Starting phenix.real_space_refine on Fri Jul 3 16:09:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9no0_49590/07_2026/9no0_49590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9no0_49590/07_2026/9no0_49590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9no0_49590/07_2026/9no0_49590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9no0_49590/07_2026/9no0_49590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9no0_49590/07_2026/9no0_49590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9no0_49590/07_2026/9no0_49590.map" } resolution = 2.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 8 5.49 5 S 60 5.16 5 C 9130 2.51 5 N 2474 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14495 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: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} 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: 3.31, per 1000 atoms: 0.23 Number of scatterers: 14495 At special positions: 0 Unit cell: (106.863, 108.573, 107.718, 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 8 15.00 O 2823 8.00 N 2474 7.00 C 9130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 705.1 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, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 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: 4.156A pdb=" N LEU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 237 through 266 removed outlier: 3.669A pdb=" N GLN A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 5.784A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.702A pdb=" N VAL A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.921A 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 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 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 567 through 593 removed outlier: 3.548A pdb=" N VAL A 571 " --> pdb=" O PRO A 567 " (cutoff:3.500A) removed outlier: 3.685A 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 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: 4.164A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 237 through 267 removed outlier: 3.630A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 5.696A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 removed outlier: 3.530A pdb=" N GLN B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.542A pdb=" N ILE B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.566A pdb=" N ILE B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 3.503A 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: 3.704A pdb=" N ILE B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 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: 3.650A pdb=" N THR B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 4.277A pdb=" N ALA B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.836A 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 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: 4.190A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.816A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.637A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 5.866A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 328 removed outlier: 3.719A pdb=" N LYS C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 327 " --> pdb=" O GLN C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 removed outlier: 3.759A pdb=" N VAL C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.556A 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 498 Processing helix chain 'C' and resid 534 through 541 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.527A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 4.198A pdb=" N ALA C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 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: 6.377A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 103 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU A 156 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 3.968A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN A 215 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 231 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 217 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 229 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A 219 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 374 removed outlier: 6.374A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (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: 6.373A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 156 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.125A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 