Starting phenix.real_space_refine on Thu Feb 5 04:22:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzf_72352/02_2026/9xzf_72352.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzf_72352/02_2026/9xzf_72352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xzf_72352/02_2026/9xzf_72352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzf_72352/02_2026/9xzf_72352.map" model { file = "/net/cci-nas-00/data/ceres_data/9xzf_72352/02_2026/9xzf_72352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzf_72352/02_2026/9xzf_72352.cif" } resolution = 2.65 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 9158 2.51 5 N 2485 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14555 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "B" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "C" Number of atoms: 4779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4779 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 31, 'TRANS': 591} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.56, per 1000 atoms: 0.18 Number of scatterers: 14555 At special positions: 0 Unit cell: (108.626, 107.611, 107.611, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 12 15.00 O 2840 8.00 N 2485 7.00 C 9158 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: 1.14 Conformation dependent library (CDL) restraints added in 372.4 milliseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 13 sheets defined 43.8% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.244A pdb=" N LEU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 237 through 266 removed outlier: 3.685A pdb=" N GLN A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 5.700A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 removed outlier: 3.632A pdb=" N GLU A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.693A pdb=" N VAL A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.137A pdb=" N ILE A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 444 through 459 removed outlier: 3.564A pdb=" N LEU A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.566A pdb=" N ALA A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 567 through 593 removed outlier: 3.598A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 625 through 636 removed outlier: 3.529A pdb=" N GLY A 636 " --> pdb=" O GLN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.333A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 removed outlier: 3.709A pdb=" N SER B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 267 removed outlier: 3.544A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 5.766A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 removed outlier: 3.522A pdb=" N GLU B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.621A pdb=" N ILE B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.624A pdb=" N ILE B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 402 through 407' Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.859A pdb=" N ILE B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.563A pdb=" N THR B 434 " --> pdb=" O PRO B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 482 through 499 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 567 through 593 removed outlier: 3.717A pdb=" N THR B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 4.280A pdb=" N ALA B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 653 through 669 removed outlier: 3.559A pdb=" N GLU B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 164 through 180 removed outlier: 4.206A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.804A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.661A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 300 removed outlier: 6.490A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 328 removed outlier: 3.518A pdb=" N GLN C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 removed outlier: 3.523A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.595A pdb=" N ILE C 406 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.513A pdb=" N ALA C 488 " --> pdb=" O SER C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 540 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.556A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 4.386A pdb=" N ALA C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 3.520A pdb=" N LYS C 629 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 668 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.432A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.102A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN A 215 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 231 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 217 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU A 229 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A 219 