Starting phenix.real_space_refine on Fri May 23 15:59:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jns_36450/05_2025/8jns_36450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jns_36450/05_2025/8jns_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_36450/05_2025/8jns_36450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jns_36450/05_2025/8jns_36450.map" model { file = "/net/cci-nas-00/data/ceres_data/8jns_36450/05_2025/8jns_36450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jns_36450/05_2025/8jns_36450.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.66, per 1000 atoms: 0.61 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: 6.43 Conformation dependent library (CDL) restraints added in 3.1 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: 3.00 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: 7.21 Time building geometry restraints manager: 7.38 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: 12914 16.90 - 33.79: 1461 33.79 - 50.69: 537 50.69 - 67.59: 267 67.59 - 84.48: 40 Dihedral angle restraints: 15219 sinusoidal: 6417 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 15216 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: 0.03 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.170 Set scattering table: 0.250 Process input model: 53.500 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.110 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 18.702 84.482 9453 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.004 TRP B 189 HIS 0.005 0.001 HIS A 466 PHE 0.018 0.003 PHE F 532 TYR 0.022 0.004 TYR A 371 ARG 0.004 0.001 ARG C 112 Details of bonding type rmsd hydrogen bonds : bond 0.25127 ( 1061) hydrogen bonds : angle 9.05686 ( 3000) covalent geometry : bond 0.00955 (24606) covalent geometry : angle 1.51588 (33282) *********************** 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 : 3.130 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: 0.8764 (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: 0.8140 (pm20) REVERT: A 290 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 332 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 434 LEU cc_start: 0.9225 (mt) cc_final: 0.8977 (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: 0.7986 (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: 0.8734 (pp) REVERT: C 290 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9007 (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: 0.8722 (p) REVERT: C 437 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8960 (tp) REVERT: D 175 LYS cc_start: 0.8708 (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: 0.9227 (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: 0.9171 (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: 0.8585 (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: 0.6564 (p) REVERT: I 68 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7377 (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: 0.3674 time to fit residues: 428.8233 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 : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 34 ASN A 123 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 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 283 GLN C 19 HIS C 34 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN 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 G 56 ASN H 14 HIS H 19 HIS I 34 ASN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.042828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.031712 restraints weight = 231322.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032562 restraints weight = 155103.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.033179 restraints weight = 114287.257| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24606 Z= 0.161 Angle : 0.761 10.365 33282 Z= 0.384 Chirality : 0.044 0.247 3819 Planarity : 0.006 0.076 4233 Dihedral : 10.801 75.344 3411 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.22 % Allowed : 3.83 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.14), residues: 2943 helix: -1.36 (0.11), residues: 1716 sheet: -2.66 (0.30), residues: 213 loop : -2.05 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP F 189 HIS 0.007 0.001 HIS G 40 PHE 0.021 0.002 PHE I 74 TYR 0.020 0.002 TYR E 305 ARG 0.007 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 1061) hydrogen bonds : angle 5.15162 ( 3000) covalent geometry : bond 0.00358 (24606) covalent geometry : angle 0.76088 (33282) *********************** 