227 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE B 561 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA B 510 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR B 531 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY B 512 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU B 529 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 514 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR B 527 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS B 516 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.260A 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: 6.412A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 156 " --> pdb=" O ARG C 103 " (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: 3.999A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN C 215 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA C 231 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 217 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 229 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 219 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 229 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.538A 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 371 removed outlier: 3.533A pdb=" N GLY C 382 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 6.292A 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 611 859 hydrogen bonds defined for protein. 2427 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: 2.74 Time building geometry restraints manager: 1.57 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: 3882 1.33 - 1.45: 2275 1.45 - 1.57: 8475 1.57 - 1.69: 10 1.69 - 1.81: 99 Bond restraints: 14741 Sorted by residual: bond pdb=" C ARG C 139 " pdb=" O ARG C 139 " ideal model delta sigma weight residual 1.244 1.208 0.035 9.80e-03 1.04e+04 1.30e+01 bond pdb=" O4 PO4 C 901 " pdb=" P PO4 C 901 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O3 PO4 C 901 " pdb=" P PO4 C 901 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.86e+00 bond pdb=" O2 PO4 C 901 " pdb=" P PO4 C 901 " ideal model delta sigma weight residual 1.567 1.504 0.063 2.00e-02 2.50e+03 9.80e+00 bond pdb=" O1 PO4 C 901 " pdb=" P PO4 C 901 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.19e+00 ... (remaining 14736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19693 2.13 - 4.26: 251 4.26 - 6.39: 37 6.39 - 8.53: 8 8.53 - 10.66: 1 Bond angle restraints: 19990 Sorted by residual: angle pdb=" C1' C D 3 " pdb=" N1 C D 3 " pdb=" C2 C D 3 " ideal model delta sigma weight residual 118.80 123.93 -5.13 1.10e+00 8.26e-01 2.18e+01 angle pdb=" CA ARG C 139 " pdb=" CB ARG C 139 " pdb=" CG ARG C 139 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 angle pdb=" CA GLU C 330 " pdb=" CB GLU C 330 " pdb=" CG GLU C 330 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 angle pdb=" CB MET A 376 " pdb=" CG MET A 376 " pdb=" SD MET A 376 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C4' A D 7 " pdb=" O4' A D 7 " pdb=" C1' A D 7 " ideal model delta sigma weight residual 109.70 106.16 3.54 1.00e+00 1.00e+00 1.25e+01 ... (remaining 19985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 8792 35.42 - 70.84: 246 70.84 - 106.27: 26 106.27 - 141.69: 0 141.69 - 177.11: 2 Dihedral angle restraints: 9066 sinusoidal: 3663 harmonic: 5403 Sorted by residual: dihedral pdb=" O4' U D 5 " pdb=" C1' U D 5 " pdb=" N1 U D 5 " pdb=" C2 U D 5 " ideal model delta sinusoidal sigma weight residual 200.00 22.89 177.11 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C D 3 " pdb=" C1' C D 3 " pdb=" N1 C D 3 " pdb=" C2 C D 3 " ideal model delta sinusoidal sigma weight residual -160.00 16.86 -176.86 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" C5' A D 7 " pdb=" C4' A D 7 " pdb=" C3' A D 7 " pdb=" O3' A D 7 " ideal model delta sinusoidal sigma weight residual 147.00 103.53 43.47 1 8.00e+00 1.56e-02 4.11e+01 ... (remaining 9063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2206 0.097 - 0.193: 132 0.193 - 0.290: 1 0.290 - 0.386: 2 0.386 - 0.483: 3 Chirality restraints: 2344 Sorted by residual: chirality pdb=" P C D 3 " pdb=" OP1 C D 3 " pdb=" OP2 C D 3 " pdb=" O5' C D 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" P A D 6 " pdb=" OP1 A D 6 " pdb=" OP2 A D 6 " pdb=" O5' A D 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" P U D 5 " pdb=" OP1 U D 5 " pdb=" OP2 U D 5 " pdb=" O5' U D 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2341 not shown) Planarity restraints: 2567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 132 " 0.778 9.50e-02 1.11e+02 3.49e-01 7.42e+01 pdb=" NE ARG