Starting phenix.real_space_refine on Sat Jun 21 02:44:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jns_36450/06_2025/8jns_36450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jns_36450/06_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_36450/06_2025/8jns_36450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jns_36450/06_2025/8jns_36450.map" model { file = "/net/cci-nas-00/data/ceres_data/8jns_36450/06_2025/8jns_36450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jns_36450/06_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-5710/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: 15.52, per 1000 atoms: 0.64 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: 6.64 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: 2.97 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: 7.74 Time building geometry restraints manager: 7.75 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 56.590 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.120 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.420 ------------------------------------------------------------------------------- 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 : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7888 (ttt90) REVERT: A 47 MET cc_start: 0.8044 (mmm) cc_final: 0.6338 (mmm) REVERT: A 58 LEU cc_start: 0.9049 (mt) cc_final: 0.8559 (pp) REVERT: A 173 LEU cc_start: 0.8974 (mt) cc_final: 0.8760 (pp) REVERT: A 180 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8101 (mm) REVERT: A 255 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: A 290 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8644 (p) REVERT: A 332 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 434 LEU cc_start: 0.9225 (mt) cc_final: 0.8976 (mt) REVERT: B 8 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7950 (tpt170) REVERT: B 216 ASP cc_start: 0.8988 (m-30) cc_final: 0.8115 (t0) REVERT: B 307 MET cc_start: 0.8125 (tpp) cc_final: 0.7869 (tpp) REVERT: B 369 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7987 (t80) REVERT: B 459 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8886 (mm) REVERT: C 47 MET cc_start: 0.8417 (mmm) cc_final: 0.8179 (mmm) REVERT: C 49 THR cc_start: 0.9057 (m) cc_final: 0.8631 (p) REVERT: C 58 LEU cc_start: 0.9132 (mt) cc_final: 0.8735 (pp) REVERT: C 290 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9006 (p) REVERT: C 296 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8392 (p0) REVERT: C 348 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8915 (tmm) REVERT: C 355 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9278 (mm) REVERT: C 363 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8721 (p) REVERT: C 437 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8960 (tp) REVERT: D 175 LYS cc_start: 0.8708 (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: 0.9226 (tp) REVERT: D 369 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7891 (t80) REVERT: F 113 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6132 (mp10) REVERT: F 144 LEU cc_start: 0.9412 (mt) cc_final: 0.9171 (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: 0.8584 (t) REVERT: F 437 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9377 (mt) REVERT: H 88 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8841 (mm-30) REVERT: I 45 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.6563 (p) REVERT: I 68 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7378 (tt) REVERT: I 76 ASN cc_start: 0.8256 (m-40) cc_final: 0.7594 (p0) outliers start: 484 outliers final: 101 residues processed: 759 average time/residue: 0.3636 time to fit residues: 421.7886 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 : 3.215 ------------------------------------------------------------------------------- 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 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN C 19 HIS C 34 ASN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 GLN D 123 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN D 262 GLN D 283 GLN E 123 ASN E 244 ASN E 283 GLN E 482 GLN F 123 ASN F 244 ASN F 458 HIS G 34 ASN H 14 HIS H 19 HIS I 34 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.044970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.034257 restraints weight = 226652.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.035087 restraints weight = 154039.