Starting phenix.real_space_refine on Thu Feb 5 03:45:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9no0_49590/02_2026/9no0_49590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9no0_49590/02_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_49590/02_2026/9no0_49590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9no0_49590/02_2026/9no0_49590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9no0_49590/02_2026/9no0_49590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9no0_49590/02_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-2.0-5952/lib/python3.9/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: 3.51, per 1000 atoms: 0.24 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: 1.33 Conformation dependent library (CDL) restraints added in 564.8 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: 0.45 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: 2.11 Time building geometry restraints manager: 1.73 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=" 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 angle pdb=" CB GLU A 330 " pdb=" CG GLU A 330 " pdb=" CD GLU A 330 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.70e+00 3.46e-01 1.19e+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: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 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= 0.339 Angle : 0.629 10.658 19990 Z= 0.335 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 covalent geometry : bond 0.00752 (14741) covalent geometry : angle 0.62945 (19990) hydrogen bonds : bond 0.19972 ( 859) hydrogen bonds : angle 7.54553 ( 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 : 0.621 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: 0.7623 time to fit residues: 91.6825 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 : 0.410 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.089810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064561 restraints weight = 22978.188| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.19 r_work: 0.2808 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14741 Z= 0.178 Angle : 0.541 5.691 19990 Z= 0.298 Chirality : 0.045 0.141 2344 Planarity : 0.004 0.044 2567 Dihedral : 8.937 179.050 2128 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.58 % Allowed : 14.41 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 1865 helix: 2.10 (0.18), residues: 737 sheet: 1.73 (0.25), residues: 431 loop : 0.41 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 617 TYR 0.019 0.002 TYR B 334 PHE 0.015 0.001 PHE C 340 TRP 0.004 0.001 TRP C 184 HIS 0.002 0.000 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00378 (14741) covalent geometry : angle 0.54063 (19990) hydrogen bonds : bond 0.06541 ( 859) hydrogen bonds : angle 5.45989 ( 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 147 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8532 (mmm-85) cc_final: 0.8106 (mmm160) REVERT: A 118 ARG cc_start: 0.6385 (mmt180) cc_final: 0.5051 (mmm160) REVERT: A 424 MET cc_start: 0.9152 (ptp) cc_final: 0.8585 (ppp) REVERT: A 616 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8405 (mmmm) REVERT: A 643 ASP cc_start: 0.8523 (m-30) cc_final: 0.8211 (m-30) REVERT: B 118 ARG cc_start: 0.7206 (tpt170) cc_final: 0.6788 (tpp-160) REVERT: B 125 ASP cc_start: 0.8518 (m-30) cc_final: 0.8305 (m-30) REVERT: B 314 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8600 (m-40) REVERT: B 645 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7923 (tm-30) REVERT: B 664 ILE cc_start: 0.8610 (pp) cc_final: 0.8248 (pp) REVERT: C 230 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8438 (tp30) REVERT: C 418 ILE cc_start: 0.8810 (tt) cc_final: 0.8595 (pp) REVERT: C 436 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: C 616 LYS cc_start: 0.9139 (tppp) cc_final: 0.8810 (mmmm) outliers start: 41 outliers final: 16 residues processed: 140 average time/residue: 0.7418 time to fit residues: 112.5375 Evaluate side-chains 118 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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 352 VAL Chi-restraints excluded: chain B residue 371 SER 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 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: 2.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 175 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3456 r_free = 0.3456 target = 0.090254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064790 restraints weight = 23075.547| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.20 r_work: 0.2816 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14741 Z= 0.171 Angle : 0.517 6.011 19990 Z= 0.283 Chirality : 0.044 0.153 2344 Planarity : 0.004 0.048 2567 Dihedral : 8.353 179.609 2097 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.02 % Allowed : 14.29 % Favored : 82.69 % 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: 2.20 (0.19), residues: 1865 helix: 2.32 (0.18), residues: 738 sheet: 1.74 (0.25), residues: 432 loop : 0.39 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 661 TYR 0.019 0.002 TYR C 334 PHE 0.016 0.001 PHE C 340 TRP 0.004 0.001 TRP B 184 HIS 0.001 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00368 (14741) covalent geometry : angle 0.51684 (19990) hydrogen bonds : bond 0.05974 ( 859) hydrogen bonds : angle 5.14042 ( 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 157 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 0.635 Fit side-chains REVERT: A 103 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8096 (mmm160) REVERT: A 424 MET cc_start: 0.9130 (ptp) cc_final: 0.8599 (ppp) REVERT: A 616 LYS cc_start: 0.9071 (tppp) cc_final: 0.8538 (mmmm) REVERT: A 643 ASP cc_start: 0.8508 (m-30) cc_final: 0.8192 (m-30) REVERT: A 645 GLU cc_start: 0.8217 (tp30) cc_final: 0.7840 (tp30) REVERT: A 657 MET cc_start: 0.8820 (tpp) cc_final: 0.8567 (tpt) REVERT: B 54 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7773 (mmt90) REVERT: B 118 ARG cc_start: 0.7165 (tpt170) cc_final: 0.6754 (tpp-160) REVERT: B 125 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8329 (m-30) REVERT: B 314 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8580 (m-40) REVERT: B 645 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7894 (tm-30) REVERT: B 664 ILE cc_start: 0.8576 (pp) cc_final: 0.8218 (pp) REVERT: C 230 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8447 (tp30) REVERT: C 436 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: C 616 LYS cc_start: 0.9155 (tppp) cc_final: 0.8833 (mmmm) REVERT: C 617 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8735 (tpt-90) outliers start: 48 outliers final: 19 residues processed: 148 average time/residue: 0.6194 time to fit residues: 100.2945 Evaluate side-chains 128 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU 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 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 533 ILE Chi-restraints excluded: chain B residue 610 VAL 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 617 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.062180 restraints weight = 23328.767| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.20 r_work: 0.2761 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 14741 Z= 0.359 Angle : 0.628 5.957 19990 Z= 0.344 Chirality : 0.050 0.166 2344 Planarity : 0.005 0.064 2567 Dihedral : 8.545 178.245 2090 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.21 % Allowed : 13.66 % Favored : 83.13 % 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: 1.93 (0.19), residues: 1865 helix: 2.10 (0.18), residues: 730 sheet: 1.75 (0.25), residues: 430 loop : 0.15 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 661 TYR 0.019 0.002 TYR C 334 PHE 0.018 0.002 PHE A 545 TRP 0.004 0.002 TRP A 184 HIS 0.004 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00814 (14741) covalent geometry : angle 0.62839 (19990) hydrogen bonds : bond 0.07086 ( 859) hydrogen bonds : angle 5.40752 ( 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 156 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 105 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8222 (mmm160) REVERT: A 294 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8783 (mtp180) REVERT: A 319 ASP cc_start: 0.8381 (t0) cc_final: 0.8135 (t0) REVERT: A 424 MET cc_start: 0.9195 (ptp) cc_final: 0.8660 (ppp) REVERT: A 616 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8563 (mmmm) REVERT: A 643 ASP cc_start: 0.8566 (m-30) cc_final: 0.8246 (m-30) REVERT: A 645 GLU cc_start: 0.8189 (tp30) cc_final: 0.7907 (tp30) REVERT: A 657 MET cc_start: 0.8896 (tpp) cc_final: 0.8584 (tpt) REVERT: B 54 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7977 (mmt90) REVERT: B 125 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8374 (m-30) REVERT: B 230 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8367 (tp30) REVERT: B 664 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8237 (pp) REVERT: C 56 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9011 (mp) REVERT: C 230 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8532 (tp30) REVERT: C 436 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: C 616 LYS cc_start: 0.9156 (tppp) cc_final: 0.8817 (mmmm) REVERT: C 617 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8667 (tpt-90) outliers start: 51 outliers final: 27 residues processed: 145 average time/residue: 0.7073 time to fit residues: 112.0670 Evaluate side-chains 139 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 440 VAL 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 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 56 LEU 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 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 547 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 36 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3464 r_free = 0.3464 target = 0.090725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.065381 restraints weight = 22986.136| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.19 r_work: 0.2828 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1131 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= 0.148 Angle : 0.519 6.331 19990 Z= 0.281 Chirality : 0.044 0.155 2344 Planarity : 0.004 0.049 2567 Dihedral : 8.237 179.565 2090 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.52 % Allowed : 14.66 % Favored : 82.82 % 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 (0.19), residues: 1865 helix: 2.41 (0.18), residues: 730 sheet: 1.72 (0.25), residues: 435 loop : 