C 132 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG C 132 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 132 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 132 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 446 " -0.700 9.50e-02 1.11e+02 3.14e-01 6.03e+01 pdb=" NE ARG C 446 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG C 446 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 446 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 446 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 139 " 0.391 9.50e-02 1.11e+02 1.75e-01 1.89e+01 pdb=" NE ARG C 139 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 139 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 139 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 139 " 0.013 2.00e-02 2.50e+03 ... (remaining 2564 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 6201 2.93 - 3.42: 14424 3.42 - 3.91: 25126 3.91 - 4.41: 29323 4.41 - 4.90: 47079 Nonbonded interactions: 122153 Sorted by model distance: nonbonded pdb=" O ILE B 196 " pdb=" OD1 ASP B 197 " model vdw 2.437 3.040 nonbonded pdb=" O ARG B 464 " pdb=" OD1 ASP B 465 " model vdw 2.455 3.040 nonbonded pdb=" N GLU A 330 " pdb=" OE1 GLU A 330 " model vdw 2.461 3.120 nonbonded pdb=" N GLU C 330 " pdb=" OE1 GLU C 330 " model vdw 2.461 3.120 nonbonded pdb=" N GLU C 293 " pdb=" OE1 GLU C 293 " model vdw 2.512 3.120 ... (remaining 122148 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: 4.840 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: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.690 Find NCS groups from input model: 0.380 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:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9235 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 : 0.008 0.063 14741 Z= 0.340 Angle : 0.629 10.658 19990 Z= 0.343 Chirality : 0.052 0.483 2344 Planarity : 0.011 0.349 2567 Dihedral : 16.179 177.108 5582 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.45 % Allowed : 15.36 % Favored : 83.20 % 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: 1.27 (0.19), residues: 1865 helix: 1.05 (0.18), residues: 740 sheet: 1.55 (0.25), residues: 426 loop : 0.30 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 661 TYR 0.018 0.002 TYR B 427 PHE 0.016 0.002 PHE C 545 TRP 0.004 0.002 TRP C 184 HIS 0.004 0.001 HIS B 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.34 (14741) covalent geometry : angle 0.62946 / 0.34 (19990) hydrogen bonds : bond 0.19972 / 13.29 ( 859) hydrogen bonds : angle 7.54553 / 5.47 ( 2427) *********************** 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 120 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.8080 (mmm160) REVERT: A 376 MET cc_start: 0.8254 (mmm) cc_final: 0.7553 (mmm) REVERT: A 424 MET cc_start: 0.9262 (ptp) cc_final: 0.8635 (ppp) REVERT: A 616 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8781 (mmmt) REVERT: A 643 ASP cc_start: 0.8537 (m-30) cc_final: 0.8245 (m-30) REVERT: B 54 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8028 (mmt90) REVERT: B 118 ARG cc_start: 0.6897 (tpt170) cc_final: 0.6455 (tpp-160) REVERT: B 125 ASP cc_start: 0.8575 (m-30) cc_final: 0.8372 (m-30) REVERT: B 230 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8433 (tp30) REVERT: B 645 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7933 (tm-30) REVERT: B 664 ILE cc_start: 0.8551 (pp) cc_final: 0.8180 (pp) REVERT: C 54 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8504 (mmt90) REVERT: C 103 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8198 (mtp85) REVERT: C 418 ILE cc_start: 0.8805 (tt) cc_final: 0.8579 (pp) REVERT: C 436 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: C 616 LYS cc_start: 0.9130 (tppp) cc_final: 0.8780 (mmmm) REVERT: C 617 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8694 (tpt-90) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 0.7663 time to fit residues: 92.2459 Evaluate side-chains 113 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 611 GLN Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.089460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.064145 restraints weight = 22990.397| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.19 r_work: 0.2802 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9212 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14741 Z= 0.187 Angle : 0.544 6.385 19990 Z= 0.303 Chirality : 0.045 0.153 2344 Planarity : 0.004 0.053 2567 Dihedral : 8.990 177.871 2128 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.45 % Allowed : 14.10 % Favored : 83.45 % 