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.035703 restraints weight = 116030.462| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24606 Z= 0.155 Angle : 0.748 9.995 33282 Z= 0.379 Chirality : 0.044 0.201 3819 Planarity : 0.006 0.074 4233 Dihedral : 10.684 77.375 3411 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.22 % Allowed : 3.72 % Favored : 96.06 % 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: -1.35 (0.11), residues: 1716 sheet: -2.64 (0.30), residues: 213 loop : -2.06 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP F 189 HIS 0.007 0.001 HIS G 40 PHE 0.020 0.002 PHE I 74 TYR 0.019 0.002 TYR B 90 ARG 0.006 0.001 ARG F 433 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 1061) hydrogen bonds : angle 5.08279 ( 3000) covalent geometry : bond 0.00346 (24606) covalent geometry : angle 0.74808 (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 : 2.991 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 30 LEU cc_start: 0.7634 (mm) cc_final: 0.7416 (mt) REVERT: A 114 MET cc_start: 0.9292 (mmp) cc_final: 0.9050 (mmm) REVERT: A 157 LEU cc_start: 0.9347 (tp) cc_final: 0.8981 (tp) REVERT: A 334 MET cc_start: 0.8582 (mmm) cc_final: 0.8227 (mmm) REVERT: B 140 VAL cc_start: 0.9341 (t) cc_final: 0.9117 (t) REVERT: B 335 MET cc_start: 0.9516 (mtp) cc_final: 0.8893 (ttm) REVERT: B 385 LEU cc_start: 0.9403 (mt) cc_final: 0.9160 (tp) REVERT: B 462 MET cc_start: 0.9036 (mtp) cc_final: 0.8736 (ttm) REVERT: C 307 MET cc_start: 0.7369 (mmt) cc_final: 0.6902 (mmt) REVERT: C 335 MET cc_start: 0.9051 (mtm) cc_final: 0.8845 (ttm) REVERT: C 374 LEU cc_start: 0.9325 (tp) cc_final: 0.9120 (tp) REVERT: C 399 MET cc_start: 0.9108 (mmm) cc_final: 0.8687 (mpp) REVERT: C 462 MET cc_start: 0.9438 (mtp) cc_final: 0.8974 (ttp) REVERT: E 128 MET cc_start: 0.8571 (tpp) cc_final: 0.7853 (tpp) REVERT: E 334 MET cc_start: 0.9131 (mtt) cc_final: 0.8689 (mtt) REVERT: E 376 MET cc_start: 0.9491 (mtm) cc_final: 0.9175 (ptp) REVERT: F 144 LEU cc_start: 0.9533 (mt) cc_final: 0.9326 (tp) REVERT: F 207 ILE cc_start: 0.9521 (mt) cc_final: 0.9317 (mt) REVERT: F 234 MET cc_start: 0.8727 (mtm) cc_final: 0.8376 (mtm) REVERT: F 462 MET cc_start: 0.9090 (mtp) cc_final: 0.8760 (tmm) REVERT: G 46 LYS cc_start: 0.9156 (pptt) cc_final: 0.8949 (ptmm) REVERT: G 47 MET cc_start: 0.5802 (mmm) cc_final: 0.4642 (mmm) REVERT: G 75 PHE cc_start: 0.9451 (m-10) cc_final: 0.9193 (m-80) REVERT: H 31 GLU cc_start: 0.6520 (mt-10) cc_final: 0.6136 (mp0) REVERT: H 73 ASP cc_start: 0.9324 (t70) cc_final: 0.8978 (p0) outliers start: 6 outliers final: 0 residues processed: 258 average time/residue: 0.3639 time to fit residues: 147.9724 Evaluate side-chains 187 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 3.024 ------------------------------------------------------------------------------- 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: 1.9990 chunk 105 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN ** 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 171 GLN 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 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 HIS H 40 HIS ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.037637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.027398 restraints weight = 255194.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.028175 restraints weight = 161914.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.028713 restraints weight = 116843.195| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.6191 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= 0.197 Angle : 0.693 8.518 33282 Z= 0.352 Chirality : 0.041 0.151 3819 Planarity : 0.006 0.066 4233 Dihedral : 10.120 86.470 3411 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % 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: -1.23 (0.15), residues: 2943 helix: -0.19 (0.12), residues: 1737 sheet: -2.17 (0.29), residues: 240 loop : -1.37 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP C 189 HIS 0.007 0.001 HIS F 225 PHE 0.025 0.002 PHE H 75 TYR 0.018 0.002 TYR B 90 ARG 0.013 0.001 ARG C 380 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 1061) hydrogen bonds : angle 4.56149 ( 3000) covalent geometry : bond 0.00433 (24606) covalent geometry : angle 0.69326 (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 208 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 2.768 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: 0.8295 (mmp) cc_final: 0.7725 (tpp) REVERT: A 144 LEU cc_start: 0.9588 (tt) cc_final: 0.9373 (pp) REVERT: A 147 MET cc_start: 0.9097 (mmt) cc_final: 0.8769 (mpp) REVERT: A 334 MET cc_start: 0.8793 (mmm) cc_final: 0.8481 (mmm) REVERT: A 399 MET cc_start: 0.8589 (tpp) cc_final: 0.8128 (tmm) REVERT: B 114 MET cc_start: 0.9225 (mmp) cc_final: 0.9016 (mmm) REVERT: B 216 ASP cc_start: 0.8202 (t0) cc_final: 0.7960 (t0) REVERT: B 307 MET cc_start: 0.8528 (mmp) cc_final: 0.8008 (mmm) REVERT: B 335 MET cc_start: 0.9538 (mtp) cc_final: 0.9316 (mtp) REVERT: B 533 MET cc_start: 0.9046 (ppp) cc_final: 0.8224 (ppp) REVERT: C 1 MET cc_start: 0.9222 (mmp) cc_final: 0.8945 (mmm) REVERT: C 335 MET cc_start: 0.9015 (mtm) cc_final: 0.8729 (mtp) REVERT: C 374 LEU cc_start: 0.9393 (tp) cc_final: 0.9132 (tp) REVERT: C 533 