0.34 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 661 TYR 0.019 0.001 TYR B 334 PHE 0.016 0.001 PHE C 340 TRP 0.008 0.002 TRP B 184 HIS 0.001 0.000 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00313 (14741) covalent geometry : angle 0.51906 (19990) hydrogen bonds : bond 0.05532 ( 859) hydrogen bonds : angle 4.98375 ( 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 148 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 424 MET cc_start: 0.9110 (ptp) cc_final: 0.8566 (ppp) REVERT: A 616 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8571 (mmmm) REVERT: A 645 GLU cc_start: 0.8132 (tp30) cc_final: 0.7720 (tp30) REVERT: A 657 MET cc_start: 0.8886 (tpp) cc_final: 0.8549 (tpt) REVERT: B 54 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7721 (mmt90) REVERT: B 125 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: B 230 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: B 664 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8227 (pp) REVERT: C 56 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8992 (mp) REVERT: C 103 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7914 (mtp85) REVERT: C 125 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: C 230 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8438 (tp30) REVERT: C 436 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: C 616 LYS cc_start: 0.9163 (tppp) cc_final: 0.8828 (mmmm) REVERT: C 617 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8713 (tpt-90) outliers start: 40 outliers final: 14 residues processed: 137 average time/residue: 0.6841 time to fit residues: 102.4593 Evaluate side-chains 128 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 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 646 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 103 ARG 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 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: 2.9990 chunk 149 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 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: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.087634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062371 restraints weight = 23237.825| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.19 r_work: 0.2777 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: 0.9058 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 14741 Z= 0.339 Angle : 0.625 6.816 19990 Z= 0.340 Chirality : 0.049 0.162 2344 Planarity : 0.005 0.062 2567 Dihedral : 8.412 178.628 2088 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.96 % Allowed : 14.41 % 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: 1.98 (0.19), residues: 1865 helix: 2.14 (0.18), residues: 736 sheet: 1.71 (0.25), residues: 433 loop : 0.20 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 661 TYR 0.019 0.002 TYR A 334 PHE 0.018 0.002 PHE C 340 TRP 0.004 0.002 TRP A 184 HIS 0.003 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00766 (14741) covalent geometry : angle 0.62461 (19990) hydrogen bonds : bond 0.06879 ( 859) hydrogen bonds : angle 5.30700 ( 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 153 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 106 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 294 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8649 (mtm180) REVERT: A 319 ASP cc_start: 0.8245 (t0) cc_final: 0.7851 (t0) REVERT: A 424 MET cc_start: 0.9148 (ptp) cc_final: 0.8644 (ppp) REVERT: A 616 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8557 (mmmm) REVERT: A 643 ASP cc_start: 0.8556 (m-30) cc_final: 0.8247 (m-30) REVERT: A 645 GLU cc_start: 0.8160 (tp30) cc_final: 0.7884 (tp30) REVERT: A 657 MET cc_start: 0.8916 (tpp) cc_final: 0.8578 (tpt) REVERT: B 54 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7967 (mmt90) REVERT: B 125 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: B 230 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8330 (tp30) REVERT: B 664 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8232 (pp) REVERT: C 56 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9002 (mp) REVERT: C 103 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8032 (mtp85) REVERT: C 230 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8516 (tp30) REVERT: C 436 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: C 616 LYS cc_start: 0.9160 (tppp) cc_final: 0.8834 (mmmm) REVERT: C 617 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8648 (tpt-90) outliers start: 47 outliers final: 21 residues processed: 142 average time/residue: 0.6251 time to fit residues: 97.0130 Evaluate side-chains 136 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 294 ARG Chi-restraints excluded: chain A residue 411 VAL 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 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 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 B residue 664 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 103 ARG 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 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 547 ILE 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: 0.7980 chunk 167 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 164 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.090376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065326 