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: 2.05 (0.19), residues: 1865 helix: 2.09 (0.18), residues: 735 sheet: 1.74 (0.25), residues: 430 loop : 0.41 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 617 TYR 0.020 0.002 TYR C 334 PHE 0.018 0.001 PHE C 340 TRP 0.004 0.001 TRP C 184 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (14741) covalent geometry : angle 0.54438 / 0.30 (19990) hydrogen bonds : bond 0.06904 / 4.63 ( 859) hydrogen bonds : angle 5.58442 / 4.04 ( 2427) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8109 (mmm160) REVERT: A 118 ARG cc_start: 0.6375 (mmt180) cc_final: 0.5034 (mmm160) REVERT: A 424 MET cc_start: 0.9161 (ptp) cc_final: 0.8589 (ppp) REVERT: A 616 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8424 (mmmm) REVERT: A 643 ASP cc_start: 0.8531 (m-30) cc_final: 0.8223 (m-30) REVERT: B 118 ARG cc_start: 0.7130 (tpt170) cc_final: 0.6779 (tpp-160) REVERT: B 125 ASP cc_start: 0.8531 (m-30) cc_final: 0.8317 (m-30) REVERT: B 314 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8600 (m110) REVERT: B 645 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7938 (tm-30) REVERT: B 664 ILE cc_start: 0.8596 (pp) cc_final: 0.8235 (pp) REVERT: C 230 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8446 (tp30) REVERT: C 418 ILE cc_start: 0.8768 (tt) cc_final: 0.8547 (pp) REVERT: C 436 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: C 616 LYS cc_start: 0.9125 (tppp) cc_final: 0.8794 (mmmm) outliers start: 39 outliers final: 15 residues processed: 137 average time/residue: 0.7435 time to fit residues: 110.6636 Evaluate side-chains 118 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 73 optimal weight: 0.1980 chunk 44 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 130 optimal weight: 0.0670 chunk 175 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066717 restraints weight = 23068.443| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.20 r_work: 0.2859 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14741 Z= 0.127 Angle : 0.487 6.172 19990 Z= 0.268 Chirality : 0.044 0.164 2344 Planarity : 0.004 0.049 2567 Dihedral : 8.198 176.420 2098 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.58 % Allowed : 15.10 % Favored : 82.32 % 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: 2.21 (0.20), residues: 1865 helix: 2.33 (0.18), residues: 736 sheet: 1.70 (0.25), residues: 434 loop : 0.43 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 617 TYR 0.020 0.001 TYR B 334 PHE 0.016 0.001 PHE C 340 TRP 0.007 0.001 TRP B 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (14741) covalent geometry : angle 0.48725 / 0.27 (19990) hydrogen bonds : bond 0.05521 / 3.71 ( 859) hydrogen bonds : angle 5.04683 / 3.62 ( 2427) *********************** 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 149 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8259 (mmm-85) REVERT: A 424 MET cc_start: 0.9083 (ptp) cc_final: 0.8550 (ppp) REVERT: A 616 LYS cc_start: 0.9053 (tppp) cc_final: 0.8504 (mmmm) REVERT: A 643 ASP cc_start: 0.8505 (m-30) cc_final: 0.8186 (m-30) REVERT: A 645 GLU cc_start: 0.8199 (tp30) cc_final: 0.7963 (tp30) REVERT: A 657 MET cc_start: 0.8805 (tpp) cc_final: 0.8524 (tpt) REVERT: B 125 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8304 (m-30) REVERT: B 314 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8601 (m-40) REVERT: B 400 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7116 (p0) REVERT: B 645 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7935 (tm-30) REVERT: B 664 ILE cc_start: 0.8584 (pp) cc_final: 0.8247 (pp) REVERT: C 230 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8406 (tp30) REVERT: C 436 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: C 616 LYS cc_start: 0.9155 (tppp) cc_final: 0.8836 (mmmm) REVERT: C 617 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8716 (tpt-90) outliers start: 41 outliers final: 13 residues processed: 142 average time/residue: 0.6518 time to fit residues: 101.3657 Evaluate side-chains 120 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 73 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 611 GLN A 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.089843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064417 restraints weight = 23171.619| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.20 r_work: 0.2807 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9209 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14741 Z= 0.217 Angle : 0.532 5.909 19990 Z= 0.293 Chirality : 0.045 0.165 2344 Planarity : 0.004 0.050 2567 Dihedral : 8.199 174.273 2092 