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 526 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.349A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A 424 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N SER A 474 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N HIS A 426 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL A 476 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLU A 428 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLU A 478 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.333A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL B 99 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N CYS B 154 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP B 101 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU B 156 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ARG B 103 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA B 158 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 6.745A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 227 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 561 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B 526 " --> pdb=" O LYS B 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.292A pdb=" N GLN B 392 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 606 through 611 Processing sheet with id=AA9, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.310A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 202 removed outlier: 3.994A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN C 215 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA C 231 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 217 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 229 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 219 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 229 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP C 526 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 370 through 374 removed outlier: 6.263A pdb=" N GLN C 392 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 606 through 611 843 hydrogen bonds defined for protein. 2373 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: 2.42 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4584 1.33 - 1.45: 1848 1.45 - 1.57: 8260 1.57 - 1.69: 17 1.69 - 1.81: 99 Bond restraints: 14808 Sorted by residual: bond pdb=" N GLY B 481 " pdb=" CA GLY B 481 " ideal model delta sigma weight residual 1.458 1.444 0.014 9.20e-03 1.18e+04 2.17e+00 bond pdb=" CB GLU C 326 " pdb=" CG GLU C 326 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CB LYS B 439 " pdb=" CG LYS B 439 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.97e-01 bond pdb=" CA GLU C 326 " pdb=" CB GLU C 326 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.66e-02 3.63e+03 9.27e-01 bond pdb=" CB GLN B 94 " pdb=" CG GLN B 94 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.11e-01 ... (remaining 14803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 19824 1.68 - 3.36: 216 3.36 - 5.04: 40 5.04 - 6.71: 4 6.71 - 8.39: 2 Bond angle restraints: 20086 Sorted by residual: angle pdb=" CB MET B 485 " pdb=" CG MET B 485 " pdb=" SD MET B 485 " ideal model delta sigma weight residual 112.70 121.09 -8.39 3.00e+00 1.11e-01 7.82e+00 angle pdb=" CA GLU C 326 " pdb=" CB GLU C 326 " pdb=" CG GLU C 326 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.81e+00 angle pdb=" CA ILE B 664 " pdb=" CB ILE B 664 " pdb=" CG1 ILE B 664 " ideal model delta sigma weight residual 110.40 115.15 -4.75 1.70e+00 3.46e-01 7.81e+00 angle pdb=" C ILE B 196 " pdb=" N ASP B 197 " pdb=" CA ASP B 197 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.51e+00 angle pdb=" CB GLU C 644 " pdb=" CG GLU C 644 " pdb=" CD GLU C 644 " ideal model delta sigma weight residual 112.60 117.11 -4.51 1.70e+00 3.46e-01 7.04e+00 ... (remaining 20081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 7983 17.84 - 35.68: 811 35.68 - 53.52: 233 53.52 - 71.36: 57 71.36 - 89.20: 25 Dihedral angle restraints: 9109 sinusoidal: 3706 harmonic: 5403 Sorted by residual: dihedral pdb=" C4' A D 7 " pdb=" C3' A D 7 " pdb=" C2' A D 7 " pdb=" C1' A D 7 " ideal model delta sinusoidal sigma weight residual 36.35 -34.98 71.32 1 3.10e+00 1.04e-01 6.79e+02 dihedral pdb=" C4' A D 8 " pdb=" C3' A D 8 " pdb=" C2' A D 8 " pdb=" C1' A D 8 " ideal model delta sinusoidal sigma weight residual 36.34 -34.35 70.70 1 3.10e+00 1.04e-01 6.69e+02 dihedral pdb=" O4' A D 7 " pdb=" C4' A D 7 " pdb=" C3' A D 7 " pdb=" C2' A D 7 " ideal model delta sinusoidal sigma weight residual -35.15 23.58 -58.73 1 4.00e+00 6.25e-02 2.89e+02 ... (remaining 9106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1932 0.056 - 0.112: 376 0.112 - 0.168: 43 0.168 - 0.224: 0 0.224 - 0.280: 4 Chirality restraints: 2355 Sorted by residual: chirality pdb=" C2' A D 7 " pdb=" C3' A D 7 " pdb=" O2' A D 7 " pdb=" C1' A D 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C2' A D 8 " pdb=" C3' A D 8 " pdb=" O2' A D 8 " pdb=" C1' A D 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' A D 8 " pdb=" C4' A D 8 " pdb=" O3' A D 8 " pdb=" C2' A D 8 " both_signs ideal model delta sigma weight residual False -2.50 -2.73 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2352 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 326 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" CD GLU C 326 " 0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU C 326 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU C 326 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 644 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" CD GLU C 644 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU C 644 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU C 644 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 221 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO B 222 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 222 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 222 " 0.021 5.00e-02 4.00e+02 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 7002 2.97 - 3.45: 14521 3.45 - 3.94: 24374 3.94 - 4.42: 28658 4.42 - 4.90: 46480 Nonbonded interactions: 121035 Sorted by model distance: nonbonded pdb=" O ILE B 196 " pdb=" OD1 ASP B 197 " model vdw 2.489 3.040 nonbonded pdb=" O5' A D 1 " pdb=" O4' A D 1 " model vdw 2.542 2.432 nonbonded pdb=" O5' A D 8 " pdb=" O4' A D 8 " model vdw 2.559 2.432 nonbonded pdb=" N GLU C 602 " pdb=" OE1 GLU C 602 " model vdw 2.576 3.120 nonbonded pdb=" O4' U D 6 " pdb=" O2 U D 6 " model vdw 2.576 3.040 ... (remaining 121030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 668 or resid 901)) selection = (chain 'B' and (resid 46 through 668 or resid 901)) selection = chain 'C' } 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 individual isotropic 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: 2.610 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: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.850 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.004 0.042 14808 Z= 0.174 Angle : 0.478 8.392 20086 Z= 0.247 Chirality : 0.045 0.280 2355 Planarity : 0.003 0.041 2570 Dihedral : 16.540 89.204 5625 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.38 % Allowed : 18.94 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1865 helix: 1.03 (0.18), residues: 723 sheet: 1.46 (0.25), residues: 436 loop : 0.32 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.016 0.001 TYR A 116 PHE 0.014 0.001 PHE B 663 TRP 0.003 0.001 TRP A 184 HIS 0.002 0.000 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00409 (14808) covalent geometry : angle 0.47806 (20086) hydrogen bonds : bond 0.21540 ( 843) hydrogen bonds : angle 7.73765 ( 2373) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8669 (tptm) cc_final: 0.8362 (tptm) REVERT: A 292 MET cc_start: 0.8636 (tmt) cc_final: 0.8292 (tmm) REVERT: A 322 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: A 332 ASP cc_start: 0.7934 (t0) cc_final: 0.7590 (t0) REVERT: A 560 ASP cc_start: 0.8459 (m-30) cc_final: 0.8213 (m-30) REVERT: A 617 ARG cc_start: 0.9208 (mmm-85) cc_final: 0.8673 (mmm-85) REVERT: A 645 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: A 658 HIS cc_start: 0.8819 (t-90) cc_final: 0.8239 (t-170) REVERT: A 666 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7625 (pp20) REVERT: A 667 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6804 (mp) REVERT: B 96 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8319 (ttm) REVERT: B 112 ILE cc_start: 0.6319 (OUTLIER) cc_final: 0.5328 (tp) REVERT: B 118 ARG cc_start: 0.6737 (tpt170) cc_final: 0.6017 (tpm170) REVERT: B 155 ASN cc_start: 0.9053 (t0) cc_final: 0.8762 (t0) REVERT: B 322 GLU cc_start: 0.8747 (mp0) cc_final: 0.8497 (mp0) REVERT: C 119 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8063 (mmm-85) outliers start: 22 outliers final: 12 residues processed: 104 average time/residue: 0.5807 time to fit residues: 66.0118 Evaluate side-chains 103 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 609 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.086724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.062841 restraints weight = 24039.909| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.54 r_work: 0.2640 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14808 Z= 0.173 Angle : 0.519 7.194 20086 Z= 0.280 Chirality : 0.047 0.502 2355 Planarity : 0.004 0.045 2570 Dihedral : 7.214 79.928 2159 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.02 % Allowed : 17.31 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.20), residues: 1865 helix: 