restraints weight = 22975.266| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.18 r_work: 0.2837 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14741 Z= 0.148 Angle : 0.534 8.391 19990 Z= 0.288 Chirality : 0.044 0.149 2344 Planarity : 0.004 0.049 2567 Dihedral : 8.142 179.517 2088 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.45 % Allowed : 14.85 % Favored : 82.69 % 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 (0.20), residues: 1865 helix: 2.45 (0.18), residues: 732 sheet: 1.70 (0.25), residues: 436 loop : 0.33 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 661 TYR 0.020 0.001 TYR B 334 PHE 0.016 0.001 PHE C 340 TRP 0.009 0.001 TRP B 184 HIS 0.002 0.000 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00316 (14741) covalent geometry : angle 0.53427 (19990) hydrogen bonds : bond 0.05463 ( 859) hydrogen bonds : angle 4.94288 ( 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 148 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.445 Fit side-chains REVERT: A 424 MET cc_start: 0.9096 (ptp) cc_final: 0.8573 (ppp) REVERT: A 616 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8561 (mmmm) REVERT: A 645 GLU cc_start: 0.8126 (tp30) cc_final: 0.7741 (tp30) REVERT: A 657 MET cc_start: 0.8905 (tpp) cc_final: 0.8538 (tpt) REVERT: B 54 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7742 (mmt90) REVERT: B 118 ARG cc_start: 0.6978 (tpm170) cc_final: 0.6677 (tpp-160) REVERT: B 125 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8274 (m-30) REVERT: B 230 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8239 (tp30) REVERT: B 645 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7808 (tm-30) REVERT: B 664 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8201 (pp) REVERT: C 56 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8973 (mp) REVERT: C 103 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7916 (mtp85) REVERT: C 230 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8434 (tp30) REVERT: C 436 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: C 616 LYS cc_start: 0.9168 (tppp) cc_final: 0.8840 (mmmm) REVERT: C 617 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8704 (tpt-90) outliers start: 39 outliers final: 20 residues processed: 136 average time/residue: 0.5543 time to fit residues: 82.9187 Evaluate side-chains 134 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 440 VAL 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 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 B residue 664 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 103 ARG 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 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: 0.0870 chunk 145 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3439 r_free = 0.3439 target = 0.088842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.063631 restraints weight = 23079.963| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.19 r_work: 0.2801 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14741 Z= 0.244 Angle : 0.581 9.322 19990 Z= 0.315 Chirality : 0.046 0.174 2344 Planarity : 0.005 0.051 2567 Dihedral : 8.255 179.591 2088 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.39 % Allowed : 15.17 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.19), residues: 1865 helix: 2.31 (0.18), residues: 736 sheet: 1.73 (0.25), residues: 435 loop : 0.28 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 661 TYR 0.020 0.002 TYR B 334 PHE 0.018 0.001 PHE C 340 TRP 0.004 0.001 TRP C 184 HIS 0.003 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00546 (14741) covalent geometry : angle 0.58118 (19990) hydrogen bonds : bond 0.06161 ( 859) hydrogen bonds : angle 5.10339 ( 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 144 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.462 Fit side-chains REVERT: A 424 MET cc_start: 0.9118 (ptp) cc_final: 0.8618 (ppp) REVERT: A 616 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8581 (mmmm) REVERT: A 643 ASP cc_start: 0.8513 (m-30) cc_final: 0.8216 (m-30) REVERT: A 645 GLU cc_start: 0.8113 (tp30) cc_final: 0.7757 (tp30) REVERT: A 657 MET cc_start: 0.8920 (tpp) cc_final: 0.8545 (tpt) REVERT: B 54 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7745 (mmt90) REVERT: B 125 ASP cc_start: 0.8520 (m-30) cc_final: 0.8310 (m-30) REVERT: B 230 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: B 415 ILE cc_start: 0.6307 (OUTLIER) cc_final: 0.6104 (pp) REVERT: B 645 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7788 (tm-30) REVERT: B 664 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8218 (pp) REVERT: C 50 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8626 (m-30) REVERT: C 56 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9002 (mp) REVERT: C 230 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8476 (tp30) REVERT: C 436 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 616 LYS cc_start: 0.9166 (tppp) cc_final: 0.8851 (mmmm) REVERT: C 617 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8661 (tpt-90) outliers start: 38 outliers final: 21 residues processed: 134 average time/residue: 0.6300 time to fit residues: 92.4713 Evaluate side-chains 133 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 440 