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 258 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 252 time to evaluate : 3.059 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: A 114 MET cc_start: 0.9234 (mmp) cc_final: 0.8958 (mmm) REVERT: A 157 LEU cc_start: 0.9354 (tp) cc_final: 0.8984 (tp) REVERT: B 140 VAL cc_start: 0.9295 (t) cc_final: 0.9077 (t) REVERT: B 216 ASP cc_start: 0.8903 (m-30) cc_final: 0.8686 (t0) REVERT: B 335 MET cc_start: 0.9466 (mtp) cc_final: 0.8816 (ttm) REVERT: B 462 MET cc_start: 0.9239 (mtp) cc_final: 0.8888 (ttm) REVERT: C 307 MET cc_start: 0.7290 (mmt) cc_final: 0.6845 (mmt) REVERT: C 374 LEU cc_start: 0.9327 (tp) cc_final: 0.9105 (tp) REVERT: C 399 MET cc_start: 0.9158 (mmm) cc_final: 0.8723 (mpp) REVERT: C 462 MET cc_start: 0.9432 (mtp) cc_final: 0.8941 (ttp) REVERT: D 307 MET cc_start: 0.7298 (mmt) cc_final: 0.6978 (mmt) REVERT: D 376 MET cc_start: 0.9428 (mtm) cc_final: 0.9206 (ptp) REVERT: E 302 LEU cc_start: 0.9468 (mt) cc_final: 0.9167 (mt) REVERT: E 376 MET cc_start: 0.9506 (mtm) cc_final: 0.9035 (ptp) REVERT: F 147 MET cc_start: 0.8859 (mmt) cc_final: 0.8572 (mmp) REVERT: F 234 MET cc_start: 0.8793 (mtm) cc_final: 0.8468 (mtp) REVERT: F 459 ILE cc_start: 0.9608 (pt) cc_final: 0.9321 (mm) REVERT: F 462 MET cc_start: 0.9099 (mtp) cc_final: 0.8735 (tmm) REVERT: G 47 MET cc_start: 0.5996 (mmm) cc_final: 0.4924 (mmm) REVERT: G 75 PHE cc_start: 0.9477 (m-10) cc_final: 0.9246 (m-80) REVERT: H 31 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6701 (mp0) REVERT: H 73 ASP cc_start: 0.9378 (t70) cc_final: 0.9025 (p0) REVERT: I 47 MET cc_start: 0.8288 (tpt) cc_final: 0.7930 (tpp) outliers start: 6 outliers final: 0 residues processed: 258 average time/residue: 0.3556 time to fit residues: 144.3790 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 : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 173 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 237 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN F 237 ASN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 HIS H 40 HIS I 14 HIS ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.037749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.027492 restraints weight = 255683.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.028274 restraints weight = 162736.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.028822 restraints weight = 117081.391| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24606 Z= 0.201 Angle : 0.689 8.785 33282 Z= 0.349 Chirality : 0.040 0.165 3819 Planarity : 0.006 0.063 4233 Dihedral : 10.240 86.682 3411 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 2943 helix: -0.26 (0.12), residues: 1734 sheet: -2.28 (0.30), residues: 213 loop : -1.51 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP F 410 HIS 0.006 0.001 HIS A 82 PHE 0.022 0.002 PHE H 74 TYR 0.018 0.002 TYR B 90 ARG 0.005 0.001 ARG C 112 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 1061) hydrogen bonds : angle 4.57338 ( 3000) covalent geometry : bond 0.00438 (24606) covalent geometry : angle 0.68864 (33282) *********************** 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 204 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 3.255 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: A 128 MET cc_start: 0.8077 (mmp) cc_final: 0.7350 (mmm) REVERT: A 144 LEU cc_start: 0.9612 (tt) cc_final: 0.9403 (pp) REVERT: A 234 MET cc_start: 0.9197 (mtm) cc_final: 0.8984 (mtm) REVERT: A 334 MET cc_start: 0.8767 (mmt) cc_final: 0.8408 (mmm) REVERT: A 399 MET cc_start: 0.8591 (tpp) cc_final: 0.8240 (tmm) REVERT: B 114 MET cc_start: 0.9268 (mmp) cc_final: 0.9056 (mmm) REVERT: B 307 MET cc_start: 0.8514 (mmp) cc_final: 0.8005 (mmm) REVERT: B 335 MET cc_start: 0.9553 (mtp) cc_final: 0.9300 (mtp) REVERT: B 533 MET cc_start: 0.9182 (ppp) cc_final: 0.8509 (ppp) REVERT: C 1 MET cc_start: 0.9328 (mmp) cc_final: 0.9037 (mmm) REVERT: C 19 HIS cc_start: 0.9646 (t70) cc_final: 0.9355 (m-70) REVERT: C 399 MET cc_start: 0.9128 (mmm) cc_final: 0.8844 (mpp) REVERT: D 334 MET cc_start: 0.9402 (tpt) cc_final: 0.9022 (tpt) REVERT: D 348 MET cc_start: 0.9630 (ptm) cc_final: 0.9242 (ptm) REVERT: E 225 HIS cc_start: 0.7810 (p90) cc_final: 0.7549 (p-80) REVERT: E 307 MET cc_start: 0.8319 (tpp) cc_final: 0.7830 (tpp) REVERT: E 334 MET cc_start: 0.9472 (mmm) cc_final: 0.9054 (mmm) REVERT: E 533 MET cc_start: 0.8520 (ppp) cc_final: 0.7556 (mmp) REVERT: F 216 ASP cc_start: 0.8822 (m-30) cc_final: 0.8580 (t0) REVERT: F 234 MET cc_start: 0.9042 (mtm) cc_final: 0.8713 (mtp) REVERT: F 309 MET cc_start: 0.8400 (ppp) cc_final: 0.8048 (ppp) REVERT: F 348 MET cc_start: 0.9006 (mtm) cc_final: 0.8647 (ptm) REVERT: F 462 MET cc_start: 0.9188 (mtp) cc_final: 0.8933 (tmm) REVERT: H 31 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6135 (mp0) REVERT: H 73 ASP cc_start: 0.9570 (t70) cc_final: 0.9263 (p0) REVERT: I 46 LYS cc_start: 0.9172 (pptt) cc_final: 0.8746 (pttm) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.3533 time to fit residues: 115.6348 Evaluate side-chains 164 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 4 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 122 optimal weight: 0.3980 chunk 147 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN C 262 GLN D 225 HIS D 237 ASN F 262 GLN H 19 HIS I 40 HIS I 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.039653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.029858 restraints weight = 243281.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.030605 restraints weight = 157591.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.031114 restraints weight = 116197.271| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24606 Z= 0.145 Angle : 0.616 10.074 33282 Z= 0.306 Chirality : 0.039 0.152 3819 Planarity : 0.005 0.058 4233 Dihedral : 9.872 85.631 3411 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2943 helix: 0.34 (0.13), residues: 1743 sheet: -1.91 (0.31), residues: 213 loop : -1.18 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 410 HIS 0.005 0.001 HIS H 19 PHE 0.020 0.001 PHE H 74 TYR 0.018 0.001 TYR I 29 ARG 0.008 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 1061) hydrogen bonds : angle 4.21489 ( 3000) covalent geometry : bond 0.00323 (24606) covalent geometry : angle 0.61565 (33282) *********************** 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 196 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 3.176 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: A 128 MET cc_start: 0.8281 (mmp) cc_final: 0.7510 (mmm) REVERT: A 157 LEU cc_start: 0.9465 (tp) cc_final: 0.9147 (tp) REVERT: A 334 MET cc_start: 0.8756 (mmt) cc_final: 0.8413 (mmm) REVERT: A 399 MET cc_start: 0.8657 (tpp) cc_final: 0.8381 (tmm) REVERT: B 114 MET cc_start: 0.9423 (mmp) cc_final: 0.9209 (mmm) REVERT: B 533 MET cc_start: 0.9206 (ppp) cc_final: 0.8826 (ppp) REVERT: C 19 HIS cc_start: 0.9661 (t70) cc_final: 0.9357 (m-70) REVERT: C 128 MET cc_start: 0.8984 (ptp) cc_final: 0.8123 (ptp) REVERT: C 334 MET cc_start: 0.9600 (tpt) cc_final: 0.9330 (tpt) REVERT: C 533 MET cc_start: 0.8326 (ppp) cc_final: 0.8098 (ppp) REVERT: D 135 TYR cc_start: 0.8261 (t80) cc_final: 0.8008 (t80) REVERT: D 147 MET cc_start: 0.8896 (mmm) cc_final: 0.8687 (mmm) REVERT: D 234 MET cc_start: 0.9337 (mtm) cc_final: 0.8942 (mtp) REVERT: D 334 MET cc_start: 0.9429 (tpt) cc_final: 0.9095 (tpt) REVERT: D 376 MET cc_start: 0.9393 (mpp) cc_final: 0.9124 (mpp) REVERT: E 128 MET cc_start: 0.8572 (tpp) cc_final: 0.8103 (tmm) REVERT: E 225 HIS cc_start: 0.7752 (p90) cc_final: 0.7516 (p-80) REVERT: E 334 MET cc_start: 0.9505 (mmm) cc_final: 0.9046 (mmm) REVERT: F 216 ASP cc_start: 0.8880 (m-30) cc_final: 0.8677 (t0) REVERT: F 234 MET cc_start: 0.9041 (mtm) cc_final: 0.8671 (mtm) REVERT: F 335 MET cc_start: 0.9258 (mtt) cc_final: 0.8972 (tpp) REVERT: F 348 MET cc_start: 0.9083 (mtm) cc_final: 0.8589 (ttp) REVERT: F 462 MET cc_start: 0.9294 (mtp) cc_final: 0.8980 (tmm) REVERT: H 19 HIS cc_start: 0.9232 (m90) cc_final: 0.9030 (m-70) REVERT: H 31 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5914 (mm-30) REVERT: H 73 ASP cc_start: 0.9456 (t70) cc_final: 0.9166 (p0) REVERT: I 46 LYS cc_start: 0.9225 (pptt) cc_final: 0.8912 (pttm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.3227 time to fit residues: 102.8667 Evaluate side-chains 162 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 157 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 294 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.037302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.026669 restraints weight = 258172.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.027439 restraints weight = 161017.