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.64 % Allowed : 14.60 % Favored : 82.76 % 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: 2.22 (0.19), residues: 1865 helix: 2.37 (0.18), residues: 730 sheet: 1.80 (0.25), residues: 434 loop : 0.34 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 118 TYR 0.017 0.002 TYR C 334 PHE 0.018 0.001 PHE C 340 TRP 0.005 0.001 TRP C 184 HIS 0.002 0.000 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (14741) covalent geometry : angle 0.53237 / 0.29 (19990) hydrogen bonds : bond 0.06064 / 4.07 ( 859) hydrogen bonds : angle 5.14444 / 3.71 ( 2427) *********************** 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 144 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8110 (mmm160) REVERT: A 424 MET cc_start: 0.9144 (ptp) cc_final: 0.8620 (ppp) REVERT: A 616 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8565 (mmmm) REVERT: A 643 ASP cc_start: 0.8511 (m-30) cc_final: 0.8198 (m-30) REVERT: A 645 GLU cc_start: 0.8150 (tp30) cc_final: 0.7741 (tp30) REVERT: A 657 MET cc_start: 0.8885 (tpp) cc_final: 0.8577 (tpt) REVERT: B 54 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7772 (mmt90) REVERT: B 118 ARG cc_start: 0.7179 (tpt170) cc_final: 0.6767 (tpp-160) REVERT: B 125 ASP cc_start: 0.8545 (m-30) cc_final: 0.8336 (m-30) REVERT: B 230 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: B 314 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8606 (m-40) REVERT: B 645 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7894 (tm-30) REVERT: B 664 ILE cc_start: 0.8585 (pp) cc_final: 0.8217 (pp) REVERT: C 56 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8957 (mp) REVERT: C 126 LYS cc_start: 0.8978 (mppt) cc_final: 0.8707 (mptt) REVERT: C 230 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: C 436 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: C 616 LYS cc_start: 0.9146 (tppp) cc_final: 0.8824 (mmmm) REVERT: C 617 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8711 (tpt-90) outliers start: 42 outliers final: 21 residues processed: 136 average time/residue: 0.6650 time to fit residues: 99.0483 Evaluate side-chains 131 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU 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 616 LYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 157 optimal weight: 0.0000 chunk 38 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 169 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.066442 restraints weight = 22985.040| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.20 r_work: 0.2853 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14741 Z= 0.131 Angle : 0.488 6.715 19990 Z= 0.267 Chirality : 0.044 0.166 2344 Planarity : 0.004 0.046 2567 Dihedral : 8.032 173.265 2092 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.64 % Allowed : 14.73 % Favored : 82.63 % 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: 2.29 (0.20), residues: 1865 helix: 2.47 (0.18), residues: 733 sheet: 1.77 (0.25), residues: 435 loop : 0.37 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 661 TYR 0.018 0.001 TYR B 334 PHE 0.015 0.001 PHE C 340 TRP 0.006 0.001 TRP B 184 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (14741) covalent geometry : angle 0.48810 / 0.27 (19990) hydrogen bonds : bond 0.05225 / 3.50 ( 859) hydrogen bonds : angle 4.88631 / 3.50 ( 2427) *********************** 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 150 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.8078 (mmm160) REVERT: A 424 MET cc_start: 0.9106 (ptp) cc_final: 0.8580 (ppp) REVERT: A 616 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8577 (mmmm) REVERT: A 643 ASP cc_start: 0.8508 (m-30) cc_final: 0.8189 (m-30) REVERT: A 645 GLU cc_start: 0.8096 (tp30) cc_final: 0.7628 (tp30) REVERT: A 657 MET cc_start: 0.8865 (tpp) cc_final: 0.8532 (tpt) REVERT: B 118 ARG cc_start: 0.7213 (tpt170) cc_final: 0.6676 (tpp-160) REVERT: B 125 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8306 (m-30) REVERT: B 230 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: B 314 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8612 (m-40) REVERT: B 645 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7902 (tm-30) REVERT: B 664 ILE cc_start: 0.8550 (pp) cc_final: 0.8210 (pp) REVERT: C 56 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8948 (mp) REVERT: C 230 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8430 (tp30) REVERT: C 436 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: C 616 LYS cc_start: 0.9144 (tppp) cc_final: 0.8836 (mmmm) REVERT: C 617 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8717 (tpt-90) outliers