MET cc_start: 0.8196 (ppp) cc_final: 0.7993 (ppp) REVERT: D 348 MET cc_start: 0.9622 (ptm) cc_final: 0.9238 (ptm) REVERT: E 128 MET cc_start: 0.8765 (tpp) cc_final: 0.8043 (tpp) REVERT: E 225 HIS cc_start: 0.7977 (p90) cc_final: 0.7588 (p-80) REVERT: E 307 MET cc_start: 0.8511 (tpp) cc_final: 0.8121 (tpp) REVERT: E 376 MET cc_start: 0.9462 (mtm) cc_final: 0.8972 (ptp) REVERT: E 449 MET cc_start: 0.8837 (pmm) cc_final: 0.8504 (pmm) REVERT: E 533 MET cc_start: 0.8528 (ppp) cc_final: 0.7560 (mmp) REVERT: F 234 MET cc_start: 0.9024 (mtm) cc_final: 0.8719 (mtp) REVERT: F 309 MET cc_start: 0.8368 (ppp) cc_final: 0.8036 (ppp) REVERT: F 334 MET cc_start: 0.9534 (tpp) cc_final: 0.9283 (tpp) REVERT: F 462 MET cc_start: 0.9165 (mtp) cc_final: 0.8942 (tmm) REVERT: G 47 MET cc_start: 0.6254 (mmm) cc_final: 0.5103 (mmm) REVERT: H 31 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6229 (mp0) REVERT: H 73 ASP cc_start: 0.9574 (t70) cc_final: 0.9269 (p0) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.3287 time to fit residues: 110.5031 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 : 2.821 ------------------------------------------------------------------------------- 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: 4.9990 chunk 122 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 192 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 262 GLN C 56 ASN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN D 237 ASN F 262 GLN H 19 HIS H 64 GLN I 40 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.039104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.029450 restraints weight = 248864.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030167 restraints weight = 160351.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.030674 restraints weight = 118529.799| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.6911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24606 Z= 0.166 Angle : 0.630 11.133 33282 Z= 0.314 Chirality : 0.039 0.159 3819 Planarity : 0.005 0.058 4233 Dihedral : 9.737 88.351 3411 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.40 % 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: -0.61 (0.16), residues: 2943 helix: 0.28 (0.13), residues: 1755 sheet: -1.89 (0.32), residues: 213 loop : -1.13 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 410 HIS 0.006 0.001 HIS F 158 PHE 0.021 0.001 PHE H 74 TYR 0.018 0.002 TYR B 61 ARG 0.029 0.001 ARG C 112 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 1061) hydrogen bonds : angle 4.24792 ( 3000) covalent geometry : bond 0.00365 (24606) covalent geometry : angle 0.62997 (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 198 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 2.867 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: 0.8525 (mmp) cc_final: 0.7771 (mmm) REVERT: A 157 LEU cc_start: 0.9472 (tp) cc_final: 0.9154 (tp) REVERT: A 173 LEU cc_start: 0.9508 (mt) cc_final: 0.9174 (pp) REVERT: A 399 MET cc_start: 0.8749 (tpp) cc_final: 0.8515 (tmm) REVERT: B 114 MET cc_start: 0.9366 (mmp) cc_final: 0.9146 (mmm) REVERT: B 216 ASP cc_start: 0.7926 (t0) cc_final: 0.7669 (t0) REVERT: B 533 MET cc_start: 0.9166 (ppp) cc_final: 0.8735 (ppp) REVERT: C 128 MET cc_start: 0.9046 (ptp) cc_final: 0.8342 (ptp) REVERT: C 335 MET cc_start: 0.9160 (mtm) cc_final: 0.8920 (mtp) REVERT: C 374 LEU cc_start: 0.9523 (tp) cc_final: 0.9266 (tp) REVERT: D 135 TYR cc_start: 0.8266 (t80) cc_final: 0.8027 (t80) REVERT: D 147 MET cc_start: 0.8899 (mmm) cc_final: 0.8684 (mmm) REVERT: D 234 MET cc_start: 0.9324 (mtm) cc_final: 0.8931 (mtp) REVERT: D 348 MET cc_start: 0.9561 (ptm) cc_final: 0.9317 (ptm) REVERT: E 128 MET cc_start: 0.8845 (tpp) cc_final: 0.8381 (tpp) REVERT: E 225 HIS cc_start: 0.7597 (p90) cc_final: 0.7197 (p-80) REVERT: F 206 ASP cc_start: 0.9112 (m-30) cc_final: 0.8864 (m-30) REVERT: F 234 MET cc_start: 0.9099 (mtm) cc_final: 0.8740 (mtm) REVERT: F 348 MET cc_start: 0.8954 (ttp) cc_final: 0.8753 (ttt) REVERT: F 462 MET cc_start: 0.9272 (mtp) cc_final: 0.8996 (tmm) REVERT: G 47 MET cc_start: 0.6469 (mmm) cc_final: 0.5383 (mmm) REVERT: H 19 HIS cc_start: 0.9178 (m90) cc_final: 0.8930 (m-70) REVERT: I 46 LYS cc_start: 0.9247 (pptt) cc_final: 0.8919 (pttm) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.3300 time to fit residues: 107.4150 Evaluate side-chains 165 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.695 ------------------------------------------------------------------------------- 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: 8.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 96 ASN B 158 HIS B 237 ASN C 56 ASN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 HIS F 458 HIS G 56 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.025053 restraints weight = 275482.