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.027996 restraints weight = 116147.468| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.7191 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= 0.126 Angle : 0.606 10.347 33282 Z= 0.298 Chirality : 0.039 0.159 3819 Planarity : 0.005 0.056 4233 Dihedral : 9.549 82.553 3411 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2943 helix: 0.64 (0.13), residues: 1743 sheet: -1.60 (0.33), residues: 213 loop : -1.02 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 410 HIS 0.004 0.001 HIS I 19 PHE 0.023 0.001 PHE H 74 TYR 0.015 0.001 TYR I 29 ARG 0.004 0.000 ARG G 16 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 1061) hydrogen bonds : angle 4.13620 ( 3000) covalent geometry : bond 0.00284 (24606) covalent geometry : angle 0.60641 (33282) *********************** 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 184 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 3.159 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: 0.8394 (mmp) cc_final: 0.7706 (mmm) REVERT: A 147 MET cc_start: 0.8939 (mpp) cc_final: 0.8581 (mpp) REVERT: A 234 MET cc_start: 0.9389 (mtm) cc_final: 0.9059 (mtm) REVERT: A 334 MET cc_start: 0.8837 (mmt) cc_final: 0.8467 (mmm) REVERT: A 399 MET cc_start: 0.8568 (tpp) cc_final: 0.8308 (tmm) REVERT: A 462 MET cc_start: 0.9368 (mpp) cc_final: 0.8896 (ttm) REVERT: B 114 MET cc_start: 0.9363 (mmp) cc_final: 0.9146 (mmm) REVERT: B 533 MET cc_start: 0.9077 (ppp) cc_final: 0.8849 (ptp) REVERT: C 19 HIS cc_start: 0.9662 (t70) cc_final: 0.9361 (m-70) REVERT: C 128 MET cc_start: 0.8810 (ptp) cc_final: 0.8212 (ptp) REVERT: C 334 MET cc_start: 0.9592 (tpt) cc_final: 0.9334 (tpt) REVERT: D 135 TYR cc_start: 0.8346 (t80) cc_final: 0.8077 (t80) REVERT: D 147 MET cc_start: 0.8903 (mmm) cc_final: 0.8653 (mmm) REVERT: D 216 ASP cc_start: 0.9173 (m-30) cc_final: 0.8918 (t0) REVERT: D 234 MET cc_start: 0.9470 (mtm) cc_final: 0.9018 (mtp) REVERT: D 334 MET cc_start: 0.9406 (tpt) cc_final: 0.9113 (tpt) REVERT: D 348 MET cc_start: 0.9560 (ptm) cc_final: 0.9163 (ptm) REVERT: D 376 MET cc_start: 0.9445 (mpp) cc_final: 0.9093 (mpp) REVERT: E 128 MET cc_start: 0.8530 (tpp) cc_final: 0.7958 (tpp) REVERT: E 147 MET cc_start: 0.8896 (mtm) cc_final: 0.8581 (ptp) REVERT: E 225 HIS cc_start: 0.7870 (p90) cc_final: 0.7664 (p-80) REVERT: E 334 MET cc_start: 0.9432 (mmm) cc_final: 0.9093 (mmm) REVERT: F 206 ASP cc_start: 0.9091 (m-30) cc_final: 0.8876 (m-30) REVERT: F 216 ASP cc_start: 0.8959 (m-30) cc_final: 0.8740 (t0) REVERT: F 234 MET cc_start: 0.9123 (mtm) cc_final: 0.8745 (mtm) REVERT: F 335 MET cc_start: 0.9220 (mtt) cc_final: 0.8984 (tpp) REVERT: F 348 MET cc_start: 0.9015 (mtm) cc_final: 0.8514 (ttm) REVERT: F 462 MET cc_start: 0.9248 (mtp) cc_final: 0.8882 (tmm) REVERT: H 31 GLU cc_start: 0.6242 (mt-10) cc_final: 0.5966 (mm-30) REVERT: H 73 ASP cc_start: 0.9536 (t70) cc_final: 0.9278 (p0) REVERT: I 46 LYS cc_start: 0.9213 (pptt) cc_final: 0.8906 (pttm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3347 time to fit residues: 101.3318 Evaluate side-chains 157 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 50 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 285 optimal weight: 20.0000 chunk 64 optimal weight: 0.0980 chunk 90 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 237 ASN B 466 HIS D 536 HIS E 536 HIS H 19 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.030007 restraints weight = 232686.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.030712 restraints weight = 151353.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.031200 restraints weight = 112913.778| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.7537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24606 Z= 0.115 Angle : 0.591 9.492 33282 Z= 0.288 Chirality : 0.038 0.145 3819 Planarity : 0.004 0.052 4233 Dihedral : 9.216 81.893 3411 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.04 % Allowed : 2.13 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2943 helix: 0.87 (0.13), residues: 1743 sheet: -1.42 (0.34), residues: 213 loop : -0.89 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 410 HIS 0.006 0.001 HIS H 19 PHE 0.019 0.001 PHE H 74 TYR 0.014 0.001 TYR A 77 ARG 0.004 0.000 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 1061) hydrogen bonds : angle 3.97597 ( 3000) covalent geometry : bond 0.00264 (24606) covalent geometry : angle 0.59134 (33282) *********************** 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 189 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 2.876 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: A 128 MET cc_start: 0.8460 (mmp) cc_final: 0.8178 (mmm) REVERT: A 157 LEU cc_start: 0.9450 (tp) cc_final: 0.9153 (tp) REVERT: A 234 MET cc_start: 0.9326 (mtm) cc_final: 