start: 42 outliers final: 21 residues processed: 139 average time/residue: 0.5974 time to fit residues: 91.8186 Evaluate side-chains 129 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 115 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 611 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.062240 restraints weight = 23177.897| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.19 r_work: 0.2776 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9240 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 14741 Z= 0.363 Angle : 0.626 6.596 19990 Z= 0.343 Chirality : 0.050 0.171 2344 Planarity : 0.005 0.069 2567 Dihedral : 8.384 171.517 2092 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.83 % Allowed : 14.22 % Favored : 82.95 % 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: 2.02 (0.19), residues: 1865 helix: 2.17 (0.18), residues: 732 sheet: 1.76 (0.25), residues: 433 loop : 0.21 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 617 TYR 0.020 0.003 TYR B 427 PHE 0.019 0.002 PHE A 340 TRP 0.004 0.002 TRP B 184 HIS 0.004 0.001 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00824 / 0.36 (14741) covalent geometry : angle 0.62584 / 0.34 (19990) hydrogen bonds : bond 0.06966 / 4.66 ( 859) hydrogen bonds : angle 5.34591 / 3.87 ( 2427) *********************** 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 150 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8101 (mmm160) REVERT: A 294 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8494 (mtm-85) REVERT: A 424 MET cc_start: 0.9158 (ptp) cc_final: 0.8655 (ppp) REVERT: A 616 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8594 (mmmm) REVERT: A 643 ASP cc_start: 0.8574 (m-30) cc_final: 0.8254 (m-30) REVERT: A 645 GLU cc_start: 0.8141 (tp30) cc_final: 0.7829 (tp30) REVERT: A 657 MET cc_start: 0.8919 (tpp) cc_final: 0.8587 (tpt) REVERT: B 54 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7872 (mmt90) REVERT: B 125 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: B 230 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8332 (tp30) REVERT: B 664 ILE cc_start: 0.8594 (pp) cc_final: 0.8242 (pp) REVERT: C 56 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8993 (mp) REVERT: C 230 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8517 (tp30) REVERT: C 436 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: C 616 LYS cc_start: 0.9150 (tppp) cc_final: 0.8836 (mmmm) REVERT: C 617 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8689 (tpt-90) outliers start: 45 outliers final: 23 residues processed: 141 average time/residue: 0.6450 time to fit residues: 99.6284 Evaluate side-chains 130 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 294 ARG 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 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 64 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 164 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.064952 restraints weight = 22804.850| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.18 r_work: 0.2832 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9203 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14741 Z= 0.154 Angle : 0.524 8.080 19990 Z= 0.286 Chirality : 0.044 0.168 2344 Planarity : 0.004 0.055 2567 Dihedral : 8.119 171.301 2092 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.14 % Allowed : 15.29 % Favored : 82.57 % 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: 2.23 (0.19), residues: 1865 helix: 2.42 (0.18), residues: 731 sheet: 1.72 (0.25), residues: 435 loop : 0.35 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 661 TYR 0.019 0.001 TYR B 334 PHE 0.016 0.001 PHE C 340 TRP 0.005 0.001 TRP B 184 HIS 0.002 0.001 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (14741) covalent geometry : angle 0.52378 / 0.29 (19990) hydrogen bonds : bond 0.05681 / 3.81 ( 859) hydrogen bonds : angle 5.00854 / 3.60 ( 2427) *********************** 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 138 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7418 (mt0) REVERT: A 103 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.8083 (mmm160) REVERT: A 424 MET cc_start: 0.9112 (ptp) cc_final: 0.8585 (ppp) REVERT: A 616 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: A 643 ASP cc_start: 0.8501 (m-30) cc_final: 0.8203 (m-30) REVERT: A 645 GLU cc_start: 0.8110 (tp30) cc_final: 0.7737 (tp30) REVERT: A 657 MET cc_start: 0.8879 (tpp) cc_final: 0.8519 (tpt) REVERT: B 118 ARG cc_start: 0.6848 (tpt170) cc_final: 0.6443 (tpm170) REVERT: B 125 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: B 230 