Starting phenix.real_space_refine on Thu Aug 6 11:58:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzf_72352/08_2026/9xzf_72352.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzf_72352/08_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_72352/08_2026/9xzf_72352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzf_72352/08_2026/9xzf_72352.map" model { file = "/net/cci-nas-00/data/ceres_data/9xzf_72352/08_2026/9xzf_72352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzf_72352/08_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-2.2rc3-6140/lib/python3.11/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: 2.77, per 1000 atoms: 0.19 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: 0.75 Conformation dependent library (CDL) restraints added in 492.9 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: 0.75 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: 2.62 Time building geometry restraints manager: 1.05 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=" C1' A D 7 " pdb=" N9 A D 7 " ideal model delta sigma weight residual 1.483 1.464 0.019 1.50e-02 4.44e+03 1.69e+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=" C1' A D 8 " pdb=" N9 A D 8 " ideal model delta sigma weight residual 1.483 1.465 0.018 1.50e-02 4.44e+03 1.50e+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 ... (remaining 14803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 19800 1.68 - 3.36: 243 3.36 - 5.04: 37 5.04 - 6.71: 4 6.71 - 8.39: 2 Bond angle restraints: 20086 Sorted by residual: angle pdb=" C1' U D 6 " pdb=" N1 U D 6 " pdb=" C2 U D 6 " ideal model delta sigma weight residual 117.70 123.10 -5.40 1.20e+00 6.94e-01 2.03e+01 angle pdb=" C1' C D 4 " pdb=" N1 C D 4 " pdb=" C2 C D 4 " ideal model delta sigma weight residual 118.80 123.26 -4.46 1.10e+00 8.26e-01 1.64e+01 angle pdb=" N1 U D 6 " pdb=" C2 U D 6 " pdb=" O2 U D 6 " ideal model delta sigma weight residual 122.80 125.27 -2.47 7.00e-01 2.04e+00 1.25e+01 angle pdb=" O2 U D 6 " pdb=" C2 U D 6 " pdb=" N3 U D 6 " ideal model delta sigma weight residual 122.20 119.77 2.43 7.00e-01 2.04e+00 1.20e+01 angle pdb=" O5' U D 6 " pdb=" C5' U D 6 " pdb=" C4' U D 6 " ideal model delta sigma weight residual 109.40 112.10 -2.70 8.00e-01 1.56e+00 1.14e+01 ... (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 - 0.051: 1861 0.051 - 0.102: 380 0.102 - 0.153: 111 0.153 - 0.204: 1 0.204 - 0.256: 2 Chirality restraints: 2355 Sorted by residual: 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 -2.48 -2.73 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C3' A D 7 " pdb=" C4' A D 7 " pdb=" O3' A D 7 " pdb=" C2' A D 7 " both_signs ideal model delta sigma weight residual False -2.48 -2.73 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASP B 197 " pdb=" N ASP B 197 " pdb=" C ASP B 197 " pdb=" CB ASP B 197 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 ... (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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.800 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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= 0.176 Angle : 0.481 8.392 20086 Z= 0.269 Chirality : 0.045 0.256 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/Z covalent geometry : bond 0.00409 / 0.18 (14808) covalent geometry : angle 0.48130 / 0.27 (20086) hydrogen bonds : bond 0.21540 / 14.35 ( 843) hydrogen bonds : angle 7.73765 / 5.57 ( 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 : 0.413 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: 0.6258 time to fit residues: 71.2910 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 : 0.495 ------------------------------------------------------------------------------- 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... C 641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.086442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.062550 restraints weight = 24073.565| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.54 r_work: 0.2635 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14808 Z= 0.178 Angle : 0.526 9.706 20086 Z= 0.290 Chirality : 0.046 0.342 2355 Planarity : 0.004 0.047 2570 Dihedral : 7.139 78.951 2159 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.89 % Allowed : 17.43 % 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: 1.89 (0.20), residues: 1865 helix: 1.98 (0.18), residues: 730 sheet: 1.57 (0.25), residues: 438 loop : 0.35 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 118 TYR 0.017 0.001 TYR A 334 PHE 0.017 0.001 PHE A 340 TRP 0.004 0.001 TRP A 184 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (14808) covalent geometry : angle 0.52568 / 0.29 (20086) hydrogen bonds : bond 0.07236 / 4.77 ( 843) hydrogen bonds : angle 5.66120 / 4.17 ( 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 137 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 91 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8682 (tptm) cc_final: 0.8381 (tptm) REVERT: A 292 MET cc_start: 0.8806 (tmt) cc_final: 0.8463 (tmm) REVERT: A 322 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8453 (mm-30) REVERT: A 332 ASP cc_start: 0.7597 (t0) cc_final: 0.7331 (t0) REVERT: A 560 ASP cc_start: 0.8474 (m-30) cc_final: 0.8239 (m-30) REVERT: A 