0.8987 (mtm) REVERT: A 317 ASP cc_start: 0.9544 (t70) cc_final: 0.9187 (m-30) REVERT: A 334 MET cc_start: 0.8864 (mmt) cc_final: 0.8544 (mmm) REVERT: A 399 MET cc_start: 0.8671 (tpp) cc_final: 0.8443 (mmm) REVERT: A 462 MET cc_start: 0.9411 (mpp) cc_final: 0.8964 (ttm) REVERT: C 19 HIS cc_start: 0.9641 (t70) cc_final: 0.9311 (m90) REVERT: C 128 MET cc_start: 0.8740 (ptp) cc_final: 0.8047 (ptp) REVERT: C 334 MET cc_start: 0.9583 (tpt) cc_final: 0.9351 (tpt) REVERT: C 533 MET cc_start: 0.8477 (ppp) cc_final: 0.8246 (ppp) REVERT: D 135 TYR cc_start: 0.8389 (t80) cc_final: 0.8094 (t80) REVERT: D 147 MET cc_start: 0.8934 (mmm) cc_final: 0.8661 (mmm) REVERT: D 216 ASP cc_start: 0.9166 (m-30) cc_final: 0.8883 (t0) REVERT: D 234 MET cc_start: 0.9405 (mtm) cc_final: 0.8967 (mtp) REVERT: D 334 MET cc_start: 0.9370 (tpt) cc_final: 0.9095 (tpp) REVERT: D 348 MET cc_start: 0.9554 (ptm) cc_final: 0.9166 (ptm) REVERT: D 376 MET cc_start: 0.9491 (mpp) cc_final: 0.9020 (mpp) REVERT: E 128 MET cc_start: 0.8480 (tpp) cc_final: 0.7907 (tpp) REVERT: E 147 MET cc_start: 0.8715 (mtm) cc_final: 0.8415 (ptp) REVERT: E 334 MET cc_start: 0.9387 (mmm) cc_final: 0.9069 (mmm) REVERT: E 376 MET cc_start: 0.9564 (mpp) cc_final: 0.9297 (mpp) REVERT: F 216 ASP cc_start: 0.8950 (m-30) cc_final: 0.8700 (t0) REVERT: F 335 MET cc_start: 0.9271 (mtt) cc_final: 0.9039 (tpp) REVERT: F 348 MET cc_start: 0.9116 (mtm) cc_final: 0.8670 (ttp) REVERT: F 462 MET cc_start: 0.9248 (mtp) cc_final: 0.8870 (tmm) REVERT: H 19 HIS cc_start: 0.9104 (m90) cc_final: 0.8882 (m-70) REVERT: H 31 GLU cc_start: 0.6195 (mt-10) cc_final: 0.5909 (mm-30) REVERT: I 46 LYS cc_start: 0.9323 (pptt) cc_final: 0.9089 (pttm) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.3229 time to fit residues: 99.9917 Evaluate side-chains 159 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 27 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 96 ASN B 158 HIS B 219 ASN D 219 ASN D 536 HIS F 171 GLN F 536 HIS H 64 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.035404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.025475 restraints weight = 267828.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.026234 restraints weight = 161448.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.026738 restraints weight = 113441.677| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.8019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24606 Z= 0.177 Angle : 0.662 10.636 33282 Z= 0.327 Chirality : 0.039 0.180 3819 Planarity : 0.005 0.049 4233 Dihedral : 9.236 75.242 3411 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2943 helix: 0.81 (0.13), residues: 1731 sheet: -1.39 (0.34), residues: 219 loop : -0.88 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 410 HIS 0.008 0.001 HIS E 225 PHE 0.024 0.002 PHE E 301 TYR 0.014 0.002 TYR A 77 ARG 0.014 0.001 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 1061) hydrogen bonds : angle 4.27423 ( 3000) covalent geometry : bond 0.00387 (24606) covalent geometry : angle 0.66178 (33282) *********************** 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 178 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8578 (mmp) cc_final: 0.8004 (mtt) REVERT: A 147 MET cc_start: 0.9112 (mpp) cc_final: 0.8843 (mpp) REVERT: A 234 MET cc_start: 0.9498 (mtm) cc_final: 0.9173 (mtm) REVERT: A 317 ASP cc_start: 0.9531 (t70) cc_final: 0.9197 (m-30) REVERT: A 334 MET cc_start: 0.8926 (mmt) cc_final: 0.8579 (mmm) REVERT: A 462 MET cc_start: 0.9348 (mpp) cc_final: 0.8886 (mpp) REVERT: B 335 MET cc_start: 0.9462 (mtp) cc_final: 0.8226 (tpp) REVERT: B 533 MET cc_start: 0.9396 (ptm) cc_final: 0.8925 (ptm) REVERT: C 19 HIS cc_start: 0.9623 (t70) cc_final: 0.9300 (m90) REVERT: C 128 MET cc_start: 0.8601 (ptp) cc_final: 0.7964 (ptp) REVERT: C 334 MET cc_start: 0.9552 (tpt) cc_final: 0.9309 (tpt) REVERT: C 374 LEU cc_start: 0.9428 (tp) cc_final: 0.9218 (tp) REVERT: C 533 MET cc_start: 0.8474 (ppp) cc_final: 0.8195 (ppp) REVERT: D 135 TYR cc_start: 0.8453 (t80) cc_final: 0.8229 (t80) REVERT: D 147 MET cc_start: 0.8990 (mmm) cc_final: 0.8670 (mpp) REVERT: D 234 MET cc_start: 0.9530 (mtm) cc_final: 0.8854 (mtm) REVERT: D 309 MET cc_start: 0.8187 (mmm) cc_final: 0.7899 (mmm) REVERT: D 334 MET cc_start: 0.9376 (tpt) cc_final: 0.9054 (tpp) REVERT: D 348 MET cc_start: 0.9593 (ptm) cc_final: 0.9176 (ptm) REVERT: D 376 MET cc_start: 0.9516 (mpp) cc_final: 0.9087 (mpp) REVERT: E 147 MET cc_start: 0.8863 (mtm) cc_final: 0.8620 (ptp) REVERT: E 334 MET cc_start: 