Starting phenix.real_space_refine on Mon Aug 25 01:32:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jns_36450/08_2025/8jns_36450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jns_36450/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jns_36450/08_2025/8jns_36450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jns_36450/08_2025/8jns_36450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jns_36450/08_2025/8jns_36450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jns_36450/08_2025/8jns_36450.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 174 5.16 5 C 15336 2.51 5 N 4041 2.21 5 O 4593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24168 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "C" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "D" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 375} Chain breaks: 2 Chain: "E" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 375} Chain breaks: 2 Chain: "F" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 375} Chain breaks: 2 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "H" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "I" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.08, per 1000 atoms: 0.25 Number of scatterers: 24168 At special positions: 0 Unit cell: (168.96, 171.6, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 174 16.00 P 18 15.00 Mg 6 11.99 O 4593 8.00 N 4041 7.00 C 15336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 13 sheets defined 61.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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: 4.86 Time building geometry restraints manager: 2.91 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: 0.02 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.330 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.88 (0.13), residues: 2943 helix: -3.31 (0.09), residues: 1650 sheet: -2.70 (0.34), residues: 195 loop : -2.90 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 112 TYR 0.022 0.004 TYR A 371 PHE 0.018 0.003 PHE F 532 TRP 0.023 0.004 TRP B 189 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00955 (24606) covalent geometry : angle 1.51588 (33282) hydrogen bonds : bond 0.25127 ( 1061) hydrogen bonds : angle 9.05686 ( 3000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 484 poor density : 354 time to evaluate : 0.940 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: 0.1818 time to fit residues: 211.9958 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 : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 34 ASN A 123 ASN A 237 ASN A 262 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 536 HIS B 34 ASN B 40 HIS B 219 ASN B 283 GLN C 19 HIS C 34 ASN ** C 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.043139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.031977 restraints weight = 232212.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032828 restraints weight = 155416.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.033466 restraints weight = 114517.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.033917 restraints weight = 89626.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.034244 restraints weight = 74798.410| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24606 Z= 0.156 Angle : 0.752 9.576 33282 Z= 0.381 Chirality : 0.043 0.208 3819 Planarity : 0.006 0.076 4233 Dihedral : 10.756 75.024 3411 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.14), residues: 2943 helix: -1.40 (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 ARG 0.005 0.001 ARG H 8 TYR 0.019 0.002 TYR B 90 PHE 0.020 0.002 PHE I 74 TRP 0.037 0.005 TRP F 189 HIS 0.007 0.001 HIS G 40 Details of bonding type rmsd covalent geometry : bond 0.00348 (24606) covalent geometry : angle 0.75194 (33282) hydrogen bonds : bond 0.04700 ( 1061) hydrogen bonds : angle 5.13312 ( 3000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 255 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7598 (mm) cc_final: 0.7378 (mt) REVERT: A 114 MET cc_start: 0.9242 (mmp) cc_final: 0.9020 (mmm) REVERT: A 157 LEU cc_start: 0.9331 (tp) cc_final: 0.8963 (tp) REVERT: B 140 VAL cc_start: 0.9301 (t) cc_final: 0.9072 (t) REVERT: B 335 MET cc_start: 0.9426 (mtp) cc_final: 0.8775 (ttm) REVERT: B 462 MET cc_start: 0.9198 (mtp) cc_final: 0.8836 (ttm) REVERT: C 307 MET cc_start: 0.7244 (mmt) cc_final: 0.6769 (mmt) REVERT: C 374 LEU cc_start: 0.9299 (tp) cc_final: 0.9083 (tp) REVERT: C 399 MET cc_start: 0.9133 (mmm) cc_final: 0.8716 (mpp) REVERT: C 462 MET cc_start: 0.9437 (mtp) cc_final: 0.8954 (ttp) REVERT: D 234 MET cc_start: 0.9319 (ttp) cc_final: 0.9119 (mtp) REVERT: D 307 MET cc_start: 0.7248 (mmt) cc_final: 0.6922 (mmt) REVERT: D 376 MET cc_start: 0.9463 (mtm) cc_final: 0.9257 (ptp) REVERT: E 128 MET cc_start: 0.8539 (tpp) cc_final: 0.7835 (tpp) REVERT: E 334 MET cc_start: 0.9151 (mtt) cc_final: 0.8613 (mtt) REVERT: E 376 MET cc_start: 0.9476 (mtm) cc_final: 0.9038 (ptp) REVERT: F 207 ILE cc_start: 0.9484 (mt) cc_final: 0.9281 (mt) REVERT: F 234 MET cc_start: 0.8777 (mtm) cc_final: 0.8401 (mtm) REVERT: F 462 MET cc_start: 0.9086 (mtp) cc_final: 0.8703 (tmm) REVERT: G 47 MET cc_start: 0.5990 (mmm) cc_final: 0.4889 (mmm) REVERT: G 75 PHE cc_start: 0.9464 (m-10) cc_final: 0.9241 (m-80) REVERT: H 31 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6567 (mp0) REVERT: H 73 ASP cc_start: 0.9388 (t70) cc_final: 0.9040 (p0) outliers start: 5 outliers final: 0 residues processed: 260 average time/residue: 0.1753 time to fit residues: 72.0249 Evaluate side-chains 188 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 248 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 294 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS H 19 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.042457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032195 restraints weight = 237597.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.033034 restraints weight = 156962.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.033612 restraints weight = 115399.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.034033 restraints weight = 92482.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.034264 restraints weight = 78493.417| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24606 Z= 0.130 Angle : 0.623 8.840 33282 Z= 0.313 Chirality : 0.040 0.177 3819 Planarity : 0.005 0.060 4233 Dihedral : 10.097 89.849 3411 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.15), residues: 2943 helix: -0.20 (0.13), residues: 1716 sheet: -2.13 (0.30), residues: 219 loop : -1.41 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 8 TYR 0.018 0.002 TYR B 90 PHE 0.022 0.002 PHE H 74 TRP 0.024 0.003 TRP C 189 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00292 (24606) covalent geometry : angle 0.62313 (33282) hydrogen bonds : bond 0.03452 ( 1061) hydrogen bonds : angle 4.41499 ( 3000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7709 (mm) cc_final: 0.7459 (mt) REVERT: A 48 SER cc_start: 0.9319 (m) cc_final: 0.9101 (p) REVERT: A 128 MET cc_start: 0.7694 (mmp) cc_final: 0.7065 (tpp) REVERT: A 334 MET cc_start: 0.8608 (mmm) cc_final: 0.8401 (mmt) REVERT: A 399 MET cc_start: 0.8399 (tpp) cc_final: 0.7987 (tmm) REVERT: B 216 ASP cc_start: 0.7848 (t0) cc_final: 0.7536 (t0) REVERT: B 335 MET cc_start: 0.9548 (mtp) cc_final: 0.8749 (ttm) REVERT: B 533 MET cc_start: 0.8983 (ppp) cc_final: 0.8180 (ppp) REVERT: C 1 MET cc_start: 0.9205 (mmp) cc_final: 0.8876 (mmm) REVERT: D 144 LEU cc_start: 0.9782 (mt) cc_final: 0.9568 (mt) REVERT: D 348 MET cc_start: 0.9531 (ptm) cc_final: 0.9182 (ptm) REVERT: E 225 HIS cc_start: 0.7616 (p90) cc_final: 0.7394 (p-80) REVERT: E 307 MET cc_start: 0.7919 (tpp) cc_final: 0.7364 (tpp) REVERT: E 334 MET cc_start: 0.9205 (mtt) cc_final: 0.8796 (mtt) REVERT: E 376 MET cc_start: 0.9484 (mtm) cc_final: 0.9078 (ptp) REVERT: E 533 MET cc_start: 0.8520 (ppp) cc_final: 0.7600 (mmp) REVERT: F 147 MET cc_start: 0.8975 (mmt) cc_final: 0.8731 (mmp) REVERT: F 207 ILE cc_start: 0.9579 (mt) cc_final: 0.9366 (mt) REVERT: F 216 ASP cc_start: 0.8726 (m-30) cc_final: 0.8517 (t0) REVERT: F 234 MET cc_start: 0.8771 (mtm) cc_final: 0.8395 (mtp) REVERT: F 334 MET cc_start: 0.9487 (tpp) cc_final: 0.9279 (tpp) REVERT: F 348 MET cc_start: 0.8952 (mtm) cc_final: 0.8430 (ttm) REVERT: F 462 MET cc_start: 0.9157 (mtp) cc_final: 0.8857 (tmm) REVERT: G 88 GLU cc_start: 0.8717 (pt0) cc_final: 0.8086 (mm-30) REVERT: H 31 GLU cc_start: 0.6397 (mt-10) cc_final: 0.6153 (mm-30) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1722 time to fit residues: 61.2310 Evaluate side-chains 174 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 237 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 262 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 262 GLN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 HIS H 40 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.041202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.031154 restraints weight = 236844.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.031919 restraints weight = 155771.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.032453 restraints weight = 115975.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032778 restraints weight = 93270.