617 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8734 (mmm-85) REVERT: A 645 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: A 658 HIS cc_start: 0.8745 (t-90) cc_final: 0.8452 (t-170) REVERT: A 663 PHE cc_start: 0.7901 (t80) cc_final: 0.7640 (t80) REVERT: A 667 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7209 (mp) REVERT: B 282 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: B 617 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7420 (tpt-90) REVERT: C 119 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8097 (mmm-85) REVERT: C 448 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8629 (mm) REVERT: C 616 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8456 (mmmt) outliers start: 46 outliers final: 17 residues processed: 126 average time/residue: 0.6649 time to fit residues: 91.4586 Evaluate side-chains 115 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 A residue 667 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 289 LYS 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 121 ILE 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 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: 0.9980 chunk 161 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3221 r_free = 0.3221 target = 0.086160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.062683 restraints weight = 24670.172| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.54 r_work: 0.2642 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14808 Z= 0.188 Angle : 0.504 6.492 20086 Z= 0.276 Chirality : 0.045 0.208 2355 Planarity : 0.004 0.052 2570 Dihedral : 6.991 77.958 2142 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.46 % Allowed : 17.24 % Favored : 79.30 % 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: 2.00 (0.20), residues: 1865 helix: 2.18 (0.18), residues: 730 sheet: 1.52 (0.25), residues: 440 loop : 0.35 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 661 TYR 0.019 0.001 TYR B 334 PHE 0.017 0.001 PHE A 340 TRP 0.004 0.001 TRP A 184 HIS 0.002 0.001 HIS B 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (14808) covalent geometry : angle 0.50371 / 0.28 (20086) hydrogen bonds : bond 0.06013 / 3.98 ( 843) hydrogen bonds : angle 5.18415 / 3.83 ( 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 153 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 98 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8731 (tptm) cc_final: 0.8468 (tptm) REVERT: A 292 MET cc_start: 0.8885 (tmt) cc_final: 0.8558 (tmm) REVERT: A 322 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8473 (mm-30) REVERT: A 332 ASP cc_start: 0.7520 (t0) cc_final: 0.7249 (t0) REVERT: A 560 ASP cc_start: 0.8558 (m-30) cc_final: 0.8334 (m-30) REVERT: A 617 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8724 (mmm-85) REVERT: A 645 GLU cc_start: 0.8750 (mp0) cc_final: 0.8493 (pm20) REVERT: A 658 HIS cc_start: 0.8880 (t-90) cc_final: 0.8081 (t-170) REVERT: A 667 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7132 (mp) REVERT: B 50 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8545 (t70) REVERT: B 112 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.6183 (pt) REVERT: B 282 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: B 617 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7416 (tpt-90) REVERT: C 54 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8170 (mmt90) REVERT: C 119 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8297 (mtp-110) REVERT: C 616 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8468 (mmmt) outliers start: 55 outliers final: 17 residues processed: 142 average time/residue: 0.5681 time to fit residues: 87.5995 Evaluate side-chains 117 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE 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 517 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 153 LEU 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: 4.9990 chunk 183 optimal weight: 0.5980 chunk 164 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3224 r_free = 0.3224 target = 0.086680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.062786 restraints weight = 24192.197| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.55 r_work: 0.2634 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14808 Z= 0.204 Angle : 0.508 8.279 20086 Z= 0.275 Chirality : 0.045 0.154 2355 Planarity : 0.004 0.052 2570 Dihedral : 6.905 77.135 2135 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.52 % Allowed : 18.00 % Favored : 78.48 % 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: 1.98 (0.20), residues: 1865 helix: 2.21 (0.18), residues: 732 sheet: 1.47 (0.24), residues: 434 loop : 0.31 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 119 TYR 0.020 0.001 TYR B 334 PHE 0.020 0.001 PHE C 663 TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (14808) covalent geometry : angle 0.50811 / 0.28 (20086) hydrogen bonds : bond 0.05693 / 3.76 ( 843) hydrogen bonds : angle 5.04981 / 3.74 ( 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 147 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 91 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8655 (tptm) cc_final: 0.8375 (tptm) REVERT: A 292 MET cc_start: 0.8888 (tmt) cc_final: 0.8587 (tmm) REVERT: A 322 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8439 (mm-30) REVERT: A 332 ASP cc_start: 0.7525 (t70) cc_final: 0.7208 (t0) REVERT: A 560 ASP cc_start: 0.8503 (m-30) cc_final: 0.8276 (m-30) REVERT: A 617 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8715 (mmm-85) REVERT: A 645 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8524 (pm20) REVERT: A 658 HIS cc_start: 0.8684 (t-90) cc_final: 0.8393 (t-170) REVERT: B 50 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8555 (t70) REVERT: B 112 ILE cc_start: 0.6572 (OUTLIER) cc_final: 0.6226 (pt) REVERT: B 282 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: B 475 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8674 (mt-10) REVERT: B 617 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7396 (tpt-90) REVERT: C 96 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.7733 (tmm) REVERT: C 616 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8472 (mmmt) outliers start: 56 outliers final: 23 residues processed: 133 average time/residue: 0.5388 time to fit residues: 78.4869 Evaluate side-chains 120 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE 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 351 ILE 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 96 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 143 optimal weight: 0.0980 chunk 16 optimal weight: 0.0030 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 121 optimal weight: 0.0270 overall best weight: 0.3048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 GLN C 632 GLN C 641 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.089331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.065944 restraints weight = 24222.791| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.51 r_work: 0.2707 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14808 Z= 0.112 Angle : 0.473 7.707 20086 Z= 0.257 Chirality : 0.043 0.141 2355 Planarity : 0.004 0.045 2570 Dihedral : 6.668 74.623 2133 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.83 % Allowed : 18.57 % 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: 2.08 (0.20), residues: 1865 helix: 2.29 (0.18), residues: 736 sheet: 1.45 (0.24), residues: 441 loop : 0.40 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.021 0.001 TYR B 334 PHE 0.018 0.001 PHE A 545 TRP 0.007 0.001 TRP B 184 HIS 0.002 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (14808) covalent geometry : angle 0.47288 / 0.26 (20086) hydrogen bonds : bond 0.04628 / 3.06 ( 843) hydrogen bonds : angle 4.76854 / 3.54 ( 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 147 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8645 (tptm) cc_final: 0.8362 (tptm) REVERT: A 155 ASN cc_start: 0.9073 (t0) cc_final: 0.8861 (t0) REVERT: A 292 MET cc_start: 0.8889 (tmt) cc_final: 0.8598 (tmm) REVERT: A 332 ASP cc_start: 0.7464 (t70) cc_final: 0.7129 (t0) REVERT: A 560 ASP cc_start: 0.8510 (m-30) cc_final: 0.8272 (m-30) REVERT: A 617 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8928 (mmm-85) REVERT: A 645 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: A 658 HIS cc_start: 0.8842 (t-90) cc_final: 0.8382 (t-170) REVERT: A 663 PHE cc_start: 0.7879 (t80) cc_final: 0.7573 (t80) REVERT: B 50 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8535 (t70) REVERT: B 112 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6128 (pt) REVERT: B 282 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: B 475 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8696 (mt-10) REVERT: B 617 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7335 (tpt-90) REVERT: C 96 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7493 (tmm) REVERT: C 119 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8050 (mmm-85) REVERT: C 448 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8616 (mm) REVERT: C 560 ASP cc_start: 0.8554 (t70) cc_final: 0.7948 (m-30) REVERT: C 616 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8423 (mmmt) outliers start: 45 outliers final: 14 residues processed: 138 average time/residue: 0.5455 time to fit residues: 82.7136 Evaluate side-chains 114 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 202 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 112 ILE 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 547 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 99 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: 1.9990 chunk 36 optimal weight: 9.9990 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: 0.