0.9413 (mmm) cc_final: 0.9161 (mmm) REVERT: E 376 MET cc_start: 0.9533 (mpp) cc_final: 0.9254 (mpp) REVERT: F 216 ASP cc_start: 0.9029 (m-30) cc_final: 0.8681 (t0) REVERT: F 234 MET cc_start: 0.9465 (mtm) cc_final: 0.9168 (mtm) REVERT: F 348 MET cc_start: 0.9054 (mtm) cc_final: 0.8624 (ttm) REVERT: F 399 MET cc_start: 0.9385 (tpp) cc_final: 0.9133 (tpp) REVERT: F 462 MET cc_start: 0.9299 (mtp) cc_final: 0.8917 (tmm) REVERT: H 31 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6089 (mp0) REVERT: H 73 ASP cc_start: 0.9518 (t70) cc_final: 0.9276 (p0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3230 time to fit residues: 95.3347 Evaluate side-chains 148 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 285 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 chunk 251 optimal weight: 0.0000 chunk 161 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 180 optimal weight: 0.0020 chunk 248 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 254 optimal weight: 6.9990 chunk 280 optimal weight: 9.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS D 219 ASN D 475 ASN D 536 HIS E 475 ASN H 19 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.036949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.026734 restraints weight = 271385.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.027504 restraints weight = 163402.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.027940 restraints weight = 113817.742| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.8169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 24606 Z= 0.099 Angle : 0.611 9.662 33282 Z= 0.295 Chirality : 0.039 0.180 3819 Planarity : 0.004 0.052 4233 Dihedral : 8.866 71.064 3411 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2943 helix: 1.05 (0.13), residues: 1731 sheet: -1.15 (0.35), residues: 219 loop : -0.70 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 410 HIS 0.010 0.001 HIS B 466 PHE 0.020 0.001 PHE D 532 TYR 0.016 0.001 TYR A 77 ARG 0.017 0.000 ARG E 233 Details of bonding type rmsd hydrogen bonds : bond 0.02641 ( 1061) hydrogen bonds : angle 4.00304 ( 3000) covalent geometry : bond 0.00228 (24606) covalent geometry : angle 0.61105 (33282) *********************** 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 193 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.809 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: 0.8566 (mmp) cc_final: 0.8115 (mtt) REVERT: A 147 MET cc_start: 0.9028 (mpp) cc_final: 0.8779 (mpp) REVERT: A 157 LEU cc_start: 0.9500 (tp) cc_final: 0.9205 (tp) REVERT: A 234 MET cc_start: 0.9511 (mtm) cc_final: 0.9214 (ptp) REVERT: A 317 ASP cc_start: 0.9493 (t70) cc_final: 0.9096 (m-30) REVERT: A 334 MET cc_start: 0.8914 (mmt) cc_final: 0.8488 (mmt) REVERT: A 462 MET cc_start: 0.9330 (mpp) cc_final: 0.8948 (mpp) REVERT: B 71 LEU cc_start: 0.9563 (mt) cc_final: 0.9270 (mt) REVERT: B 335 MET cc_start: 0.9317 (mtp) cc_final: 0.8090 (tpp) REVERT: B 533 MET cc_start: 0.9244 (ptm) cc_final: 0.8831 (ptm) REVERT: C 19 HIS cc_start: 0.9644 (t70) cc_final: 0.9310 (m90) REVERT: C 128 MET cc_start: 0.8710 (ptp) cc_final: 0.7987 (ptp) REVERT: C 334 MET cc_start: 0.9550 (tpt) cc_final: 0.9285 (tpt) REVERT: C 533 MET cc_start: 0.8494 (ppp) cc_final: 0.8200 (ppp) REVERT: D 147 MET cc_start: 0.8973 (mmm) cc_final: 0.8645 (mpp) REVERT: D 234 MET cc_start: 0.9524 (mtm) cc_final: 0.9080 (mtp) REVERT: D 309 MET cc_start: 0.8160 (mmm) cc_final: 0.7876 (mmm) REVERT: D 334 MET cc_start: 0.9325 (tpt) cc_final: 0.9011 (tpp) REVERT: D 348 MET cc_start: 0.9560 (ptm) cc_final: 0.9133 (ptm) REVERT: D 376 MET cc_start: 0.9542 (mpp) cc_final: 0.9077 (mpp) REVERT: E 307 MET cc_start: 0.8523 (tpt) cc_final: 0.8311 (tpt) REVERT: E 334 MET cc_start: 0.9404 (mmm) cc_final: 0.9175 (mmm) REVERT: E 376 MET cc_start: 0.9561 (mpp) cc_final: 0.9277 (mpp) REVERT: F 216 ASP cc_start: 0.9181 (m-30) cc_final: 0.8811 (t0) REVERT: F 234 MET cc_start: 0.9406 (mtm) cc_final: 0.9031 (mtm) REVERT: F 335 MET cc_start: 0.8429 (tpp) cc_final: 0.8068 (tpp) REVERT: F 348 MET cc_start: 0.9134 (mtm) cc_final: 0.8792 (mpp) REVERT: F 462 MET cc_start: 0.9266 (mtp) cc_final: 0.8881 (tmm) REVERT: F 533 MET cc_start: 0.9181 (ppp) cc_final: 0.8843 (ppp) REVERT: G 47 MET cc_start: 0.7546 (mmm) cc_final: 0.6685 (tpp) REVERT: G 88 GLU cc_start: 0.8911 (pt0) cc_final: 0.8592 (pt0) REVERT: H 31 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6279 (mm-30) REVERT: H 73 ASP cc_start: 0.9496 (t70) cc_final: 0.9289 (p0) REVERT: I 47 MET cc_start: 0.6894 (ttp) cc_final: 0.6591 (ttp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3461 time to fit residues: 107.1209 Evaluate side-chains 157 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 225 optimal weight: 0.0980 chunk 19 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS B 466 HIS D 536 HIS F 171 GLN F 461 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.035267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.025388 restraints weight = 272050.