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.033107 restraints weight = 80632.156| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24606 Z= 0.132 Angle : 0.613 10.681 33282 Z= 0.303 Chirality : 0.039 0.165 3819 Planarity : 0.005 0.062 4233 Dihedral : 9.616 81.893 3411 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.16), residues: 2943 helix: 0.35 (0.13), residues: 1716 sheet: -1.87 (0.30), residues: 219 loop : -1.08 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 16 TYR 0.019 0.001 TYR B 90 PHE 0.019 0.001 PHE H 74 TRP 0.025 0.003 TRP F 410 HIS 0.005 0.001 HIS F 158 Details of bonding type rmsd covalent geometry : bond 0.00296 (24606) covalent geometry : angle 0.61322 (33282) hydrogen bonds : bond 0.03046 ( 1061) hydrogen bonds : angle 4.13918 ( 3000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.046 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 30 LEU cc_start: 0.7859 (mm) cc_final: 0.7623 (mt) REVERT: A 128 MET cc_start: 0.8075 (mmp) cc_final: 0.7562 (tpp) REVERT: A 157 LEU cc_start: 0.9468 (tp) cc_final: 0.9147 (tp) REVERT: A 334 MET cc_start: 0.8687 (mmm) cc_final: 0.8477 (mmm) REVERT: A 399 MET cc_start: 0.8432 (tpp) cc_final: 0.8141 (tmm) REVERT: B 462 MET cc_start: 0.9264 (ttm) cc_final: 0.9060 (ttm) REVERT: B 533 MET cc_start: 0.9069 (ppp) cc_final: 0.8502 (ppp) REVERT: C 334 MET cc_start: 0.9514 (tpt) cc_final: 0.9234 (tpt) REVERT: C 376 MET cc_start: 0.9420 (mpp) cc_final: 0.9174 (ptp) REVERT: D 234 MET cc_start: 0.9328 (mtm) cc_final: 0.8950 (mtp) REVERT: D 348 MET cc_start: 0.9503 (ptm) cc_final: 0.9286 (ptm) REVERT: D 376 MET cc_start: 0.9366 (mpp) cc_final: 0.9090 (ptp) REVERT: E 128 MET cc_start: 0.9100 (mmm) cc_final: 0.8337 (tpp) REVERT: E 225 HIS cc_start: 0.7632 (p90) cc_final: 0.7403 (p-80) REVERT: E 307 MET cc_start: 0.7973 (tpp) cc_final: 0.7714 (tpp) REVERT: F 147 MET cc_start: 0.9195 (mmt) cc_final: 0.8980 (mmp) REVERT: F 207 ILE cc_start: 0.9569 (mt) cc_final: 0.9352 (mt) REVERT: F 309 MET cc_start: 0.8644 (ppp) cc_final: 0.7958 (ppp) REVERT: F 348 MET cc_start: 0.8997 (mtm) cc_final: 0.8365 (mtt) REVERT: F 399 MET cc_start: 0.9215 (mmp) cc_final: 0.9009 (mmt) REVERT: F 462 MET cc_start: 0.9204 (mtp) cc_final: 0.8883 (tmm) REVERT: G 47 MET cc_start: 0.6254 (mmm) cc_final: 0.5232 (tmm) REVERT: G 88 GLU cc_start: 0.8743 (pt0) cc_final: 0.8010 (mm-30) REVERT: H 31 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5904 (mm-30) REVERT: H 73 ASP cc_start: 0.9474 (t70) cc_final: 0.9153 (p0) REVERT: I 46 LYS cc_start: 0.9131 (pptt) cc_final: 0.8808 (pttm) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.1636 time to fit residues: 55.2220 Evaluate side-chains 168 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 8 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 244 ASN A 283 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN B 237 ASN B 244 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN F 262 GLN H 19 HIS I 14 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.039944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030247 restraints weight = 236934.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.030954 restraints weight = 155139.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.031422 restraints weight = 115912.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.031783 restraints weight = 94143.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.031977 restraints weight = 80863.160| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24606 Z= 0.159 Angle : 0.636 10.791 33282 Z= 0.313 Chirality : 0.039 0.153 3819 Planarity : 0.005 0.059 4233 Dihedral : 9.470 76.944 3411 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2943 helix: 0.56 (0.13), residues: 1746 sheet: -1.65 (0.32), residues: 213 loop : -0.97 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 63 TYR 0.014 0.001 TYR B 90 PHE 0.024 0.002 PHE H 74 TRP 0.025 0.003 TRP F 410 HIS 0.006 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00348 (24606) covalent geometry : angle 0.63628 (33282) hydrogen bonds : bond 0.03006 ( 1061) hydrogen bonds : angle 4.10228 ( 3000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8359 (mmp) cc_final: 0.7598 (mmm) REVERT: A 147 MET cc_start: 0.8935 (mpp) cc_final: 0.8653 (mpp) REVERT: A 399 MET cc_start: 0.8671 (tpp) cc_final: 0.8421 (tmm) REVERT: A 462 MET cc_start: 0.9329 (mpp) cc_final: 0.8809 (ttm) REVERT: B 114 MET cc_start: 0.9321 (mmp) cc_final: 0.9008 (mmm) REVERT: B 462 MET cc_start: 0.9294 (ttm) cc_final: 0.9093 (ttm) REVERT: B 533 MET cc_start: 0.9050 (ppp) cc_final: 0.8582 (ppp) REVERT: C 19 HIS cc_start: 0.9634 (t70) cc_final: 0.9341 (m-70) REVERT: C 128 MET cc_start: 0.9156 (ptp) cc_final: 0.8464 (ptp) REVERT: C 144 LEU cc_start: 0.9793 (mm) cc_final: 0.9561 (mt) REVERT: C 334 MET cc_start: 0.9587 (tpt) cc_final: 0.9317 (tpt) REVERT: C 376 MET cc_start: 0.9388 (mpp) cc_final: 0.9050 (ptp) REVERT: D 147 MET cc_start: 0.8706 (mmp) cc_final: 