2.04 (0.18), residues: 730 sheet: 1.57 (0.25), residues: 431 loop : 0.34 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 118 TYR 0.015 0.001 TYR B 334 PHE 0.014 0.001 PHE A 340 TRP 0.004 0.001 TRP B 184 HIS 0.003 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00379 (14808) covalent geometry : angle 0.51932 (20086) hydrogen bonds : bond 0.06637 ( 843) hydrogen bonds : angle 5.48580 ( 2373) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8718 (tptm) cc_final: 0.8404 (tptm) REVERT: A 292 MET cc_start: 0.8773 (tmt) cc_final: 0.8465 (tmm) REVERT: A 322 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8524 (mm-30) REVERT: A 332 ASP cc_start: 0.7512 (t0) cc_final: 0.7235 (t0) REVERT: A 560 ASP cc_start: 0.8495 (m-30) cc_final: 0.8265 (m-30) REVERT: A 617 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8738 (mmm-85) REVERT: A 645 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: A 658 HIS cc_start: 0.8735 (t-90) cc_final: 0.8406 (t-170) REVERT: A 663 PHE cc_start: 0.7866 (t80) cc_final: 0.7619 (t80) REVERT: A 667 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7156 (mp) REVERT: B 112 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6063 (pt) REVERT: B 118 ARG cc_start: 0.6958 (tpt170) cc_final: 0.6143 (tpm170) REVERT: B 282 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: B 322 GLU cc_start: 0.8538 (mp0) cc_final: 0.8231 (mp0) REVERT: B 617 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7411 (tpt-90) REVERT: C 119 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8035 (mmm-85) REVERT: C 120 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: C 448 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8608 (mm) REVERT: C 616 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8461 (mmmt) outliers start: 48 outliers final: 10 residues processed: 133 average time/residue: 0.6271 time to fit residues: 90.8443 Evaluate side-chains 114 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 616 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 101 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN C 641 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.085819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.061985 restraints weight = 24429.511| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.56 r_work: 0.2618 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14808 Z= 0.239 Angle : 0.533 7.280 20086 Z= 0.284 Chirality : 0.047 0.319 2355 Planarity : 0.004 0.055 2570 Dihedral : 6.900 78.762 2138 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.78 % Allowed : 16.49 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.20), residues: 1865 helix: 2.14 (0.18), residues: 732 sheet: 1.50 (0.25), residues: 439 loop : 0.26 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 661 TYR 0.019 0.002 TYR B 334 PHE 0.020 0.001 PHE C 663 TRP 0.003 0.001 TRP A 184 HIS 0.002 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00557 (14808) covalent geometry : angle 0.53282 (20086) hydrogen bonds : bond 0.06063 ( 843) hydrogen bonds : angle 5.13769 ( 2373) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 96 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8706 (tptm) cc_final: 0.8446 (tptm) REVERT: A 292 MET cc_start: 0.8867 (tmt) cc_final: 0.8557 (tmm) REVERT: A 322 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8437 (mm-30) REVERT: A 332 ASP cc_start: 0.7504 (t0) cc_final: 0.7201 (t0) REVERT: A 560 ASP cc_start: 0.8532 (m-30) cc_final: 0.8299 (m-30) REVERT: A 617 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8718 (mmm-85) REVERT: A 645 GLU cc_start: 0.8756 (mp0) cc_final: 0.8487 (pm20) REVERT: A 658 HIS cc_start: 0.8858 (t-90) cc_final: 0.8372 (t-170) REVERT: A 667 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7181 (mp) REVERT: B 50 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8549 (t70) REVERT: B 56 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8815 (mp) REVERT: B 282 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: B 326 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 475 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8673 (mt-10) REVERT: B 617 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7390 (tpt-90) REVERT: C 119 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8128 (mmm-85) REVERT: C 616 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8489 (mmmt) outliers start: 60 outliers final: 20 residues processed: 141 average time/residue: 0.5456 time to fit residues: 83.8602 Evaluate side-chains 122 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 616 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 39 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN C 641 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.062480 restraints weight = 24518.760| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.52 