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8238 (tp30) REVERT: B 282 GLU cc_start: 0.8236 (pm20) cc_final: 0.8034 (pp20) REVERT: B 664 ILE cc_start: 0.8551 (pp) cc_final: 0.8215 (pp) REVERT: C 56 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8963 (mp) REVERT: C 230 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8452 (tp30) REVERT: C 436 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: C 616 LYS cc_start: 0.9145 (tppp) cc_final: 0.8829 (mmmm) REVERT: C 617 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8716 (tpt-90) outliers start: 34 outliers final: 18 residues processed: 129 average time/residue: 0.6373 time to fit residues: 90.5967 Evaluate side-chains 125 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 75 optimal weight: 0.1980 chunk 145 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.090737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065476 restraints weight = 22880.353| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.19 r_work: 0.2846 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9195 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14741 Z= 0.147 Angle : 0.520 9.535 19990 Z= 0.282 Chirality : 0.044 0.169 2344 Planarity : 0.004 0.048 2567 Dihedral : 7.911 170.492 2088 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.14 % Allowed : 15.48 % Favored : 82.38 % 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: 2.29 (0.20), residues: 1865 helix: 2.53 (0.18), residues: 727 sheet: 1.75 (0.25), residues: 435 loop : 0.33 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 617 TYR 0.019 0.001 TYR B 334 PHE 0.016 0.001 PHE C 340 TRP 0.006 0.001 TRP B 184 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (14741) covalent geometry : angle 0.51954 / 0.28 (19990) hydrogen bonds : bond 0.05399 / 3.62 ( 859) hydrogen bonds : angle 4.90452 / 3.52 ( 2427) *********************** 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 137 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8067 (mmm160) REVERT: A 424 MET cc_start: 0.9106 (ptp) cc_final: 0.8586 (ppp) REVERT: A 616 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: A 643 ASP cc_start: 0.8494 (m-30) cc_final: 0.8217 (m-30) REVERT: A 645 GLU cc_start: 0.8089 (tp30) cc_final: 0.7700 (tp30) REVERT: A 657 MET cc_start: 0.8893 (tpp) cc_final: 0.8535 (tpt) REVERT: B 118 ARG cc_start: 0.6820 (tpt170) cc_final: 0.6405 (tpm170) REVERT: B 125 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: B 230 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: B 664 ILE cc_start: 0.8569 (pp) cc_final: 0.8190 (pp) REVERT: C 56 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8962 (mp) REVERT: C 230 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8425 (tp30) REVERT: C 436 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: C 616 LYS cc_start: 0.9162 (tppp) cc_final: 0.8844 (mmmm) REVERT: C 617 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8697 (tpt-90) outliers start: 34 outliers final: 20 residues processed: 128 average time/residue: 0.6758 time to fit residues: 94.9901 Evaluate side-chains 127 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 122 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.090849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065611 restraints weight = 23054.819| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.20 r_work: 0.2848 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9191 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14741 Z= 0.149 Angle : 0.526 10.197 19990 Z= 0.284 Chirality : 0.044 0.170 2344 Planarity : 0.004 0.061 2567 Dihedral : 7.868 169.621 2088 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.01 % Allowed : 15.86 % Favored : 82.13 % 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: 2.31 (0.20), residues: 1865 helix: 2.52 (0.18), residues: 732 sheet: 1.77 (0.25), residues: 435 loop : 0.35 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 661 TYR 0.020 0.001 TYR B 334 PHE 0.016 0.001 PHE C 340 TRP 0.007 0.001 TRP B 184 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (14741) covalent geometry : angle 0.52570 / 0.28 (19990) hydrogen bonds : bond 0.05313 / 3.56 ( 859) hydrogen bonds : angle 4.86379 / 3.49 ( 2427) *********************** 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 135 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7362 (mt0) REVERT: A 103 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8087 (mmm160) REVERT: A 424 MET cc_start: 0.9108 (ptp) cc_final: 0.8593 (ppp) REVERT: A 616 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8584 (mmmm) REVERT: A 643 ASP cc_start: 0.8497 (m-30) cc_final: 