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.026148 restraints weight = 162399.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.026672 restraints weight = 113056.741| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.8464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24606 Z= 0.151 Angle : 0.628 9.287 33282 Z= 0.308 Chirality : 0.039 0.161 3819 Planarity : 0.004 0.053 4233 Dihedral : 8.759 67.513 3411 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2943 helix: 1.02 (0.13), residues: 1737 sheet: -1.14 (0.36), residues: 219 loop : -0.64 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 410 HIS 0.005 0.001 HIS D 461 PHE 0.020 0.002 PHE D 532 TYR 0.014 0.001 TYR A 77 ARG 0.009 0.000 ARG E 233 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 1061) hydrogen bonds : angle 4.12879 ( 3000) covalent geometry : bond 0.00333 (24606) covalent geometry : angle 0.62804 (33282) *********************** 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 179 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8594 (mmp) cc_final: 0.8304 (mtt) REVERT: A 147 MET cc_start: 0.9169 (mpp) cc_final: 0.8937 (mpp) REVERT: A 234 MET cc_start: 0.9553 (mtm) cc_final: 0.9184 (mtm) REVERT: A 317 ASP cc_start: 0.9569 (t70) cc_final: 0.9205 (m-30) REVERT: A 334 MET cc_start: 0.8940 (mmt) cc_final: 0.8614 (mmm) REVERT: A 462 MET cc_start: 0.9360 (mpp) cc_final: 0.9109 (ttm) REVERT: B 335 MET cc_start: 0.9475 (mtp) cc_final: 0.8326 (tpp) REVERT: B 533 MET cc_start: 0.9334 (ptm) cc_final: 0.8839 (ptm) REVERT: C 19 HIS cc_start: 0.9621 (t70) cc_final: 0.9334 (m90) REVERT: C 128 MET cc_start: 0.8578 (ptp) cc_final: 0.7876 (ptp) REVERT: C 147 MET cc_start: 0.9147 (mmt) cc_final: 0.8755 (mpp) REVERT: C 334 MET cc_start: 0.9540 (tpt) cc_final: 0.9284 (tpt) REVERT: D 128 MET cc_start: 0.7605 (tpp) cc_final: 0.7298 (tpp) REVERT: D 147 MET cc_start: 0.9017 (mmm) cc_final: 0.8679 (mpp) REVERT: D 234 MET cc_start: 0.9475 (mtm) cc_final: 0.9004 (mtp) REVERT: D 334 MET cc_start: 0.9396 (tpt) cc_final: 0.9034 (tpp) REVERT: D 348 MET cc_start: 0.9588 (ptm) cc_final: 0.9141 (ptm) REVERT: D 376 MET cc_start: 0.9490 (mpp) cc_final: 0.9061 (mpp) REVERT: E 147 MET cc_start: 0.8176 (ptp) cc_final: 0.7549 (ptp) REVERT: E 307 MET cc_start: 0.8846 (tpt) cc_final: 0.8631 (tpt) REVERT: E 334 MET cc_start: 0.9449 (mmm) cc_final: 0.9148 (mmm) REVERT: E 376 MET cc_start: 0.9569 (mpp) cc_final: 0.9290 (mpp) REVERT: F 128 MET cc_start: 0.9487 (mtp) cc_final: 0.9231 (mtm) REVERT: F 147 MET cc_start: 0.9145 (mmp) cc_final: 0.8537 (mpp) REVERT: F 216 ASP cc_start: 0.9082 (m-30) cc_final: 0.8748 (t0) REVERT: F 234 MET cc_start: 0.9487 (mtm) cc_final: 0.9148 (mtm) REVERT: F 335 MET cc_start: 0.8476 (tpp) cc_final: 0.8097 (tpp) REVERT: F 348 MET cc_start: 0.9338 (mtm) cc_final: 0.8797 (ttp) REVERT: F 462 MET cc_start: 0.9284 (mtp) cc_final: 0.8929 (tmm) REVERT: F 533 MET cc_start: 0.9187 (ppp) cc_final: 0.8817 (ppp) REVERT: G 47 MET cc_start: 0.7623 (mmm) cc_final: 0.6514 (tpp) REVERT: H 73 ASP cc_start: 0.9487 (t70) cc_final: 0.9239 (p0) REVERT: I 47 MET cc_start: 0.7276 (ttp) cc_final: 0.6908 (ttp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3288 time to fit residues: 98.0921 Evaluate side-chains 147 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 252 optimal weight: 5.9990 chunk 188 optimal weight: 0.0870 chunk 285 optimal weight: 0.9980 chunk 286 optimal weight: 8.9990 chunk 241 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.038439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.028931 restraints weight = 241949.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.029617 restraints weight = 154339.