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.025777 restraints weight = 167722.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.026284 restraints weight = 118452.089| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24606 Z= 0.258 Angle : 0.754 11.280 33282 Z= 0.375 Chirality : 0.041 0.171 3819 Planarity : 0.005 0.056 4233 Dihedral : 9.878 78.303 3411 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -0.79 (0.15), residues: 2943 helix: 0.07 (0.12), residues: 1761 sheet: -1.77 (0.34), residues: 213 loop : -1.12 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 410 HIS 0.009 0.002 HIS C 158 PHE 0.030 0.002 PHE H 74 TYR 0.015 0.002 TYR F 184 ARG 0.006 0.001 ARG G 16 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 1061) hydrogen bonds : angle 4.62251 ( 3000) covalent geometry : bond 0.00547 (24606) covalent geometry : angle 0.75422 (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 180 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8773 (mmp) cc_final: 0.8409 (mmm) REVERT: A 147 MET cc_start: 0.9028 (mpp) cc_final: 0.8754 (mpp) REVERT: A 334 MET cc_start: 0.9020 (mmt) cc_final: 0.8753 (mmm) REVERT: A 399 MET cc_start: 0.9025 (tpp) cc_final: 0.8728 (tmm) REVERT: A 462 MET cc_start: 0.9420 (mpp) cc_final: 0.9091 (ttm) REVERT: B 216 ASP cc_start: 0.8421 (t0) cc_final: 0.8194 (t0) REVERT: B 307 MET cc_start: 0.8347 (mmp) cc_final: 0.7596 (mmm) REVERT: B 334 MET cc_start: 0.9710 (tpp) cc_final: 0.9476 (tpp) REVERT: B 348 MET cc_start: 0.8882 (ppp) cc_final: 0.8595 (ppp) REVERT: B 533 MET cc_start: 0.9275 (ppp) cc_final: 0.8772 (ppp) REVERT: C 19 HIS cc_start: 0.9597 (t-90) cc_final: 0.9379 (t-90) REVERT: C 128 MET cc_start: 0.8683 (ptp) cc_final: 0.8168 (ptp) REVERT: C 147 MET cc_start: 0.9174 (mmt) cc_final: 0.8895 (mpp) REVERT: C 374 LEU cc_start: 0.9449 (tp) cc_final: 0.9160 (tp) REVERT: C 533 MET cc_start: 0.8535 (ppp) cc_final: 0.8219 (ppp) REVERT: D 147 MET cc_start: 0.9030 (mmm) cc_final: 0.8721 (mpp) REVERT: D 234 MET cc_start: 0.9442 (mtm) cc_final: 0.9034 (mtp) REVERT: D 348 MET cc_start: 0.9620 (ptm) cc_final: 0.9220 (ptm) REVERT: E 128 MET cc_start: 0.8931 (tpp) cc_final: 0.8540 (tpp) REVERT: E 225 HIS cc_start: 0.7844 (p90) cc_final: 0.7458 (p-80) REVERT: E 335 MET cc_start: 0.9661 (mtp) cc_final: 0.9381 (mtp) REVERT: E 376 MET cc_start: 0.9478 (mpp) cc_final: 0.9250 (mpp) REVERT: F 234 MET cc_start: 0.9291 (mtm) cc_final: 0.8938 (mtm) REVERT: F 334 MET cc_start: 0.9616 (tpp) cc_final: 0.9396 (tpp) REVERT: F 348 MET cc_start: 0.8845 (ttp) cc_final: 0.8607 (ttt) REVERT: F 462 MET cc_start: 0.9266 (mtp) cc_final: 0.8939 (tmm) REVERT: H 19 HIS cc_start: 0.9114 (m90) cc_final: 0.8885 (m-70) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3569 time to fit residues: 104.4839 Evaluate side-chains 144 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 3.111 ------------------------------------------------------------------------------- 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: 5.9990 chunk 135 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 285 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** C 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.035661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.025652 restraints weight = 262580.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.026416 restraints weight = 158932.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.026942 restraints weight = 111941.320| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.8017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 24606 Z= 0.107 Angle : 0.608 9.341 33282 Z= 0.297 Chirality : 0.039 0.144 3819 Planarity : 0.004 0.060 4233 Dihedral : 9.496 77.130 3411 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -0.10 (0.16), residues: 2943 helix: 0.68 (0.13), residues: 1728 sheet: -1.51 (0.35), residues: 213 loop : -0.91 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 410 HIS 0.003 0.001 HIS D 461 PHE 0.020 0.001 PHE I 74 TYR 0.013 0.001 TYR A 77 ARG 0.003 0.000 ARG G 16 Details of bonding type rmsd hydrogen bonds : bond 0.02863 ( 1061) hydrogen bonds : angle 4.07452 ( 3000) covalent geometry : bond 0.00246 (24606) covalent geometry : angle 0.60753 (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 184 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 2.722 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: 0.8661 (mmp) cc_final: 0.8176 (mtt) REVERT: A 147 MET cc_start: 0.9106 (mpp) cc_final: 0.8821 (mpp) REVERT: A 157 LEU cc_start: 0.9467 (tp) cc_final: 0.9134 (tp) REVERT: A 317 ASP cc_start: 0.9636 (t0) cc_final: 0.9223 (m-30) REVERT: A 334 MET cc_start: 0.8957 (mmt) cc_final: 0.8527 (mmm) REVERT: A 348 MET cc_start: 0.7908 (tmm) cc_final: 0.7673 (tmm) REVERT: A 399 MET cc_start: 0.8926 (tpp) cc_final: 0.8678 (tmm) REVERT: A 462 MET cc_start: 0.9447 (mpp) cc_final: 0.9071 (ttm) REVERT: B 307 MET cc_start: 0.8435 (mmp) cc_final: 0.7897 (mpp) REVERT: B 309 MET cc_start: 0.8055 (tpp) cc_final: 0.7834 (tpp) REVERT: B 334 MET cc_start: 0.9685 (tpp) cc_final: 0.9349 (tpp) REVERT: B 335 MET cc_start: 0.9560 (mtm) cc_final: 0.9319 (mtp) REVERT: B 348 MET cc_start: 0.8713 (ppp) cc_final: 0.8465 (ppp) REVERT: B 462 MET cc_start: 0.9486 (ttt) cc_final: 0.9066 (tpp) REVERT: C 19 HIS cc_start: 0.9598 (t-90) cc_final: 0.9357 (t-90) REVERT: C 128 MET cc_start: 0.8753 (ptp) cc_final: 0.8063 (ptp) REVERT: C 374 LEU cc_start: 0.9463 (tp) cc_final: 0.9235 (tp) REVERT: D 147 MET cc_start: 0.8970 (mmm) cc_final: 0.8639 (mpp) REVERT: D 234 MET cc_start: 0.9490 (mtm) cc_final: 0.9065 (mtp) REVERT: D 348 MET cc_start: 0.9621 (ptm) cc_final: 0.9358 (ptm) REVERT: E 128 MET cc_start: 0.8805 (tpp) cc_final: 0.8305 (tpp) REVERT: E 147 MET cc_start: 0.8920 (mtm) cc_final: 0.8582 (ptp) REVERT: E 376 MET cc_start: 0.9532 (mpp) cc_final: 0.9301 (mpp) REVERT: F 234 MET cc_start: 0.9220 (mtm) cc_final: 0.8954 (mtm) REVERT: F 348 MET cc_start: 0.8834 (ttp) cc_final: 0.8574 (ttt) REVERT: F 462 MET cc_start: 0.9291 (mtp) cc_final: 0.8859 (tmm) REVERT: G 47 MET cc_start: 0.4860 (mtp) cc_final: 0.2750 (tpp) REVERT: H 19 HIS cc_start: 0.9113 (m90) cc_final: 0.8874 (m-70) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3198 time to fit residues: 96.7067 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 : 2.689 ------------------------------------------------------------------------------- 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: 5.9990 chunk 292 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 C 536 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.025437 restraints weight = 267978.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.026196 restraints weight = 160867.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.026717 restraints weight = 112747.757| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.8262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24606 Z= 0.126 Angle : 0.613 10.733 33282 Z= 0.298 Chirality : 0.039 0.191 3819 Planarity : 0.004 0.048 4233 Dihedral : 9.155 77.471 3411 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: 0.08 (0.16), residues: 2943 helix: 0.80 (0.13), residues: 1734 sheet: -1.32 (0.35), residues: 219 loop : -0.82 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 410 HIS 0.003 0.001 HIS H 82 PHE 0.022 0.001 PHE D 532 TYR 0.015 0.001 TYR D 540 ARG 0.005 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.02789 ( 1061) hydrogen bonds : angle 4.10056 ( 3000) covalent geometry : bond 0.00287 (24606) covalent geometry : angle 0.61322 (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 181 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 3.353 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: 0.8674 (mmp) cc_final: 0.8281 (mtt) REVERT: A 147 MET cc_start: 0.9150 (mpp) cc_final: 0.8928 (mpp) REVERT: A 317 ASP cc_start: 0.9676 (t0) cc_final: 0.9250 (m-30) REVERT: A 334 MET cc_start: 0.8926 (mmt) cc_final: 0.8536 (mmm) REVERT: A 399 MET cc_start: 0.8804 (tpp) cc_final: 0.8428 (tmm) REVERT: A 462 MET cc_start: 0.9423 (mpp) cc_final: 0.9100 (ttm) REVERT: B 307 MET cc_start: 0.8450 (mmp) cc_final: 0.7904 (mpp) REVERT: B 309 MET cc_start: 0.8132 (tpp) cc_final: 0.7909 (tpp) REVERT: B 334 MET cc_start: 0.9673 (tpp) cc_final: 0.9318 (tpp) REVERT: B 335 MET cc_start: 0.9569 (mtm) cc_final: 0.9353 (mtp) REVERT: B 348 MET cc_start: 0.8712 (ppp) cc_final: 0.8416 (ppp) REVERT: B 462 MET cc_start: 0.9495 (ttt) cc_final: 0.8991 (tpp) REVERT: B 533 MET cc_start: 0.9206 (ptm) cc_final: 0.8930 (ptm) REVERT: C 19 HIS cc_start: 0.9608 (t-90) cc_final: 0.9374 (t-90) REVERT: C 128 MET cc_start: 0.8691 (ptp) cc_final: 0.7982 (ptp) REVERT: C 147 MET cc_start: 0.9105 (mmt) cc_final: 0.8685 (mpp) REVERT: C 334 MET cc_start: 0.9615 (tpt) cc_final: 0.9277 (tpt) REVERT: C 335 MET cc_start: 0.8893 (ttm) cc_final: 0.8563 (ttm) REVERT: C 374 LEU cc_start: 0.9465 (tp) cc_final: 0.9222 (tp) REVERT: C 462 MET cc_start: 0.9655 (mtp) cc_final: 0.9128 (ttt) REVERT: D 147 MET cc_start: 0.9000 (mmm) cc_final: 0.8663 (mpp) REVERT: D 234 MET cc_start: 0.9486 (mtm) cc_final: 0.9046 (mtp) REVERT: D 334 MET cc_start: 0.9586 (tpp) cc_final: 0.9322 (tpp) REVERT: D 348 MET cc_start: 0.9622 (ptm) cc_final: 0.9232 (ptm) REVERT: E 128 MET cc_start: 0.8860 (tpp) cc_final: 0.8312 (tpp) REVERT: E 376 MET cc_start: 0.9538 (mpp) cc_final: 0.9276 (mpp) REVERT: F 128 MET cc_start: 0.9057 (tpp) cc_final: 0.8817 (mtt) REVERT: F 210 MET cc_start: 0.9166 (tpp) cc_final: 0.8924 (tpp) REVERT: F 234 MET cc_start: 0.9256 (mtm) cc_final: 0.8932 (mtm) REVERT: F 335 MET cc_start: 0.9062 (mtp) cc_final: 0.8786 (tpp) REVERT: F 348 MET cc_start: 0.8844 (ttp) cc_final: 0.8590 (ttt) REVERT: F 462 MET cc_start: 0.9277 (mtp) cc_final: 0.8862 (tmm) REVERT: F 533 MET cc_start: 0.9265 (ppp) cc_final: 0.8965 (ppp) REVERT: G 47 MET cc_start: 0.4990 (mtp) cc_final: 0.2813 (tpp) REVERT: G 88 GLU cc_start: 0.9025 (pt0) cc_final: 0.8619 (pt0) REVERT: H 19 HIS cc_start: 0.9132 (m90) cc_final: 0.8881 (m-70) REVERT: I 46 LYS cc_start: 0.9315 (pptt) cc_final: 0.9073 (pttm) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3694 time to fit residues: 109.9811 Evaluate side-chains 146 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 2.774 ------------------------------------------------------------------------------- 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: 10.0000 chunk 294 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 180 optimal weight: 0.0070 chunk 248 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 280 optimal weight: 0.0000 overall best weight: 0.5204 ------------------------------------------------------------------------------- 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** D 475 ASN E 225 HIS E 475 ASN F 171 GLN F 536 HIS G 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.036655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.026516 restraints weight = 271907.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.027245 restraints weight = 163538.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.027762 restraints weight = 115693.062| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.8414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 24606 Z= 0.100 Angle : 0.612 10.763 33282 Z= 0.295 Chirality : 0.039 0.177 3819 Planarity : 0.004 0.048 4233 Dihedral : 8.822 68.689 3411 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: 0.30 (0.16), residues: 2943 helix: 0.97 (0.13), residues: 1725 sheet: -1.05 (0.36), residues: 219 loop : -0.75 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 410 HIS 0.005 0.001 HIS H 14 PHE 0.023 0.001 PHE A 301 TYR 0.016 0.001 TYR A 77 ARG 0.010 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.02611 ( 1061) hydrogen bonds : angle 3.98903 ( 3000) covalent geometry : bond 0.00223 (24606) covalent geometry : angle 0.61189 (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 191 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8678 (mmp) cc_final: 0.8201 (mtt) REVERT: A 147 MET cc_start: 0.9084 (mpp) cc_final: 0.8837 (mpp) REVERT: A 317 ASP cc_start: 0.9657 (t0) cc_final: 0.9238 (m-30) REVERT: A 334 MET cc_start: 0.9010 (mmt) cc_final: 0.8581 (mmm) REVERT: A 399 MET cc_start: 0.8572 (tpp) cc_final: 0.8308 (tmm) REVERT: A 462 MET cc_start: 0.9341 (mpp) cc_final: 0.8966 (mpp) REVERT: B 71 LEU cc_start: 0.9601 (mt) cc_final: 0.9320 (mt) REVERT: B 114 MET cc_start: 0.9383 (mmp) cc_final: 0.9092 (mmm) REVERT: B 216 ASP cc_start: 0.8401 (t0) cc_final: 0.8172 (t0) REVERT: B 307 MET cc_start: 0.8370 (mmp) cc_final: 0.8064 (mpp) REVERT: B 309 MET cc_start: 0.8086 (tpp) cc_final: 0.7828 (tpp) REVERT: B 334 MET cc_start: 0.9668 (tpp) cc_final: 0.9317 (tpp) REVERT: B 348 MET cc_start: 0.8705 (ppp) cc_final: 0.8405 (ppp) REVERT: B 462 MET cc_start: 0.9445 (ttt) cc_final: 0.9045 (tpp) REVERT: B 533 MET cc_start: 0.9175 (ptm) cc_final: 0.8875 (ptm) REVERT: C 19 HIS cc_start: 0.9613 (t-90) cc_final: 0.9340 (m90) REVERT: C 128 MET cc_start: 0.8724 (ptp) cc_final: 0.8361 (ptp) REVERT: C 334 MET cc_start: 0.9592 (tpt) cc_final: 0.9269 (tpt) REVERT: C 335 MET cc_start: 0.8926 (ttm) cc_final: 0.8595 (ttm) REVERT: C 374 LEU cc_start: 0.9440 (tp) cc_final: 0.9213 (tp) REVERT: C 462 MET cc_start: 0.9645 (mtp) cc_final: 0.9086 (ttt) REVERT: C 533 MET cc_start: 0.8404 (ppp) cc_final: 0.8027 (ppp) REVERT: D 147 MET cc_start: 0.8978 (mmm) cc_final: 0.8659 (mpp) REVERT: D 216 ASP cc_start: 0.9301 (m-30) cc_final: 0.9091 (t0) REVERT: D 234 MET cc_start: 0.9514 (mtm) cc_final: 0.9087 (mtp) REVERT: D 309 MET cc_start: 0.8499 (mmm) cc_final: 0.8258 (mmm) REVERT: D 334 MET cc_start: 0.9578 (tpp) cc_final: 0.9377 (tpp) REVERT: D 348 MET cc_start: 0.9629 (ptm) cc_final: 0.9290 (ptm) REVERT: D 462 MET cc_start: 0.9036 (mpp) cc_final: 0.8778 (tmm) REVERT: E 128 MET cc_start: 0.8811 (tpp) cc_final: 0.8309 (tpp) REVERT: E 376 MET cc_start: 0.9551 (mpp) cc_final: 0.9262 (mpp) REVERT: F 128 MET cc_start: 0.8913 (tpp) cc_final: 0.8671 (mtt) REVERT: F 210 MET cc_start: 0.9207 (tpp) cc_final: 0.8896 (tpp) REVERT: F 234 MET cc_start: 0.9227 (mtm) cc_final: 0.8927 (mtm) REVERT: F 335 MET cc_start: 0.9062 (mtp) cc_final: 0.8724 (tpp) REVERT: F 348 MET cc_start: 0.8885 (ttp) cc_final: 0.8617 (ttt) REVERT: F 462 MET cc_start: 0.9245 (mtp) cc_final: 0.8859 (tmm) REVERT: F 533 MET cc_start: 0.9107 (ppp) cc_final: 0.8776 (ppp) REVERT: G 47 MET cc_start: 0.5730 (mtp) cc_final: 0.4069 (tpp) REVERT: I 46 LYS cc_start: 0.9200 (pptt) cc_final: 0.8989 (pttm) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.3384 time to fit residues: 105.9465 Evaluate side-chains 149 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 2.745 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.026017 restraints weight = 278790.