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3233 r_free = 0.3233 target = 0.087081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.063659 restraints weight = 24416.821| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.51 r_work: 0.2661 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14808 Z= 0.194 Angle : 0.500 8.008 20086 Z= 0.271 Chirality : 0.045 0.147 2355 Planarity : 0.004 0.050 2570 Dihedral : 6.547 73.948 2130 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.71 % Allowed : 19.07 % 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: 2.07 (0.20), residues: 1865 helix: 2.29 (0.18), residues: 734 sheet: 1.45 (0.24), residues: 441 loop : 0.39 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.020 0.001 TYR B 334 PHE 0.017 0.001 PHE C 663 TRP 0.003 0.001 TRP C 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (14808) covalent geometry : angle 0.49966 / 0.27 (20086) hydrogen bonds : bond 0.05109 / 3.38 ( 843) hydrogen bonds : angle 4.78028 / 3.53 ( 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 135 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8101 (ttp) REVERT: A 126 LYS cc_start: 0.8678 (tptm) cc_final: 0.8409 (tptm) REVERT: A 155 ASN cc_start: 0.9103 (t0) cc_final: 0.8894 (t0) REVERT: A 292 MET cc_start: 0.8928 (tmt) cc_final: 0.8628 (tmm) REVERT: A 332 ASP cc_start: 0.7551 (t70) cc_final: 0.7197 (t0) REVERT: A 560 ASP cc_start: 0.8524 (m-30) cc_final: 0.8290 (m-30) REVERT: A 617 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8997 (mmm-85) REVERT: A 645 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8528 (pm20) REVERT: A 658 HIS cc_start: 0.8847 (t-90) cc_final: 0.8397 (t-170) REVERT: B 50 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8522 (t70) REVERT: B 112 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6257 (pt) REVERT: B 282 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: B 475 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8666 (mt-10) REVERT: B 617 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7373 (tpt-90) REVERT: C 96 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7650 (tmm) REVERT: C 560 ASP cc_start: 0.8578 (t70) cc_final: 0.7925 (m-30) REVERT: C 616 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8499 (mmmt) outliers start: 43 outliers final: 19 residues processed: 125 average time/residue: 0.5586 time to fit residues: 76.7609 Evaluate side-chains 120 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 202 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 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 112 ILE Chi-restraints excluded: chain B residue 123 THR 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 475 GLU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 96 MET 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 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: 0.9990 chunk 48 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 0.0570 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.087583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.064096 restraints weight = 24376.722| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.52 r_work: 0.2671 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14808 Z= 0.156 Angle : 0.487 7.686 20086 Z= 0.265 Chirality : 0.044 0.143 2355 Planarity : 0.004 0.048 2570 Dihedral : 6.508 73.261 2130 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.77 % Allowed : 18.75 % Favored : 78.48 % 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: 2.32 (0.18), residues: 733 sheet: 1.43 (0.24), residues: 441 loop : 0.37 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.020 0.001 TYR B 334 PHE 0.019 0.001 PHE C 663 TRP 0.003 0.001 TRP B 184 HIS 0.002 0.000 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (14808) covalent geometry : angle 0.48739 / 0.26 (20086) hydrogen bonds : bond 0.04932 / 3.26 ( 843) hydrogen bonds : angle 4.72737 / 3.50 ( 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 142 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7943 (ttp) REVERT: A 126 LYS cc_start: 0.8676 (tptm) cc_final: 0.8404 (tptm) REVERT: A 155 ASN cc_start: 0.9103 (t0) cc_final: 0.8886 (t0) REVERT: A 292 MET cc_start: 0.8920 (tmt) cc_final: 0.8614 (tmm) REVERT: A 332 ASP cc_start: 0.7569 (t70) cc_final: 0.7223 (t0) REVERT: A 560 ASP cc_start: 0.8518 (m-30) cc_final: 0.8275 (m-30) REVERT: A 617 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8921 (mmm-85) REVERT: A 645 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: A 658 HIS cc_start: 0.8837 (t-90) cc_final: 0.8396 (t-170) REVERT: B 50 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8524 (t70) REVERT: B 112 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6177 (pt) REVERT: B 282 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: B 475 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8663 (mt-10) REVERT: B 617 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7385 (tpt-90) REVERT: C 96 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7640 (tmm) REVERT: C 448 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8524 (mm) REVERT: C 560 ASP cc_start: 0.8614 (t70) cc_final: 0.7936 (m-30) REVERT: C 616 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8488 (mmmt) outliers start: 44 outliers final: 20 residues processed: 132 average time/residue: 0.5012 time to fit residues: 73.0359 Evaluate side-chains 124 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 96 MET Chi-restraints excluded: chain A residue 202 VAL 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 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 112 ILE 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 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 610 VAL Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 96 MET 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 448 LEU Chi-restraints excluded: chain C residue 609 THR 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: 0.0980 