r_work: 0.2632 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14808 Z= 0.211 Angle : 0.517 7.122 20086 Z= 0.276 Chirality : 0.046 0.278 2355 Planarity : 0.004 0.054 2570 Dihedral : 6.782 77.423 2133 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.52 % Allowed : 17.62 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.20), residues: 1865 helix: 2.18 (0.18), residues: 732 sheet: 1.44 (0.24), residues: 440 loop : 0.26 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 119 TYR 0.019 0.001 TYR B 334 PHE 0.016 0.001 PHE B 663 TRP 0.004 0.001 TRP B 184 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00492 (14808) covalent geometry : angle 0.51672 (20086) hydrogen bonds : bond 0.05635 ( 843) hydrogen bonds : angle 4.99703 ( 2373) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 97 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8702 (tptm) cc_final: 0.8439 (tptm) REVERT: A 292 MET cc_start: 0.8904 (tmt) cc_final: 0.8632 (tmm) REVERT: A 322 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8434 (mm-30) REVERT: A 332 ASP cc_start: 0.7540 (t70) cc_final: 0.7221 (t0) REVERT: A 560 ASP cc_start: 0.8487 (m-30) cc_final: 0.8268 (m-30) REVERT: A 617 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8989 (mmm-85) REVERT: A 645 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: A 658 HIS cc_start: 0.8851 (t-90) cc_final: 0.8392 (t-170) REVERT: B 50 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8551 (t70) REVERT: B 56 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8829 (mp) REVERT: B 282 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8081 (pm20) REVERT: B 326 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 617 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7367 (tpt-90) REVERT: C 119 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8252 (mtp-110) REVERT: C 616 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8472 (mmmt) outliers start: 56 outliers final: 23 residues processed: 140 average time/residue: 0.5171 time to fit residues: 79.8375 Evaluate side-chains 125 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 616 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 38 optimal weight: 0.0970 chunk 121 optimal weight: 0.0170 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 632 GLN C 641 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.088565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.065044 restraints weight = 24231.861| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.53 r_work: 0.2694 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14808 Z= 0.117 Angle : 0.483 7.437 20086 Z= 0.256 Chirality : 0.045 0.275 2355 Planarity : 0.003 0.047 2570 Dihedral : 6.522 74.447 2131 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.45 % Allowed : 18.94 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.20), residues: 1865 helix: 2.32 (0.18), residues: 735 sheet: 1.47 (0.24), residues: 441 loop : 0.38 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 119 TYR 0.020 0.001 TYR B 334 PHE 0.017 0.001 PHE C 663 TRP 0.007 0.001 TRP B 184 HIS 0.002 0.000 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00247 (14808) covalent geometry : angle 0.48335 (20086) hydrogen bonds : bond 0.04678 ( 843) hydrogen bonds : angle 4.73454 ( 2373) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8681 (tptm) cc_final: 0.8408 (tptm) REVERT: A 155 ASN cc_start: 0.9096 (t0) cc_final: 0.8886 (t0) REVERT: A 292 MET cc_start: 0.8903 (tmt) cc_final: 0.8630 (tmm) REVERT: A 322 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: A 325 LYS cc_start: 0.8476 (mttm) cc_final: 0.8255 (mtpt) REVERT: A 332 ASP cc_start: 0.7468 (t70) cc_final: 0.7127 (t0) REVERT: A 560 ASP cc_start: 0.8506 (m-30) cc_final: 0.8262 (m-30) REVERT: A 617 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8924 (mmm-85) REVERT: A 645 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8504 (pm20) REVERT: A 658 HIS cc_start: 0.8820 (t-90) cc_final: 0.8369 (t-170) REVERT: B 50 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8548 (t70) REVERT: B 59 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8745 (p) REVERT: B 230 GLU cc_start: 0.9144 (tp30) cc_final: 0.8927 (tp30) REVERT: B 282 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: B 617 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7355 (tpt-90) REVERT: C 119 ARG cc_start: 0.8542 (ttp80) cc_final: 0.7994 (mmm-85) REVERT: C 448 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8541 (mm) REVERT: C 560 ASP cc_start: 0.8689 (t70) cc_final: 0.8111 (m-30) REVERT: C 616 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8485 (mmmt) outliers start: 39 outliers final: 15 residues processed: 133 average time/residue: 0.5693 time to fit residues: 82.9339 Evaluate side-chains 