0.8489 (mpp) REVERT: D 234 MET cc_start: 0.9308 (mtm) cc_final: 0.8910 (mtp) REVERT: D 376 MET cc_start: 0.9454 (mpp) cc_final: 0.9078 (mpp) REVERT: E 128 MET cc_start: 0.9209 (mmm) cc_final: 0.8648 (tmm) REVERT: E 225 HIS cc_start: 0.7693 (p90) cc_final: 0.7471 (p-80) REVERT: E 307 MET cc_start: 0.8352 (tpp) cc_final: 0.7888 (tpp) REVERT: E 533 MET cc_start: 0.8936 (ppp) cc_final: 0.8706 (ppp) REVERT: F 207 ILE cc_start: 0.9636 (mt) cc_final: 0.9433 (mt) REVERT: F 234 MET cc_start: 0.9322 (mtm) cc_final: 0.9040 (mtm) REVERT: F 348 MET cc_start: 0.9002 (mtm) cc_final: 0.8524 (ttm) REVERT: F 399 MET cc_start: 0.9189 (mmp) cc_final: 0.8846 (mpp) REVERT: F 462 MET cc_start: 0.9222 (mtp) cc_final: 0.8948 (tmm) REVERT: H 19 HIS cc_start: 0.9182 (m90) cc_final: 0.8946 (m-70) REVERT: H 31 GLU cc_start: 0.6085 (mt-10) cc_final: 0.5804 (mm-30) REVERT: H 73 ASP cc_start: 0.9450 (t70) cc_final: 0.9220 (p0) REVERT: I 46 LYS cc_start: 0.9110 (pptt) cc_final: 0.8754 (pttm) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.1581 time to fit residues: 50.6530 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 : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 263 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 276 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 288 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 219 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 536 HIS E 536 HIS G 56 ASN H 64 GLN I 40 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.036017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.025950 restraints weight = 263883.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.026706 restraints weight = 160943.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.027247 restraints weight = 113867.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.027623 restraints weight = 88213.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.027878 restraints weight = 73148.394| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24606 Z= 0.174 Angle : 0.647 10.710 33282 Z= 0.320 Chirality : 0.039 0.220 3819 Planarity : 0.005 0.059 4233 Dihedral : 9.294 72.511 3411 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 2943 helix: 0.60 (0.13), residues: 1749 sheet: -1.52 (0.35), residues: 213 loop : -0.95 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 440 TYR 0.014 0.002 TYR F 540 PHE 0.023 0.002 PHE H 74 TRP 0.029 0.002 TRP F 410 HIS 0.005 0.001 HIS F 158 Details of bonding type rmsd covalent geometry : bond 0.00382 (24606) covalent geometry : angle 0.64701 (33282) hydrogen bonds : bond 0.03061 ( 1061) hydrogen bonds : angle 4.17290 ( 3000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8615 (mmp) cc_final: 0.7980 (mtt) REVERT: A 144 LEU cc_start: 0.9606 (tt) cc_final: 0.9347 (pp) REVERT: A 147 MET cc_start: 0.9074 (mpp) cc_final: 0.8855 (mpp) REVERT: A 157 LEU cc_start: 0.9486 (tp) cc_final: 0.9196 (tp) REVERT: A 317 ASP cc_start: 0.9582 (t0) cc_final: 0.9189 (m-30) REVERT: A 334 MET cc_start: 0.8790 (mmm) cc_final: 0.8482 (mmm) REVERT: A 399 MET cc_start: 0.8725 (tpp) cc_final: 0.8450 (tmm) REVERT: A 462 MET cc_start: 0.9392 (mpp) cc_final: 0.9053 (ttm) REVERT: B 114 MET cc_start: 0.9290 (mmp) cc_final: 0.9068 (mmm) REVERT: B 147 MET cc_start: 0.9202 (mmm) cc_final: 0.8900 (mmm) REVERT: B 348 MET cc_start: 0.8721 (ppp) cc_final: 0.8496 (ppp) REVERT: B 533 MET cc_start: 0.9295 (ppp) cc_final: 0.8811 (ptp) REVERT: C 19 HIS cc_start: 0.9602 (t70) cc_final: 0.9358 (t-90) REVERT: C 128 MET cc_start: 0.8644 (ptp) cc_final: 0.8139 (ptp) REVERT: C 144 LEU cc_start: 0.9846 (mm) cc_final: 0.9619 (mt) REVERT: C 210 MET cc_start: 0.9128 (mmp) cc_final: 0.8842 (mmp) REVERT: C 334 MET cc_start: 0.9554 (tpt) cc_final: 0.9290 (tpt) REVERT: C 335 MET cc_start: 0.8876 (ttm) cc_final: 0.8670 (ttm) REVERT: C 376 MET cc_start: 0.9416 (mpp) cc_final: 0.9146 (ptp) REVERT: C 462 MET cc_start: 0.9727 (mtp) cc_final: 0.9453 (mtp) REVERT: C 533 MET cc_start: 0.8432 (ppp) cc_final: 0.8225 (ppp) REVERT: D 234 MET cc_start: 0.9540 (mtm) cc_final: 0.9320 (mtm) REVERT: D 348 MET cc_start: 0.9549 (ptt) cc_final: 0.9129 (ptm) REVERT: D 376 MET cc_start: 0.9481 (mpp) cc_final: 0.9081 (mpp) REVERT: E 128 MET cc_start: 0.9184 (mmm) cc_final: 0.8717 (tpp) REVERT: E 225 HIS cc_start: 0.7826 (p90) cc_final: 0.7622 (p-80) REVERT: E 307 MET cc_start: 0.8596 (tpp) cc_final: 0.8297 (tpp) REVERT: F 234 MET cc_start: 0.9432 (mtm) cc_final: 0.9056 (mtm) REVERT: F 348 MET cc_start: 0.8984 (mtm) cc_final: 0.8601 (ttp) REVERT: F 462 MET cc_start: 0.9228 (mtp) cc_final: 0.8858 (tmm) REVERT: H 19 HIS cc_start: 0.9126 (m90) cc_final: 0.8909 (m-70) REVERT: H 31 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5934 (mm-30) REVERT: H 47 MET cc_start: 0.6255 (mtt) cc_final: 0.5492 (mtp) REVERT: H 73 ASP cc_start: 0.9496 (t70) cc_final: 0.9199 (p0) REVERT: I 46 LYS cc_start: 0.9278 (pptt) cc_final: 0.8909 (pttm) REVERT: I 47 MET cc_start: 0.7848 (tpp) cc_final: 0.7536 (ttp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1426 time to fit residues: 44.8567 Evaluate side-chains 158 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 40 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 295 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 244 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS B 262 GLN D 536 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.025300 restraints weight = 269997.