0.8220 (m-30) REVERT: A 645 GLU cc_start: 0.8021 (tp30) cc_final: 0.7591 (tp30) REVERT: A 657 MET cc_start: 0.8900 (tpp) cc_final: 0.8499 (tpt) REVERT: B 125 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: B 230 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: B 664 ILE cc_start: 0.8536 (pp) cc_final: 0.8202 (pp) REVERT: C 56 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8943 (mp) REVERT: C 230 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8441 (tp30) REVERT: C 436 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: C 616 LYS cc_start: 0.9161 (tppp) cc_final: 0.8850 (mmmm) REVERT: C 617 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8690 (tpt-90) outliers start: 32 outliers final: 21 residues processed: 127 average time/residue: 0.6402 time to fit residues: 89.6942 Evaluate side-chains 127 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 129 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 183 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 611 GLN A 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.089067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063694 restraints weight = 23019.509| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.19 r_work: 0.2807 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9222 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14741 Z= 0.253 Angle : 0.587 10.965 19990 Z= 0.319 Chirality : 0.047 0.174 2344 Planarity : 0.004 0.049 2567 Dihedral : 8.031 169.562 2088 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.95 % Allowed : 15.98 % Favored : 82.06 % 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: 2.19 (0.20), residues: 1865 helix: 2.37 (0.18), residues: 736 sheet: 1.75 (0.25), residues: 436 loop : 0.28 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 617 TYR 0.021 0.002 TYR B 334 PHE 0.018 0.001 PHE C 340 TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (14741) covalent geometry : angle 0.58722 / 0.32 (19990) hydrogen bonds : bond 0.06097 / 4.08 ( 859) hydrogen bonds : angle 5.07914 / 3.67 ( 2427) ********************** 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 131 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.615 Fit side-chains REVERT: A 424 MET cc_start: 0.9105 (ptp) cc_final: 0.8623 (ppp) REVERT: A 616 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8596 (mmmm) REVERT: A 643 ASP cc_start: 0.8536 (m-30) cc_final: 0.8244 (m-30) REVERT: A 645 GLU cc_start: 0.8045 (tp30) cc_final: 0.7642 (tp30) REVERT: A 657 MET cc_start: 0.8917 (tpp) cc_final: 0.8528 (tpt) REVERT: B 118 ARG cc_start: 0.7034 (tpm170) cc_final: 0.6762 (tpp-160) REVERT: B 125 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: B 230 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: B 645 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7667 (tm-30) REVERT: B 661 ARG cc_start: 0.8374 (tpt170) cc_final: 0.8171 (mtm110) REVERT: B 664 ILE cc_start: 0.8574 (pp) cc_final: 0.8203 (pp) REVERT: C 56 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8981 (mp) REVERT: C 230 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8497 (tp30) REVERT: C 436 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: C 616 LYS cc_start: 0.9160 (tppp) cc_final: 0.8849 (mmmm) REVERT: C 617 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8681 (tpt-90) outliers start: 31 outliers final: 19 residues processed: 124 average time/residue: 0.6554 time to fit residues: 89.3849 Evaluate side-chains 126 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 29 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.065075 restraints weight = 22932.811| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.19 r_work: 0.2835 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14741 Z= 0.158 Angle : 0.546 11.117 19990 Z= 0.295 Chirality : 0.044 0.171 2344 Planarity : 0.004 0.048 2567 Dihedral : 7.906 169.163 2088 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.76 % Allowed : 16.43 % Favored : 81.81 % 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: 2.30 (0.20), residues: 1865 helix: 2.52 (0.18), residues: 730 sheet: 1.75 (0.25), residues: 436 loop : 0.35 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 617 TYR 0.020 0.001 TYR B 334 PHE 0.016 0.001 PHE C 340 TRP 0.006 0.001 TRP B 184 HIS 0.001 0.000 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (14741) covalent geometry : angle 0.54635 / 0.30 (19990) hydrogen bonds : bond 0.05477 / 3.67 ( 859) hydrogen bonds : angle 4.92500 / 3.55 ( 2427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7845.24 seconds wall clock time: 134 minutes 2.67 seconds (8042.67 seconds total)