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.030084 restraints weight = 113662.027| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.8683 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= 0.118 Angle : 0.612 9.406 33282 Z= 0.298 Chirality : 0.039 0.149 3819 Planarity : 0.004 0.052 4233 Dihedral : 8.661 63.426 3411 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2943 helix: 1.13 (0.13), residues: 1728 sheet: -0.98 (0.36), residues: 219 loop : -0.61 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 410 HIS 0.003 0.001 HIS H 82 PHE 0.024 0.001 PHE I 75 TYR 0.017 0.001 TYR D 540 ARG 0.009 0.000 ARG E 233 Details of bonding type rmsd hydrogen bonds : bond 0.02677 ( 1061) hydrogen bonds : angle 4.02559 ( 3000) covalent geometry : bond 0.00271 (24606) covalent geometry : angle 0.61235 (33282) ********************** 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 179 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8570 (mmp) cc_final: 0.8242 (mtp) REVERT: A 147 MET cc_start: 0.9089 (mpp) cc_final: 0.8852 (mpp) REVERT: A 157 LEU cc_start: 0.9437 (tp) cc_final: 0.9134 (tp) REVERT: A 234 MET cc_start: 0.9446 (mtm) cc_final: 0.9046 (mtm) REVERT: A 317 ASP cc_start: 0.9593 (t70) cc_final: 0.9249 (m-30) REVERT: A 334 MET cc_start: 0.9037 (mmt) cc_final: 0.8651 (mmt) REVERT: A 376 MET cc_start: 0.9268 (pmm) cc_final: 0.9038 (pmm) REVERT: A 462 MET cc_start: 0.9372 (mpp) cc_final: 0.9087 (ttm) REVERT: B 71 LEU cc_start: 0.9590 (mt) cc_final: 0.9261 (mt) REVERT: B 335 MET cc_start: 0.9495 (mtp) cc_final: 0.8281 (tpp) REVERT: B 462 MET cc_start: 0.9451 (ttt) cc_final: 0.9138 (tmm) REVERT: B 533 MET cc_start: 0.9345 (ptm) cc_final: 0.8851 (ptm) REVERT: C 19 HIS cc_start: 0.9625 (t70) cc_final: 0.9345 (m90) REVERT: C 128 MET cc_start: 0.8661 (ptp) cc_final: 0.7904 (ptp) REVERT: C 147 MET cc_start: 0.9116 (mmt) cc_final: 0.8733 (mpp) REVERT: C 334 MET cc_start: 0.9558 (tpt) cc_final: 0.9324 (tpt) REVERT: D 147 MET cc_start: 0.9020 (mmm) cc_final: 0.8709 (mpp) REVERT: D 234 MET cc_start: 0.9349 (mtm) cc_final: 0.8931 (mtp) REVERT: D 334 MET cc_start: 0.9417 (tpt) cc_final: 0.9103 (tpp) REVERT: D 348 MET cc_start: 0.9565 (ptm) cc_final: 0.9146 (ptm) REVERT: D 376 MET cc_start: 0.9516 (mpp) cc_final: 0.8987 (mpp) REVERT: E 128 MET cc_start: 0.8414 (tpp) cc_final: 0.8084 (tpp) REVERT: E 147 MET cc_start: 0.8190 (ptp) cc_final: 0.7512 (ptp) REVERT: E 334 MET cc_start: 0.9413 (mmm) cc_final: 0.9151 (mmm) REVERT: E 376 MET cc_start: 0.9571 (mpp) cc_final: 0.9260 (mpp) REVERT: F 216 ASP cc_start: 0.9087 (m-30) cc_final: 0.8785 (t0) REVERT: F 234 MET cc_start: 0.9434 (mtm) cc_final: 0.9147 (mtm) REVERT: F 335 MET cc_start: 0.8608 (tpp) cc_final: 0.8181 (tpp) REVERT: F 348 MET cc_start: 0.9355 (mtm) cc_final: 0.8805 (ttp) REVERT: F 462 MET cc_start: 0.9305 (mtp) cc_final: 0.8934 (tmm) REVERT: F 533 MET cc_start: 0.9139 (ppp) cc_final: 0.8710 (ppp) REVERT: G 47 MET cc_start: 0.7752 (mmm) cc_final: 0.6653 (tpp) REVERT: H 1 MET cc_start: 0.6520 (tpp) cc_final: 0.5872 (mmt) REVERT: H 19 HIS cc_start: 0.9177 (m90) cc_final: 0.8906 (m90) REVERT: H 73 ASP cc_start: 0.9373 (t70) cc_final: 0.9120 (p0) REVERT: I 47 MET cc_start: 0.7304 (ttp) cc_final: 0.6888 (ttp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3062 time to fit residues: 91.3351 Evaluate side-chains 148 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 213 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 127 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 141 optimal weight: 0.0050 overall best weight: 0.6614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.038927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029324 restraints weight = 240883.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030042 restraints weight = 152115.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.030530 restraints weight = 111186.554| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.8819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 24606 Z= 0.095 Angle : 0.592 9.286 33282 Z= 0.288 Chirality : 0.039 0.192 3819 Planarity : 0.004 0.052 4233 Dihedral : 8.406 58.909 3411 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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 : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2943 helix: 1.21 (0.13), residues: 1731 sheet: -0.89 (0.35), residues: 219 loop : -0.49 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 410 HIS 0.003 0.000 HIS B 40 PHE 0.021 0.001 PHE I 75 TYR 0.012 0.001 TYR D 540 ARG 0.015 0.000 ARG E 233 Details of bonding type rmsd hydrogen bonds : bond 0.02565 ( 1061) hydrogen bonds : angle 3.92193 ( 3000) covalent geometry : bond 0.00220 (24606) covalent geometry : angle 0.59248 (33282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7097.78 seconds wall clock time: 125 minutes 35.89 seconds (7535.89 seconds total)