chunk 100 optimal weight: 0.0670 chunk 163 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3269 r_free = 0.3269 target = 0.089265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.065805 restraints weight = 24101.945| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.51 r_work: 0.2712 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14808 Z= 0.114 Angle : 0.477 8.481 20086 Z= 0.259 Chirality : 0.043 0.137 2355 Planarity : 0.003 0.046 2570 Dihedral : 6.345 73.259 2128 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.27 % Allowed : 19.51 % 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: 2.12 (0.20), residues: 1865 helix: 2.38 (0.18), residues: 737 sheet: 1.42 (0.24), residues: 441 loop : 0.38 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 661 TYR 0.019 0.001 TYR B 334 PHE 0.016 0.001 PHE A 545 TRP 0.007 0.001 TRP B 184 HIS 0.002 0.000 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (14808) covalent geometry : angle 0.47709 / 0.26 (20086) hydrogen bonds : bond 0.04470 / 2.96 ( 843) hydrogen bonds : angle 4.61759 / 3.42 ( 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 134 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7658 (ttp) REVERT: A 126 LYS cc_start: 0.8667 (tptm) cc_final: 0.8389 (tptm) REVERT: A 155 ASN cc_start: 0.9070 (t0) cc_final: 0.8854 (t0) REVERT: A 292 MET cc_start: 0.8933 (tmt) cc_final: 0.8664 (tmm) REVERT: A 332 ASP cc_start: 0.7486 (t70) cc_final: 0.7120 (t0) REVERT: A 617 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8932 (mmm-85) REVERT: A 645 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: A 658 HIS cc_start: 0.8873 (t-90) cc_final: 0.8452 (t-170) REVERT: B 50 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8546 (t70) REVERT: B 112 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6132 (pt) REVERT: B 118 ARG cc_start: 0.6430 (tpm170) cc_final: 0.5961 (tpm170) REVERT: B 230 GLU cc_start: 0.9093 (tp30) cc_final: 0.8876 (tp30) REVERT: B 282 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: B 475 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8695 (mt-10) REVERT: B 560 ASP cc_start: 0.8166 (t0) cc_final: 0.7876 (m-30) REVERT: B 617 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7360 (tpt-90) REVERT: C 96 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7522 (tmm) REVERT: C 448 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8553 (mm) REVERT: C 487 SER cc_start: 0.9133 (m) cc_final: 0.8911 (m) REVERT: C 560 ASP cc_start: 0.8620 (t70) cc_final: 0.7958 (m-30) REVERT: C 616 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8475 (mmmt) outliers start: 36 outliers final: 15 residues processed: 124 average time/residue: 0.5377 time to fit residues: 73.5224 Evaluate side-chains 120 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 202 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 112 ILE 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 475 GLU 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 96 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 153 LEU 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=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: 4.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3236 r_free = 0.3236 target = 0.087370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.063944 restraints weight = 24433.962| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.51 r_work: 0.2665 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14808 Z= 0.185 Angle : 0.501 8.579 20086 Z= 0.271 Chirality : 0.045 0.142 2355 Planarity : 0.004 0.048 2570 Dihedral : 6.348 73.331 2128 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.27 % Allowed : 19.57 % 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: 2.10 (0.20), residues: 1865 helix: 2.35 (0.18), residues: 736 sheet: 1.43 (0.24), residues: 441 loop : 0.38 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.022 0.002 TYR B 334 PHE 0.018 0.001 PHE C 663 TRP 0.003 0.001 TRP C 184 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (14808) covalent geometry : angle 0.50144 / 0.27 (20086) hydrogen bonds : bond 0.04949 / 3.27 ( 843) hydrogen bonds : angle 4.68735 / 3.46 ( 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 128 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7895 (ttp) REVERT: A 126 LYS cc_start: 0.8677 (tptm) cc_final: 0.8407 (tptm) REVERT: A 155 ASN cc_start: 0.9101 (t0) cc_final: 0.8884 (t0) REVERT: A 292 MET cc_start: 0.8933 (tmt) cc_final: 0.8624 (tmm) REVERT: A 332 ASP cc_start: 0.7527 (t70) cc_final: 0.7164 (t0) REVERT: A 560 ASP cc_start: 0.8561 (m-30) cc_final: 0.8352 (m-30) REVERT: A 617 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8927 (mmm-85) REVERT: A 645 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8524 (pm20) REVERT: A 658 HIS cc_start: 0.8850 (t-90) cc_final: 0.8431 (t-170) REVERT: B 50 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8537 (t70) REVERT: B 118 ARG cc_start: 0.6392 (tpm170) cc_final: 0.6116 (tpm170) REVERT: B 282 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: B 475 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8677 (mt-10) REVERT: B 560 ASP cc_start: 0.8181 (t0) cc_final: 0.7849 (m-30) REVERT: B 617 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7343 (tpt-90) REVERT: C 96 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.7607 (tmm) REVERT: C 560 ASP cc_start: 0.8622 (t70) cc_final: 0.7959 (m-30) REVERT: C 616 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8505 (mmmt) outliers start: 36 outliers final: 21 residues processed: 119 average time/residue: 0.5105 time to fit residues: 67.1418 Evaluate side-chains 121 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 96 MET Chi-restraints excluded: chain A residue 202 VAL 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 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 112 ILE 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 475 GLU 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 96 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 121 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 123 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 180 optimal weight: 0.2980 chunk 128 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3259 r_free = 0.3259 target = 0.088740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.065292 restraints weight = 24185.655| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.51 r_work: 0.2697 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14808 Z= 0.125 Angle : 0.482 8.871 20086 Z= 0.261 Chirality : 0.043 0.137 2355 Planarity : 0.003 0.047 2570 Dihedral : 6.242 73.255 2128 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.01 % Allowed : 19.89 % Favored : 78.10 % 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: 2.39 (0.18), residues: 738 sheet: 1.40 (0.24), residues: 441 loop : 0.38 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.022 0.001 TYR B 334 PHE 0.015 0.001 PHE A 340 TRP 0.006 0.001 TRP B 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (14808) covalent geometry : angle 0.48187 / 0.26 (20086) hydrogen bonds : bond 0.04582 / 3.03 ( 843) hydrogen bonds : angle 4.60699 / 3.41 ( 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 123 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7660 (ttp) REVERT: A 126 LYS cc_start: 0.8685 (tptm) cc_final: 0.8417 (tptm) REVERT: A 155 ASN cc_start: 0.9094 (t0) cc_final: 0.8866 (t0) REVERT: A 292 MET cc_start: 0.8945 (tmt) cc_final: 0.8672 (tmm) REVERT: A 332 ASP cc_start: 0.7464 (t70) cc_final: 0.7114 (t0) REVERT: A 560 ASP cc_start: 0.8542 (m-30) cc_final: 0.8324 (m-30) REVERT: A 617 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8935 (mmm-85) REVERT: A 645 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: A 658 HIS cc_start: 0.8824 (t-90) cc_final: 0.8415 (t-170) REVERT: B 50 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8541 (t70) REVERT: B 118 ARG cc_start: 0.6401 (tpm170) cc_final: 0.6127 (tpm170) REVERT: B 155 ASN cc_start: 0.8960 (t0) cc_final: 0.8710 (t0) REVERT: B 230 GLU cc_start: 0.9113 (tp30) cc_final: 0.8876 (tp30) REVERT: B 282 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: B 475 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8693 (mt-10) REVERT: B 560 ASP cc_start: 0.8144 (t0) cc_final: 0.7893 (m-30) REVERT: C 96 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7545 (tmm) REVERT: C 119 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8179 (mmm-85) REVERT: C 487 SER cc_start: 0.9116 (m) cc_final: 0.8873 (m) REVERT: C 560 ASP cc_start: 0.8640 (t70) cc_final: 0.7881 (m-30) REVERT: C 616 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8488 (mmmt) outliers start: 32 outliers final: 21 residues processed: 118 average time/residue: 0.5061 time to fit residues: 66.2816 Evaluate side-chains 120 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 202 VAL 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 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 112 ILE 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 475 GLU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 121 ILE 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 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: 4.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 140 optimal weight: 0.0000 chunk 151 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3259 r_free = 0.3259 target = 0.088705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.065303 restraints weight = 24194.442| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.51 r_work: 0.2698 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1625 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= 0.130 Angle : 0.479 9.459 20086 Z= 0.260 Chirality : 0.044 0.137 2355 Planarity : 0.003 0.045 2570 Dihedral : 6.156 73.282 2127 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.01 % Allowed : 20.08 % 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: 2.14 (0.20), residues: 1865 helix: 2.40 (0.18), residues: 740 sheet: 1.41 (0.24), residues: 441 loop : 0.40 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 119 TYR 0.023 0.001 TYR B 334 PHE 0.014 0.001 PHE A 340 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (14808) covalent geometry : angle 0.47940 / 0.26 (20086) hydrogen bonds : bond 0.04532 / 3.00 ( 843) hydrogen bonds : angle 4.56627 / 3.38 ( 2373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3879.09 seconds wall clock time: 66 minutes 54.89 seconds (4014.89 seconds total)