122 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 616 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 76 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.087808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.064096 restraints weight = 24296.816| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.57 r_work: 0.2672 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14808 Z= 0.151 Angle : 0.488 7.920 20086 Z= 0.259 Chirality : 0.045 0.275 2355 Planarity : 0.004 0.049 2570 Dihedral : 6.447 73.328 2131 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.02 % Allowed : 18.75 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1865 helix: 2.37 (0.18), residues: 735 sheet: 1.45 (0.24), residues: 441 loop : 0.37 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.020 0.001 TYR B 334 PHE 0.015 0.001 PHE B 663 TRP 0.004 0.001 TRP A 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00343 (14808) covalent geometry : angle 0.48820 (20086) hydrogen bonds : bond 0.04819 ( 843) hydrogen bonds : angle 4.68471 ( 2373) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8670 (tptm) cc_final: 0.8402 (tptm) REVERT: A 155 ASN cc_start: 0.9101 (t0) cc_final: 0.8881 (t0) REVERT: A 292 MET cc_start: 0.8915 (tmt) cc_final: 0.8632 (tmm) REVERT: A 322 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8479 (mm-30) REVERT: A 325 LYS cc_start: 0.8451 (mttm) cc_final: 0.8224 (mtpt) REVERT: A 332 ASP cc_start: 0.7477 (t70) cc_final: 0.7126 (t0) REVERT: A 560 ASP cc_start: 0.8474 (m-30) cc_final: 0.8222 (m-30) REVERT: A 617 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8922 (mmm-85) REVERT: A 645 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8541 (pm20) REVERT: A 658 HIS cc_start: 0.8830 (t-90) cc_final: 0.8394 (t-170) REVERT: A 664 ILE cc_start: 0.8483 (mt) cc_final: 0.8275 (mp) REVERT: B 50 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8539 (t70) REVERT: B 89 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8741 (mppt) REVERT: B 118 ARG cc_start: 0.6406 (tpm170) cc_final: 0.6098 (tpm170) REVERT: B 282 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: B 475 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: B 560 ASP cc_start: 0.8174 (t0) cc_final: 0.7861 (m-30) REVERT: B 617 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7385 (tpt-90) REVERT: C 119 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8191 (mmm-85) REVERT: C 560 ASP cc_start: 0.8632 (t70) cc_final: 0.8015 (m-30) REVERT: C 616 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8481 (mmmt) outliers start: 48 outliers final: 22 residues processed: 136 average time/residue: 0.6012 time to fit residues: 89.3287 Evaluate side-chains 127 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 616 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 21 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.086332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.062388 restraints weight = 24291.545| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.53 r_work: 0.2625 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14808 Z= 0.233 Angle : 0.539 8.494 20086 Z= 0.286 Chirality : 0.047 0.277 2355 Planarity : 0.004 0.113 2570 Dihedral : 6.494 73.413 2131 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.77 % Allowed : 19.32 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.20), residues: 1865 helix: 2.27 (0.18), residues: 733 sheet: 1.41 (0.24), residues: 442 loop : 0.27 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.021 0.002 TYR B 334 PHE 0.021 0.001 PHE C 663 TRP 0.003 0.001 TRP A 184 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00547 (14808) covalent geometry : angle 0.53926 (20086) hydrogen bonds : bond 0.05426 ( 843) hydrogen bonds : angle 4.80714 ( 2373) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8664 (tptm) cc_final: 0.8405 (tptm) REVERT: A 292 MET cc_start: 0.8922 (tmt) cc_final: 0.8629 (tmm) REVERT: A 322 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8404 (mm-30) REVERT: A 325 LYS cc_start: 0.8478 (mttm) cc_final: 0.8247 (mtpt) REVERT: A 332 ASP cc_start: 0.7591 (t70) cc_final: 0.7238 (t0) REVERT: A 560 ASP cc_start: 0.8511 (m-30) cc_final: 0.8279 (m-30) REVERT: A 617 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8932 (mmm-85) REVERT: A 645 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: A 658 HIS cc_start: 0.8840 (t-90) cc_final: 0.8422 (t-170) REVERT: B 50 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8516 (t70) REVERT: B 89 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8756 (mppt) REVERT: B 282 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: B 475 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: C 119 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8239 (ttp-110) REVERT: C 560 ASP cc_start: 0.8692 (t70) cc_final: 