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.026046 restraints weight = 162503.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.026572 restraints weight = 114014.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.026927 restraints weight = 87822.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.027181 restraints weight = 72672.017| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.8299 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= 0.195 Angle : 0.681 11.388 33282 Z= 0.334 Chirality : 0.040 0.183 3819 Planarity : 0.005 0.056 4233 Dihedral : 9.285 82.865 3411 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2943 helix: 0.66 (0.13), residues: 1731 sheet: -1.48 (0.36), residues: 213 loop : -0.94 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 16 TYR 0.016 0.002 TYR B 540 PHE 0.024 0.002 PHE H 74 TRP 0.023 0.002 TRP F 410 HIS 0.005 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00423 (24606) covalent geometry : angle 0.68100 (33282) hydrogen bonds : bond 0.03144 ( 1061) hydrogen bonds : angle 4.23456 ( 3000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8713 (mmp) cc_final: 0.8278 (mtt) REVERT: A 144 LEU cc_start: 0.9620 (tt) cc_final: 0.9411 (pp) REVERT: A 147 MET cc_start: 0.9163 (mpp) cc_final: 0.8937 (mpp) REVERT: A 317 ASP cc_start: 0.9565 (t0) cc_final: 0.9188 (m-30) REVERT: A 334 MET cc_start: 0.8676 (mmm) cc_final: 0.8339 (mmm) REVERT: A 399 MET cc_start: 0.8804 (tpp) cc_final: 0.8483 (tmm) REVERT: A 462 MET cc_start: 0.9393 (mpp) cc_final: 0.9087 (ttm) REVERT: B 307 MET cc_start: 0.8596 (mmp) cc_final: 0.8158 (mmm) REVERT: B 335 MET cc_start: 0.9510 (mtp) cc_final: 0.8102 (tpp) REVERT: B 348 MET cc_start: 0.8670 (ppp) cc_final: 0.8414 (ppp) REVERT: B 462 MET cc_start: 0.9388 (ttt) cc_final: 0.8941 (tpp) REVERT: B 533 MET cc_start: 0.9151 (ppp) cc_final: 0.8725 (ppp) REVERT: C 19 HIS cc_start: 0.9583 (t70) cc_final: 0.9326 (m90) REVERT: C 114 MET cc_start: 0.9050 (ptp) cc_final: 0.8786 (ptp) REVERT: C 128 MET cc_start: 0.8735 (ptp) cc_final: 0.8196 (ptp) REVERT: C 147 MET cc_start: 0.9149 (mmt) cc_final: 0.8717 (mpp) REVERT: C 210 MET cc_start: 0.9069 (mmp) cc_final: 0.8829 (mmp) REVERT: C 334 MET cc_start: 0.9541 (tpt) cc_final: 0.9236 (tpt) REVERT: C 376 MET cc_start: 0.9415 (mpp) cc_final: 0.9140 (ptp) REVERT: C 533 MET cc_start: 0.8565 (ppp) cc_final: 0.8270 (ppp) REVERT: D 234 MET cc_start: 0.9476 (mtm) cc_final: 0.9238 (mtm) REVERT: D 334 MET cc_start: 0.9493 (tpp) cc_final: 0.9238 (tpt) REVERT: D 348 MET cc_start: 0.9539 (ptt) cc_final: 0.9126 (ptm) REVERT: D 376 MET cc_start: 0.9481 (mpp) cc_final: 0.9108 (mpp) REVERT: E 128 MET cc_start: 0.9103 (mmm) cc_final: 0.8676 (tpp) REVERT: E 147 MET cc_start: 0.8238 (ptp) cc_final: 0.7689 (ptp) REVERT: E 307 MET cc_start: 0.8491 (tpp) cc_final: 0.8221 (tpp) REVERT: E 399 MET cc_start: 0.9203 (mpp) cc_final: 0.8902 (mpp) REVERT: F 234 MET cc_start: 0.9496 (mtm) cc_final: 0.9181 (mtm) REVERT: F 348 MET cc_start: 0.9111 (mtm) cc_final: 0.8699 (ttp) REVERT: F 462 MET cc_start: 0.9282 (mtp) cc_final: 0.8965 (tmm) REVERT: F 533 MET cc_start: 0.9306 (ppp) cc_final: 0.8976 (ppp) REVERT: G 47 MET cc_start: 0.6858 (mmm) cc_final: 0.5770 (tpt) REVERT: H 19 HIS cc_start: 0.9116 (m90) cc_final: 0.8900 (m-70) REVERT: H 31 GLU cc_start: 0.5940 (mt-10) cc_final: 0.5705 (mm-30) REVERT: H 47 MET cc_start: 0.6825 (mtt) cc_final: 0.6008 (mtp) REVERT: I 46 LYS cc_start: 0.9374 (pptt) cc_final: 0.9052 (pttm) REVERT: I 47 MET cc_start: 0.8374 (tpp) cc_final: 0.8019 (ttp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1578 time to fit residues: 46.1595 Evaluate side-chains 143 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 0.1980 chunk 272 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 247 optimal weight: 0.0070 chunk 83 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 238 optimal weight: 0.6980 overall best weight: 0.5802 ------------------------------------------------------------------------------- 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** B 158 HIS D 219 ASN E 237 ASN E 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.035863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.025751 restraints weight = 262008.