERT: A 462 MET cc_start: 0.9333 (mpp) cc_final: 0.9015 (mpp) REVERT: B 47 MET cc_start: 0.8666 (mmp) cc_final: 0.8429 (mmm) REVERT: B 114 MET cc_start: 0.9326 (mmp) cc_final: 0.9055 (mmm) REVERT: B 147 MET cc_start: 0.9276 (mmm) cc_final: 0.8973 (mmm) REVERT: B 216 ASP cc_start: 0.8335 (t0) cc_final: 0.8097 (t0) REVERT: B 234 MET cc_start: 0.9377 (tpp) cc_final: 0.9160 (tpt) REVERT: B 334 MET cc_start: 0.9648 (tpp) cc_final: 0.9371 (tpp) REVERT: B 533 MET cc_start: 0.9423 (ptm) cc_final: 0.8942 (ptp) REVERT: C 19 HIS cc_start: 0.9585 (t70) cc_final: 0.9323 (m90) REVERT: C 128 MET cc_start: 0.8959 (ptp) cc_final: 0.8204 (ptp) REVERT: C 147 MET cc_start: 0.9190 (mmt) cc_final: 0.8803 (mpp) REVERT: C 210 MET cc_start: 0.9119 (mmp) cc_final: 0.8855 (mmp) REVERT: C 334 MET cc_start: 0.9375 (tpt) cc_final: 0.9036 (ttt) REVERT: D 135 TYR cc_start: 0.8568 (t80) cc_final: 0.8343 (t80) REVERT: D 234 MET cc_start: 0.9535 (mtm) cc_final: 0.9302 (mtm) REVERT: D 348 MET cc_start: 0.9597 (ptm) cc_final: 0.9153 (ptm) REVERT: E 128 MET cc_start: 0.8987 (tpp) cc_final: 0.8617 (tpp) REVERT: E 307 MET cc_start: 0.8612 (tpp) cc_final: 0.8220 (tpp) REVERT: E 334 MET cc_start: 0.9273 (mtt) cc_final: 0.9003 (mtt) REVERT: E 376 MET cc_start: 0.9510 (mpp) cc_final: 0.9258 (mpp) REVERT: F 147 MET cc_start: 0.9145 (mmp) cc_final: 0.8891 (mpp) REVERT: F 399 MET cc_start: 0.8883 (mpp) cc_final: 0.8582 (mpp) REVERT: F 462 MET cc_start: 0.9244 (mtp) cc_final: 0.8951 (tmm) REVERT: F 533 MET cc_start: 0.9298 (ppp) cc_final: 0.8894 (ppp) REVERT: G 47 MET cc_start: 0.5007 (mtp) cc_final: 0.3131 (tpp) REVERT: I 47 MET cc_start: 0.7302 (ttp) cc_final: 0.6606 (ttp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1436 time to fit residues: 41.4507 Evaluate side-chains 141 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 269 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 295 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS F 461 HIS F 475 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.025312 restraints weight = 267302.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.026077 restraints weight = 160530.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.026593 restraints weight = 112508.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.026974 restraints weight = 86792.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.027245 restraints weight = 71964.789| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.8704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24606 Z= 0.108 Angle : 0.622 9.770 33282 Z= 0.302 Chirality : 0.039 0.225 3819 Planarity : 0.004 0.051 4233 Dihedral : 5.263 59.536 3225 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2943 helix: 0.78 (0.13), residues: 1728 sheet: -1.34 (0.36), residues: 219 loop : -0.84 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 8 TYR 0.015 0.001 TYR A 77 PHE 0.033 0.001 PHE G 75 TRP 0.020 0.002 TRP F 410 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (24606) covalent geometry : angle 0.62205 / 0.30 (33282) hydrogen bonds : bond 0.02788 / 1.83 ( 1061) hydrogen bonds : angle 4.09729 / 2.89 ( 3000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8646 (mmp) cc_final: 0.8302 (mtm) REVERT: A 147 MET cc_start: 0.9139 (mpp) cc_final: 0.8870 (mpp) REVERT: A 157 LEU cc_start: 0.9482 (tp) cc_final: 0.9136 (tt) REVERT: A 234 MET cc_start: 0.9551 (mtm) cc_final: 0.9031 (mtm) REVERT: A 317 ASP cc_start: 0.9497 (t70) cc_final: 0.9123 (m-30) REVERT: A 399 MET cc_start: 0.8669 (tpp) cc_final: 0.8416 (tmm) REVERT: B 114 MET cc_start: 0.9378 (mmp) cc_final: 0.9096 (mmm) REVERT: B 147 MET cc_start: 0.9215 (mmm) cc_final: 0.8922 (mmm) REVERT: B 216 ASP cc_start: 0.8266 (t0) cc_final: 0.7999 (t0) REVERT: B 234 MET cc_start: 0.9305 (tpp) cc_final: 0.9052 (tpt) REVERT: B 334 MET cc_start: 0.9628 (tpp) cc_final: 0.9304 (tpp) REVERT: B 443 LEU cc_start: 0.9419 (mt) cc_final: 0.9091 (mp) REVERT: B 462 MET cc_start: 0.9424 (ttt) cc_final: 0.8844 (tpp) REVERT: B 533 MET cc_start: 0.9313 (ptm) cc_final: 0.8820 (ptp) REVERT: C 19 HIS cc_start: 0.9583 (t70) cc_final: 0.9315 (m90) REVERT: C 128 MET cc_start: 0.8786 (ptp) cc_final: 0.7885 (ptp) REVERT: C 210 MET cc_start: 0.9059 (mmp) cc_final: 0.8825 (mmp) REVERT: C 334 MET cc_start: 0.9407 (tpt) cc_final: 0.9146 (tpt) REVERT: C 462 MET cc_start: 0.9630 (mtp) cc_final: 0.9162 (ttt) REVERT: D 234 MET cc_start: 0.9514 (mtm) cc_final: 0.9086 (mtp) REVERT: D 348 MET cc_start: 0.9578 (ptm) cc_final: 0.9118 (ptm) REVERT: E 334 MET cc_start: 0.9305 (mtt) cc_final: 0.9027 (mtt) REVERT: E 376 MET cc_start: 0.9508 (mpp) cc_final: 0.9270 (mpp) REVERT: F 348 MET cc_start: 0.8733 (ttm) cc_final: 0.8310 (ttt) REVERT: F 399 MET cc_start: 0.8843 (mpp) cc_final: 0.8640 (mpp) REVERT: F 462 MET cc_start: 0.9166 (mtp) cc_final: 0.8825 (tmm) REVERT: F 533 MET cc_start: 0.9116 (ppp) cc_final: 0.8796 (ppp) REVERT: G 47 MET cc_start: 0.5373 (mtp) cc_final: 0.3508 (tpp) REVERT: I 47 MET cc_start: 0.7378 (ttp) cc_final: 0.7086 (ttp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1448 time to fit residues: 44.2043 Evaluate side-chains 149 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 73 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 280 optimal weight: 7.9990 chunk 136 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 143 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.034948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.025024 restraints weight = 267825.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.025751 restraints weight = 162834.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.026254 restraints weight = 115438.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.026621 restraints weight = 90134.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.026858 restraints weight = 74832.937| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.8886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24606 Z= 0.132 Angle : 0.625 11.195 33282 Z= 0.304 Chirality : 0.039 0.168 3819 Planarity : 0.004 0.051 4233 Dihedral : 5.181 59.158 3225 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2943 helix: 0.84 (0.13), residues: 1743 sheet: -1.28 (0.36), residues: 219 loop : -0.81 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 8 TYR 0.014 0.001 TYR A 77 PHE 0.021 0.001 PHE I 74 TRP 0.023 0.002 TRP F 410 HIS 0.003 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (24606) covalent geometry : angle 0.62474 / 0.30 (33282) hydrogen bonds : bond 0.02814 / 1.84 ( 1061) hydrogen bonds : angle 4.13270 / 2.92 ( 3000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3893.52 seconds wall clock time: 68 minutes 25.20 seconds (4105.20 seconds total)