0.8039 (m-30) REVERT: C 616 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8484 (mmmt) outliers start: 44 outliers final: 26 residues processed: 128 average time/residue: 0.5414 time to fit residues: 76.2269 Evaluate side-chains 129 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 616 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 100 optimal weight: 0.0870 chunk 163 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.088174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.064178 restraints weight = 23971.480| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.57 r_work: 0.2667 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14808 Z= 0.129 Angle : 0.486 8.358 20086 Z= 0.258 Chirality : 0.045 0.275 2355 Planarity : 0.004 0.056 2570 Dihedral : 6.284 73.287 2128 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.58 % Allowed : 19.26 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.20), residues: 1865 helix: 2.38 (0.18), residues: 735 sheet: 1.40 (0.24), residues: 442 loop : 0.30 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.023 0.001 TYR B 334 PHE 0.016 0.001 PHE C 663 TRP 0.006 0.001 TRP B 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00286 (14808) covalent geometry : angle 0.48573 (20086) hydrogen bonds : bond 0.04731 ( 843) hydrogen bonds : angle 4.64087 ( 2373) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8628 (tptm) cc_final: 0.8361 (tptm) REVERT: A 155 ASN cc_start: 0.9105 (t0) cc_final: 0.8894 (t0) REVERT: A 292 MET cc_start: 0.8908 (tmt) cc_final: 0.8647 (tmm) REVERT: A 322 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8504 (mm-30) REVERT: A 325 LYS cc_start: 0.8476 (mttm) cc_final: 0.8247 (mttt) REVERT: A 332 ASP cc_start: 0.7563 (t70) cc_final: 0.7187 (t0) REVERT: A 560 ASP cc_start: 0.8455 (m-30) cc_final: 0.8215 (m-30) REVERT: A 617 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8912 (mmm-85) REVERT: A 645 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: A 658 HIS cc_start: 0.8813 (t-90) cc_final: 0.8419 (t-170) REVERT: A 664 ILE cc_start: 0.8464 (mt) cc_final: 0.8258 (mp) REVERT: B 50 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8499 (t70) REVERT: B 96 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8270 (ttm) REVERT: B 118 ARG cc_start: 0.6431 (tpm170) cc_final: 0.5965 (tpm170) REVERT: B 282 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: B 475 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8694 (mt-10) REVERT: B 560 ASP cc_start: 0.8153 (t0) cc_final: 0.7833 (m-30) REVERT: C 119 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8308 (ttp-110) REVERT: C 560 ASP cc_start: 0.8639 (t70) cc_final: 0.8028 (m-30) REVERT: C 616 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8481 (mmmt) outliers start: 41 outliers final: 25 residues processed: 130 average time/residue: 0.5506 time to fit residues: 78.6382 Evaluate side-chains 127 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 616 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 120 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 85 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN C 426 HIS C 641 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.088684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.064749 restraints weight = 24087.486| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.57 r_work: 0.2673 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14808 Z= 0.128 Angle : 0.488 9.174 20086 Z= 0.257 Chirality : 0.044 0.275 2355 Planarity : 0.004 0.048 2570 Dihedral : 6.201 73.305 2128 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.45 % Allowed : 19.63 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.20), residues: 1865 helix: 2.42 (0.18), residues: 737 sheet: 1.43 (0.24), residues: 442 loop : 0.32 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.022 0.001 TYR B 334 PHE 0.014 0.001 PHE A 340 TRP 0.006 0.001 TRP B 184 HIS 0.002 0.000 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00284 (14808) covalent geometry : angle 0.48810 (20086) hydrogen bonds : bond 0.04555 ( 843) hydrogen bonds : angle 4.56252 ( 2373) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8629 (tptm) cc_final: 0.8366 (tptm) REVERT: A 155 ASN cc_start: 0.9081 (t0) cc_final: 0.8859 (t0) REVERT: A 292 MET cc_start: 0.8906 (tmt) cc_final: 0.8636 (tmm) REVERT: A 322 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8496 (mm-30) REVERT: A 325 LYS cc_start: 0.8467 (mttm) cc_final: 0.8236 (mtpt) REVERT: A 332 ASP cc_start: 0.7371 (t70) cc_final: 0.7038 (t0) REVERT: A 617 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8921 (mmm-85) REVERT: A 645 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: A 658 HIS cc_start: 0.8818 (t-90) cc_final: 0.8431 (t-170) REVERT: A 664 ILE cc_start: 0.8462 (mt) cc_final: 