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.026531 restraints weight = 157789.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.027079 restraints weight = 110530.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.027458 restraints weight = 85275.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.027700 restraints weight = 70591.700| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.8427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 24606 Z= 0.102 Angle : 0.618 9.707 33282 Z= 0.298 Chirality : 0.039 0.200 3819 Planarity : 0.004 0.052 4233 Dihedral : 8.890 68.957 3411 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.16), residues: 2943 helix: 0.96 (0.13), residues: 1728 sheet: -1.26 (0.36), residues: 213 loop : -0.75 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 448 TYR 0.015 0.001 TYR A 77 PHE 0.024 0.001 PHE D 532 TRP 0.017 0.002 TRP F 410 HIS 0.008 0.001 HIS D 461 Details of bonding type rmsd covalent geometry : bond 0.00234 (24606) covalent geometry : angle 0.61795 (33282) hydrogen bonds : bond 0.02681 ( 1061) hydrogen bonds : angle 3.93641 ( 3000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9072 (mmp) cc_final: 0.8757 (mmm) REVERT: A 128 MET cc_start: 0.8590 (mmp) cc_final: 0.8273 (mtt) REVERT: A 144 LEU cc_start: 0.9620 (tt) cc_final: 0.9365 (pp) REVERT: A 147 MET cc_start: 0.8978 (mpp) cc_final: 0.8762 (mpp) REVERT: A 157 LEU cc_start: 0.9469 (tp) cc_final: 0.9183 (tp) REVERT: A 317 ASP cc_start: 0.9603 (t0) cc_final: 0.9180 (m-30) REVERT: A 334 MET cc_start: 0.8625 (mmm) cc_final: 0.8334 (mmm) REVERT: A 399 MET cc_start: 0.8600 (tpp) cc_final: 0.8354 (tmm) REVERT: A 462 MET cc_start: 0.9301 (mpp) cc_final: 0.8933 (mpp) REVERT: B 114 MET cc_start: 0.9373 (mmp) cc_final: 0.9125 (mmm) REVERT: B 147 MET cc_start: 0.9184 (mmm) cc_final: 0.8837 (mmm) REVERT: B 210 MET cc_start: 0.9668 (tpt) cc_final: 0.9456 (tpp) REVERT: B 307 MET cc_start: 0.8471 (mmp) cc_final: 0.8092 (mpp) REVERT: B 348 MET cc_start: 0.8723 (ppp) cc_final: 0.8508 (ppp) REVERT: B 533 MET cc_start: 0.8940 (ppp) cc_final: 0.8625 (ppp) REVERT: C 19 HIS cc_start: 0.9593 (t70) cc_final: 0.9318 (m90) REVERT: C 128 MET cc_start: 0.8656 (ptp) cc_final: 0.8281 (ptp) REVERT: C 144 LEU cc_start: 0.9850 (mm) cc_final: 0.9593 (mt) REVERT: C 147 MET cc_start: 0.9044 (mmt) cc_final: 0.8602 (mpp) REVERT: C 210 MET cc_start: 0.9010 (mmp) cc_final: 0.8742 (mmp) REVERT: C 334 MET cc_start: 0.9546 (tpt) cc_final: 0.9254 (tpt) REVERT: C 335 MET cc_start: 0.8964 (ttm) cc_final: 0.8624 (ttm) REVERT: C 376 MET cc_start: 0.9459 (mpp) cc_final: 0.9127 (ptp) REVERT: C 533 MET cc_start: 0.8315 (ppp) cc_final: 0.7979 (ppp) REVERT: D 234 MET cc_start: 0.9507 (mtm) cc_final: 0.9069 (mtp) REVERT: D 334 MET cc_start: 0.9530 (tpp) cc_final: 0.9279 (tpp) REVERT: D 348 MET cc_start: 0.9490 (ptt) cc_final: 0.9042 (ptm) REVERT: D 376 MET cc_start: 0.9518 (mpp) cc_final: 0.9049 (mpp) REVERT: E 128 MET cc_start: 0.9249 (mmm) cc_final: 0.8518 (tpp) REVERT: E 307 MET cc_start: 0.8468 (tpp) cc_final: 0.8124 (tpp) REVERT: E 376 MET cc_start: 0.9499 (mpp) cc_final: 0.9215 (mpp) REVERT: F 128 MET cc_start: 0.9093 (tpp) cc_final: 0.8732 (mtt) REVERT: F 234 MET cc_start: 0.9464 (mtm) cc_final: 0.9145 (mtm) REVERT: F 348 MET cc_start: 0.9218 (mtm) cc_final: 0.8661 (ttp) REVERT: F 462 MET cc_start: 0.9258 (mtp) cc_final: 0.8891 (tmm) REVERT: F 533 MET cc_start: 0.9100 (ppp) cc_final: 0.8806 (ppp) REVERT: G 47 MET cc_start: 0.7297 (mmm) cc_final: 0.6061 (tpp) REVERT: H 19 HIS cc_start: 0.9124 (m90) cc_final: 0.8911 (m-70) REVERT: H 31 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6087 (mp0) REVERT: H 47 MET cc_start: 0.6594 (mtt) cc_final: 0.5744 (mtp) REVERT: I 46 LYS cc_start: 0.9202 (pptt) cc_final: 0.8908 (pttm) REVERT: I 47 MET cc_start: 0.8342 (tpp) cc_final: 0.8073 (ttp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1491 time to fit residues: 46.2758 Evaluate side-chains 152 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 6 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 277 optimal weight: 50.0000 chunk 147 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS E 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.025488 restraints weight = 277698.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.026178 restraints weight = 165590.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.026673 restraints weight = 116331.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.026971 restraints weight = 89742.