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.026734 restraints weight = 166450.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.027145 restraints weight = 116304.228| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.8623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24606 Z= 0.122 Angle : 0.605 11.933 33282 Z= 0.295 Chirality : 0.038 0.161 3819 Planarity : 0.004 0.049 4233 Dihedral : 8.626 70.459 3411 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 0.38 (0.16), residues: 2943 helix: 1.00 (0.13), residues: 1731 sheet: -0.96 (0.36), residues: 219 loop : -0.67 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 410 HIS 0.008 0.001 HIS H 19 PHE 0.018 0.001 PHE I 74 TYR 0.017 0.001 TYR D 540 ARG 0.007 0.000 ARG H 8 Details of bonding type rmsd hydrogen bonds : bond 0.02657 ( 1061) hydrogen bonds : angle 4.10416 ( 3000) covalent geometry : bond 0.00277 (24606) covalent geometry : angle 0.60511 (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 177 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8630 (mmp) cc_final: 0.8151 (mtt) REVERT: A 147 MET cc_start: 0.9142 (mpp) cc_final: 0.8905 (mpp) REVERT: A 317 ASP cc_start: 0.9673 (t0) cc_final: 0.9274 (m-30) REVERT: A 334 MET cc_start: 0.9026 (mmt) cc_final: 0.8588 (mmm) REVERT: A 399 MET cc_start: 0.8574 (tpp) cc_final: 0.8316 (tmm) REVERT: A 462 MET cc_start: 0.9299 (mpp) cc_final: 0.9029 (ttm) REVERT: B 71 LEU cc_start: 0.9599 (mt) cc_final: 0.9297 (mt) REVERT: B 114 MET cc_start: 0.9346 (mmp) cc_final: 0.9012 (mmm) REVERT: B 210 MET cc_start: 0.9540 (tpt) cc_final: 0.9322 (tpp) REVERT: B 216 ASP cc_start: 0.8438 (t0) cc_final: 0.8219 (t0) REVERT: B 307 MET cc_start: 0.8437 (mmp) cc_final: 0.8179 (mpp) REVERT: B 309 MET cc_start: 0.8228 (tpp) cc_final: 0.7982 (tpp) REVERT: B 334 MET cc_start: 0.9654 (tpp) cc_final: 0.9325 (tpp) REVERT: B 348 MET cc_start: 0.8768 (ppp) cc_final: 0.8435 (ppp) REVERT: B 462 MET cc_start: 0.9428 (ttt) cc_final: 0.8940 (tpp) REVERT: B 533 MET cc_start: 0.9205 (ptm) cc_final: 0.8769 (ptm) REVERT: C 1 MET cc_start: 0.8712 (mmp) cc_final: 0.7663 (ppp) REVERT: C 19 HIS cc_start: 0.9609 (t-90) cc_final: 0.9341 (m90) REVERT: C 128 MET cc_start: 0.8685 (ptp) cc_final: 0.7961 (ptp) REVERT: C 147 MET cc_start: 0.9053 (mmt) cc_final: 0.8663 (mpp) REVERT: C 334 MET cc_start: 0.9571 (tpt) cc_final: 0.9240 (tpt) REVERT: C 335 MET cc_start: 0.8907 (ttm) cc_final: 0.8577 (ttm) REVERT: C 374 LEU cc_start: 0.9469 (tp) cc_final: 0.9224 (tp) REVERT: C 462 MET cc_start: 0.9679 (mtp) cc_final: 0.9060 (ttt) REVERT: D 147 MET cc_start: 0.9003 (mmm) cc_final: 0.8707 (mpp) REVERT: D 234 MET cc_start: 0.9495 (mtm) cc_final: 0.9094 (mtp) REVERT: D 309 MET cc_start: 0.8289 (mmm) cc_final: 0.8070 (mmm) REVERT: D 334 MET cc_start: 0.9571 (tpp) cc_final: 0.9324 (tpp) REVERT: D 348 MET cc_start: 0.9619 (ptm) cc_final: 0.9252 (ptp) REVERT: E 128 MET cc_start: 0.8912 (tpp) cc_final: 0.8484 (tpp) REVERT: E 376 MET cc_start: 0.9544 (mpp) cc_final: 0.9274 (mpp) REVERT: F 128 MET cc_start: 0.9005 (tpp) cc_final: 0.8677 (mtt) REVERT: F 210 MET cc_start: 0.9145 (tpp) cc_final: 0.8856 (tpp) REVERT: F 234 MET cc_start: 0.9179 (mtm) cc_final: 0.8875 (mtm) REVERT: F 335 MET cc_start: 0.9078 (mtp) cc_final: 0.8610 (tpp) REVERT: F 348 MET cc_start: 0.8913 (ttp) cc_final: 0.8636 (ttt) REVERT: F 462 MET cc_start: 0.9239 (mtp) cc_final: 0.8870 (tmm) REVERT: F 533 MET cc_start: 0.9057 (ppp) cc_final: 0.8697 (ppp) REVERT: G 47 MET cc_start: 0.5882 (mtp) cc_final: 0.4160 (tpp) REVERT: I 47 MET cc_start: 0.7457 (ttp) cc_final: 0.6673 (tmm) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3373 time to fit residues: 99.7013 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 : 2.752 ------------------------------------------------------------------------------- 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: 0.1980 chunk 188 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.036262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.026240 restraints weight = 275215.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.026968 restraints weight = 164784.