0.8250 (mp) REVERT: B 50 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8551 (t70) REVERT: B 96 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8249 (ttm) REVERT: B 118 ARG cc_start: 0.6342 (tpm170) cc_final: 0.6050 (tpm170) REVERT: B 155 ASN cc_start: 0.8969 (t0) cc_final: 0.8710 (t0) REVERT: B 282 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: B 475 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8698 (mt-10) REVERT: B 560 ASP cc_start: 0.8129 (t0) cc_final: 0.7865 (m-30) REVERT: C 487 SER cc_start: 0.9111 (m) cc_final: 0.8875 (m) REVERT: C 560 ASP cc_start: 0.8666 (t70) cc_final: 0.8027 (m-30) REVERT: C 616 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8475 (mmmt) outliers start: 39 outliers final: 25 residues processed: 129 average time/residue: 0.5499 time to fit residues: 78.0610 Evaluate side-chains 128 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 616 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.088792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.064928 restraints weight = 24101.552| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.54 r_work: 0.2681 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14808 Z= 0.133 Angle : 0.490 9.856 20086 Z= 0.259 Chirality : 0.044 0.276 2355 Planarity : 0.004 0.044 2570 Dihedral : 6.168 73.310 2128 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.14 % Allowed : 19.95 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1865 helix: 2.39 (0.18), residues: 740 sheet: 1.42 (0.24), residues: 441 loop : 0.35 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.023 0.001 TYR B 334 PHE 0.014 0.001 PHE A 545 TRP 0.005 0.001 TRP B 184 HIS 0.017 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00300 (14808) covalent geometry : angle 0.49011 (20086) hydrogen bonds : bond 0.04559 ( 843) hydrogen bonds : angle 4.54473 ( 2373) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8640 (tptm) cc_final: 0.8375 (tptm) REVERT: A 155 ASN cc_start: 0.9080 (t0) cc_final: 0.8858 (t0) REVERT: A 292 MET cc_start: 0.8904 (tmt) cc_final: 0.8642 (tmm) REVERT: A 322 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8486 (mm-30) REVERT: A 325 LYS cc_start: 0.8469 (mttm) cc_final: 0.8238 (mtpt) REVERT: A 332 ASP cc_start: 0.7353 (t70) cc_final: 0.7012 (t0) REVERT: A 560 ASP cc_start: 0.8515 (m-30) cc_final: 0.8271 (m-30) REVERT: A 617 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8923 (mmm-85) REVERT: A 645 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: A 658 HIS cc_start: 0.8829 (t-90) cc_final: 0.8449 (t-170) REVERT: B 50 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8545 (t70) REVERT: B 96 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8241 (ttm) REVERT: B 118 ARG cc_start: 0.6407 (tpm170) cc_final: 0.6110 (tpm170) REVERT: B 155 ASN cc_start: 0.8957 (t0) cc_final: 0.8710 (t0) REVERT: B 282 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: B 475 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8699 (mt-10) REVERT: B 560 ASP cc_start: 0.8112 (t0) cc_final: 0.7867 (m-30) REVERT: C 119 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8422 (ttp-110) REVERT: C 311 GLU cc_start: 0.8100 (tp30) cc_final: 0.7731 (tp30) REVERT: C 487 SER cc_start: 0.9111 (m) cc_final: 0.8884 (m) REVERT: C 560 ASP cc_start: 0.8631 (t70) cc_final: 0.8032 (m-30) REVERT: C 616 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8479 (mmmt) outliers start: 34 outliers final: 23 residues processed: 121 average time/residue: 0.5990 time to fit residues: 79.5033 Evaluate side-chains 125 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 616 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 140 optimal weight: 0.0470 chunk 151 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.088235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.064377 restraints weight = 24097.129| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.56 r_work: 0.2667 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14808 Z= 0.147 Angle : 0.499 9.121 20086 Z= 0.264 Chirality : 0.045 0.276 2355 Planarity : 0.004 0.046 2570 Dihedral : 6.161 73.329 2128 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.27 % Allowed : 19.82 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.20), residues: 1865 helix: 2.37 (0.18), residues: 738 sheet: 1.41 (0.24), residues: 441 loop : 0.34 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 661 TYR 0.023 0.001 TYR C 334 PHE 0.014 0.001 PHE A 340 TRP 0.004 0.001 TRP B 184 HIS 0.012 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00338 (14808) covalent geometry : angle 0.49918 (20086) hydrogen bonds : bond 0.04678 ( 843) hydrogen bonds : angle 4.57785 ( 2373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3922.31 seconds wall clock time: 67 minutes 47.84 seconds (4067.84 seconds total)