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.027213 restraints weight = 75168.512| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.8721 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= 0.168 Angle : 0.652 11.040 33282 Z= 0.319 Chirality : 0.040 0.202 3819 Planarity : 0.004 0.054 4233 Dihedral : 8.810 73.178 3411 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.16), residues: 2943 helix: 0.86 (0.13), residues: 1734 sheet: -1.24 (0.35), residues: 219 loop : -0.78 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 233 TYR 0.019 0.001 TYR D 540 PHE 0.023 0.002 PHE B 301 TRP 0.018 0.002 TRP E 260 HIS 0.004 0.001 HIS D 461 Details of bonding type rmsd covalent geometry : bond 0.00368 (24606) covalent geometry : angle 0.65165 (33282) hydrogen bonds : bond 0.02936 ( 1061) hydrogen bonds : angle 4.17261 ( 3000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.924 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 1 MET cc_start: 0.9101 (mmp) cc_final: 0.8748 (mmm) REVERT: A 128 MET cc_start: 0.8628 (mmp) cc_final: 0.8294 (mtm) REVERT: A 147 MET cc_start: 0.9101 (mpp) cc_final: 0.8897 (mpp) REVERT: A 317 ASP cc_start: 0.9601 (t0) cc_final: 0.9173 (m-30) REVERT: A 334 MET cc_start: 0.8780 (mmm) cc_final: 0.8493 (mmm) REVERT: A 399 MET cc_start: 0.8758 (tpp) cc_final: 0.8479 (tmm) REVERT: A 462 MET cc_start: 0.9308 (mpp) cc_final: 0.8953 (mpp) REVERT: B 114 MET cc_start: 0.9348 (mmp) cc_final: 0.9068 (mmm) REVERT: B 307 MET cc_start: 0.8261 (mmp) cc_final: 0.8026 (mmm) REVERT: B 348 MET cc_start: 0.8721 (ppp) cc_final: 0.8445 (ppp) REVERT: C 19 HIS cc_start: 0.9585 (t70) cc_final: 0.9322 (m90) REVERT: C 128 MET cc_start: 0.8604 (ptp) cc_final: 0.8036 (ptp) REVERT: C 147 MET cc_start: 0.9130 (mmt) cc_final: 0.8697 (mpp) REVERT: C 210 MET cc_start: 0.9061 (mmp) cc_final: 0.8817 (mmp) REVERT: C 334 MET cc_start: 0.9509 (tpt) cc_final: 0.9226 (tpt) REVERT: C 335 MET cc_start: 0.8976 (ttm) cc_final: 0.8639 (ttm) REVERT: C 376 MET cc_start: 0.9424 (mpp) cc_final: 0.9052 (ptp) REVERT: C 533 MET cc_start: 0.8553 (ppp) cc_final: 0.8189 (ppp) REVERT: D 234 MET cc_start: 0.9488 (mtm) cc_final: 0.8807 (mtm) REVERT: D 348 MET cc_start: 0.9543 (ptt) cc_final: 0.9121 (ptm) REVERT: D 376 MET cc_start: 0.9482 (mpp) cc_final: 0.9059 (mpp) REVERT: E 128 MET cc_start: 0.9217 (mmm) cc_final: 0.8776 (tpp) REVERT: E 147 MET cc_start: 0.8390 (ptp) cc_final: 0.7981 (ptp) REVERT: E 307 MET cc_start: 0.8636 (tpp) cc_final: 0.8341 (tpp) REVERT: E 376 MET cc_start: 0.9510 (mpp) cc_final: 0.9247 (mpp) REVERT: F 128 MET cc_start: 0.9160 (tpp) cc_final: 0.8773 (mtt) REVERT: F 234 MET cc_start: 0.9497 (mtm) cc_final: 0.9161 (mtm) REVERT: F 348 MET cc_start: 0.9293 (mtm) cc_final: 0.8782 (ttp) REVERT: F 399 MET cc_start: 0.9182 (tpp) cc_final: 0.8970 (tpp) REVERT: F 462 MET cc_start: 0.9260 (mtp) cc_final: 0.8909 (tmm) REVERT: F 533 MET cc_start: 0.9186 (ppp) cc_final: 0.8831 (ppp) REVERT: H 31 GLU cc_start: 0.6284 (mt-10) cc_final: 0.5946 (mp0) REVERT: H 47 MET cc_start: 0.7305 (mtt) cc_final: 0.6739 (mtp) REVERT: H 73 ASP cc_start: 0.9508 (t70) cc_final: 0.9279 (p0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1343 time to fit residues: 40.5192 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 : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 269 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 169 optimal weight: 0.0670 chunk 132 optimal weight: 0.3980 chunk 211 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 295 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 overall best weight: 0.8522 ------------------------------------------------------------------------------- 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** ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 HIS H 19 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.026181 restraints weight = 272787.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.026929 restraints weight = 163182.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.027420 restraints weight = 113847.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.027749 restraints weight = 88843.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.027951 restraints weight = 74210.476| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.8836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 24606 Z= 0.102 Angle : 0.615 9.182 33282 Z= 0.297 Chirality : 0.039 0.197 3819 Planarity : 0.004 0.050 4233 Dihedral : 8.585 62.931 3411 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.16), residues: 2943 helix: 1.03 (0.13), residues: 1731 sheet: -1.11 (0.36), residues: 219 loop : -0.67 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 233 TYR 0.015 0.001 TYR D 540 PHE 0.039 0.001 PHE G 75 TRP 0.016 0.002 TRP D 410 HIS 0.008 0.001 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00237 (24606) covalent