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.027463 restraints weight = 115235.437| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.8801 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= 0.104 Angle : 0.601 9.404 33282 Z= 0.291 Chirality : 0.039 0.158 3819 Planarity : 0.004 0.049 4233 Dihedral : 8.443 65.192 3411 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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: 0.48 (0.16), residues: 2943 helix: 1.08 (0.13), residues: 1725 sheet: -0.87 (0.36), residues: 219 loop : -0.63 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 410 HIS 0.004 0.001 HIS H 14 PHE 0.018 0.001 PHE I 74 TYR 0.016 0.001 TYR A 77 ARG 0.007 0.000 ARG H 8 Details of bonding type rmsd hydrogen bonds : bond 0.02549 ( 1061) hydrogen bonds : angle 4.03378 ( 3000) covalent geometry : bond 0.00240 (24606) covalent geometry : angle 0.60150 (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 178 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8705 (mmp) cc_final: 0.8347 (mtt) REVERT: A 147 MET cc_start: 0.9148 (mpp) cc_final: 0.8897 (mpp) REVERT: A 157 LEU cc_start: 0.9502 (tp) cc_final: 0.9278 (tt) REVERT: A 317 ASP cc_start: 0.9666 (t0) cc_final: 0.9281 (m-30) REVERT: A 334 MET cc_start: 0.9097 (mmt) cc_final: 0.8534 (mmm) REVERT: A 376 MET cc_start: 0.9265 (pmm) cc_final: 0.9028 (pmm) REVERT: A 399 MET cc_start: 0.8537 (tpp) cc_final: 0.8302 (tmm) REVERT: A 462 MET cc_start: 0.9303 (mpp) cc_final: 0.9039 (ttm) REVERT: B 71 LEU cc_start: 0.9551 (mt) cc_final: 0.9262 (mt) REVERT: B 114 MET cc_start: 0.9363 (mmp) cc_final: 0.9045 (mmm) REVERT: B 210 MET cc_start: 0.9587 (tpt) cc_final: 0.9373 (tpp) REVERT: B 307 MET cc_start: 0.8454 (mmp) cc_final: 0.8211 (mpp) REVERT: B 309 MET cc_start: 0.8239 (tpp) cc_final: 0.7993 (tpp) REVERT: B 334 MET cc_start: 0.9670 (tpp) cc_final: 0.9330 (tpp) REVERT: B 348 MET cc_start: 0.8761 (ppp) cc_final: 0.8450 (ppp) REVERT: B 462 MET cc_start: 0.9428 (ttt) cc_final: 0.8951 (tpp) REVERT: B 533 MET cc_start: 0.9170 (ptm) cc_final: 0.8771 (ptm) REVERT: C 19 HIS cc_start: 0.9622 (t-90) cc_final: 0.9395 (m90) REVERT: C 128 MET cc_start: 0.8674 (ptp) cc_final: 0.8330 (ptp) REVERT: C 334 MET cc_start: 0.9581 (tpt) cc_final: 0.9267 (tpt) REVERT: C 335 MET cc_start: 0.8913 (ttm) cc_final: 0.8588 (ttm) REVERT: C 374 LEU cc_start: 0.9453 (tp) cc_final: 0.9214 (tp) REVERT: C 462 MET cc_start: 0.9727 (mtp) cc_final: 0.9112 (ttt) REVERT: C 533 MET cc_start: 0.8788 (ptm) cc_final: 0.8425 (ptm) REVERT: D 147 MET cc_start: 0.9010 (mmm) cc_final: 0.8719 (mpp) REVERT: D 234 MET cc_start: 0.9504 (mtm) cc_final: 0.9101 (mtp) REVERT: D 309 MET cc_start: 0.8282 (mmm) cc_final: 0.8063 (mmm) REVERT: D 334 MET cc_start: 0.9560 (tpp) cc_final: 0.9329 (tpp) REVERT: D 348 MET cc_start: 0.9638 (ptm) cc_final: 0.9302 (ptm) REVERT: D 533 MET cc_start: 0.8446 (ppp) cc_final: 0.8227 (ppp) REVERT: E 128 MET cc_start: 0.8874 (tpp) cc_final: 0.8414 (tpp) REVERT: E 147 MET cc_start: 0.7778 (ptp) cc_final: 0.7396 (pmm) REVERT: E 376 MET cc_start: 0.9513 (mpp) cc_final: 0.9257 (mpp) REVERT: F 128 MET cc_start: 0.8906 (tpp) cc_final: 0.8628 (mtt) REVERT: F 210 MET cc_start: 0.9175 (tpp) cc_final: 0.8826 (tpp) REVERT: F 234 MET cc_start: 0.9206 (mtm) cc_final: 0.8918 (mtm) REVERT: F 335 MET cc_start: 0.9071 (mtp) cc_final: 0.8628 (tpp) REVERT: F 348 MET cc_start: 0.8895 (ttp) cc_final: 0.8621 (ttt) REVERT: F 462 MET cc_start: 0.9215 (mtp) cc_final: 0.8858 (tmm) REVERT: F 533 MET cc_start: 0.8929 (ppp) cc_final: 0.8690 (ppp) REVERT: G 47 MET cc_start: 0.6175 (mtp) cc_final: 0.4331 (tpp) REVERT: I 47 MET cc_start: 0.7382 (ttp) cc_final: 0.6977 (tmm) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3437 time to fit residues: 101.8154 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 : 3.330 ------------------------------------------------------------------------------- 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: 5.9990 chunk 294 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 247 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 0.0040 chunk 141 optimal weight: 0.9990 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 HIS E 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.036632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.026553 restraints weight = 273127.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.027266 restraints weight = 163942.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.027768 restraints weight = 115614.345| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.8924 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= 0.095 Angle : 0.589 9.068 33282 Z= 0.285 Chirality : 0.039 0.158 3819 Planarity : 0.004 0.050 4233 Dihedral : 8.210 59.661 3411 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.55 (0.16), residues: 2943 helix: 1.12 (0.13), residues: 1722 sheet: -0.83 (0.36), residues: 219 loop : -0.58 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 410 HIS 0.004 0.001 HIS H 14 PHE 0.018 0.001 PHE I 74 TYR 0.013 0.001 TYR D 540 ARG 0.007 0.000 ARG H 8 Details of bonding type rmsd hydrogen bonds : bond 0.02485 ( 1061) hydrogen bonds : angle 3.95820 ( 3000) covalent geometry : bond 0.00216 (24606) covalent geometry : angle 0.58907 (33282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7560.21 seconds wall clock time: 133 minutes 9.33 seconds (7989.33 seconds total)