geometry : angle 0.61497 (33282) hydrogen bonds : bond 0.02661 ( 1061) hydrogen bonds : angle 3.93854 ( 3000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.943 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: 0.8604 (mmp) cc_final: 0.8361 (mtt) REVERT: A 147 MET cc_start: 0.9017 (mpp) cc_final: 0.8771 (mpp) REVERT: A 157 LEU cc_start: 0.9474 (tp) cc_final: 0.9198 (tt) REVERT: A 317 ASP cc_start: 0.9594 (t0) cc_final: 0.9194 (m-30) REVERT: A 334 MET cc_start: 0.8775 (mmm) cc_final: 0.8481 (mmm) REVERT: A 399 MET cc_start: 0.8573 (tpp) cc_final: 0.8362 (tmm) REVERT: A 462 MET cc_start: 0.9268 (mpp) cc_final: 0.8997 (ttm) REVERT: B 114 MET cc_start: 0.9378 (mmp) cc_final: 0.9110 (mmm) REVERT: B 210 MET cc_start: 0.9597 (tpt) cc_final: 0.9266 (tpp) REVERT: B 307 MET cc_start: 0.8326 (mmp) cc_final: 0.7728 (mpp) REVERT: B 309 MET cc_start: 0.7942 (tpt) cc_final: 0.7676 (tpp) REVERT: B 348 MET cc_start: 0.8721 (ppp) cc_final: 0.8502 (ppp) REVERT: B 462 MET cc_start: 0.9416 (ttt) cc_final: 0.9067 (tmm) REVERT: B 533 MET cc_start: 0.9257 (ptm) cc_final: 0.8849 (ptm) REVERT: C 19 HIS cc_start: 0.9583 (t70) cc_final: 0.9324 (m90) REVERT: C 128 MET cc_start: 0.8652 (ptp) cc_final: 0.8259 (ptp) REVERT: C 147 MET cc_start: 0.9053 (mmt) cc_final: 0.8617 (mpp) REVERT: C 210 MET cc_start: 0.8991 (mmp) cc_final: 0.8720 (mmp) REVERT: C 334 MET cc_start: 0.9525 (tpt) cc_final: 0.9242 (tpt) REVERT: C 335 MET cc_start: 0.8990 (ttm) cc_final: 0.8661 (ttm) REVERT: C 376 MET cc_start: 0.9450 (mpp) cc_final: 0.9098 (ptp) REVERT: C 533 MET cc_start: 0.8311 (ppp) cc_final: 0.7949 (ppp) REVERT: D 147 MET cc_start: 0.8699 (mmp) cc_final: 0.8435 (mpp) REVERT: D 234 MET cc_start: 0.9540 (mtm) cc_final: 0.9119 (mtp) REVERT: D 334 MET cc_start: 0.9429 (tpt) cc_final: 0.8941 (tpp) REVERT: D 348 MET cc_start: 0.9496 (ptt) cc_final: 0.9088 (ptm) REVERT: D 376 MET cc_start: 0.9490 (mpp) cc_final: 0.9037 (mpp) REVERT: E 128 MET cc_start: 0.9152 (mmm) cc_final: 0.8703 (tpp) REVERT: E 147 MET cc_start: 0.8319 (ptp) cc_final: 0.7695 (ptp) REVERT: E 307 MET cc_start: 0.8593 (tpp) cc_final: 0.8229 (tpp) REVERT: E 376 MET cc_start: 0.9508 (mpp) cc_final: 0.9269 (mpp) REVERT: F 128 MET cc_start: 0.9072 (tpp) cc_final: 0.8734 (mtt) REVERT: F 147 MET cc_start: 0.9076 (mmp) cc_final: 0.8300 (mpp) REVERT: F 234 MET cc_start: 0.9460 (mtm) cc_final: 0.9147 (mtm) REVERT: F 348 MET cc_start: 0.9258 (mtm) cc_final: 0.8665 (ttp) REVERT: F 399 MET cc_start: 0.9084 (tpp) cc_final: 0.8879 (tpp) REVERT: F 462 MET cc_start: 0.9185 (mtp) cc_final: 0.8829 (tmm) REVERT: F 533 MET cc_start: 0.9000 (ppp) cc_final: 0.8778 (ppp) REVERT: G 47 MET cc_start: 0.7683 (mmm) cc_final: 0.6773 (tpp) REVERT: H 31 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6566 (mp0) REVERT: H 47 MET cc_start: 0.7423 (mtt) cc_final: 0.6715 (mtp) REVERT: H 73 ASP cc_start: 0.9488 (t70) cc_final: 0.9266 (p0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1371 time to fit residues: 42.7594 Evaluate side-chains 150 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 73 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 280 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 chunk 19 optimal weight: 0.0070 chunk 143 optimal weight: 0.0270 chunk 42 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 244 ASN ** B 158 HIS ** 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 = 0.3041 r_free = 0.3041 target = 0.035918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.025903 restraints weight = 274937.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.026622 restraints weight = 164633.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.027108 restraints weight = 115927.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.027444 restraints weight = 90227.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.027651 restraints weight = 75234.364| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.8969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24606 Z= 0.114 Angle : 0.612 9.121 33282 Z= 0.298 Chirality : 0.039 0.194 3819 Planarity : 0.004 0.050 4233 Dihedral : 8.443 62.959 3411 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.16), residues: 2943 helix: 1.03 (0.13), residues: 1740 sheet: -1.10 (0.36), residues: 219 loop : -0.63 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 233 TYR 0.016 0.001 TYR D 540 PHE 0.020 0.001 PHE I 74 TRP 0.013 0.002 TRP F 410 HIS 0.004 0.001 HIS D 461 Details of bonding type rmsd covalent geometry : bond 0.00263 (24606) covalent geometry : angle 0.61161 (33282) hydrogen bonds : bond 0.02639 ( 1061) hydrogen bonds : angle 3.98469 ( 3000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4106.53 seconds wall clock time: 72 minutes 1.57 seconds (4321.57 seconds total)