VAL 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 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 415 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 B residue 664 ILE Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 56 LEU 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 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: 0.9990 chunk 161 optimal weight: 1.9990 chunk 109 optimal weight: 0.0170 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3472 r_free = 0.3472 target = 0.090860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.065798 restraints weight = 23094.508| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.19 r_work: 0.2852 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1288 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= 0.142 Angle : 0.540 10.880 19990 Z= 0.288 Chirality : 0.044 0.150 2344 Planarity : 0.004 0.053 2567 Dihedral : 8.035 179.062 2088 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.45 % Allowed : 15.42 % 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: 2.30 (0.20), residues: 1865 helix: 2.51 (0.18), residues: 734 sheet: 1.73 (0.24), residues: 436 loop : 0.36 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 661 TYR 0.022 0.001 TYR B 334 PHE 0.015 0.001 PHE C 340 TRP 0.010 0.002 TRP B 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00307 (14741) covalent geometry : angle 0.53963 (19990) hydrogen bonds : bond 0.05185 ( 859) hydrogen bonds : angle 4.83331 ( 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 144 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.455 Fit side-chains REVERT: A 103 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.8151 (mmm160) REVERT: A 424 MET cc_start: 0.9088 (ptp) cc_final: 0.8571 (ppp) REVERT: A 616 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: A 645 GLU cc_start: 0.8035 (tp30) cc_final: 0.7601 (tp30) REVERT: A 657 MET cc_start: 0.8911 (tpp) cc_final: 0.8528 (tpt) REVERT: B 54 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7679 (mmt90) REVERT: B 125 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: B 230 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8230 (tp30) REVERT: B 645 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7746 (tm-30) REVERT: B 664 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8198 (pp) REVERT: C 56 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8976 (mp) REVERT: C 230 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8423 (tp30) REVERT: C 436 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: C 616 LYS cc_start: 0.9167 (tppp) cc_final: 0.8856 (mmmm) REVERT: C 617 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8681 (tpt-90) outliers start: 39 outliers final: 20 residues processed: 134 average time/residue: 0.6389 time to fit residues: 93.9850 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 : 0.607 ------------------------------------------------------------------------------- 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 411 VAL 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 406 ILE 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 B residue 664 ILE Chi-restraints excluded: chain C residue 56 LEU 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 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: 1.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 0.0980 chunk 183 optimal weight: 0.9990 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: 0.9980 chunk 148 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3463 r_free = 0.3463 target = 0.090287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.065187 restraints weight = 23136.686| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.19 r_work: 0.2837 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14741 Z= 0.169 Angle : 0.556 11.121 19990 Z= 0.297 Chirality : 0.044 0.166 2344 Planarity : 0.004 0.053 2567 Dihedral : 8.062 179.379 2088 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.01 % Allowed : 16.11 % Favored : 81.88 % 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: 2.32 (0.20), residues: 1865 helix: 2.53 (0.18), residues: 731 sheet: 1.76 (0.24), residues: 436 loop : 0.36 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 661 TYR 0.021 0.002 TYR B 334 PHE 0.016 0.001 PHE C 340 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00372 (14741) covalent geometry : angle 0.55563 (19990) hydrogen bonds : bond 0.05428 ( 859) hydrogen bonds : angle 4.87571 ( 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 134 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8216 (mmm160) REVERT: A 424 MET cc_start: 0.9101 (ptp) cc_final: 0.8586 (ppp) REVERT: A 616 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8552 (mmmm) REVERT: A 643 ASP cc_start: 0.8480 (m-30) cc_final: 0.8179 (m-30) REVERT: A 657 MET cc_start: 0.8922 (tpp) cc_final: 0.8535 (tpt) REVERT: B 54 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7652 (mmt90) REVERT: B 125 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: B 230 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: B 645 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7737 (tm-30) REVERT: B 664 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8186 (pp) REVERT: C 56 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8963 (mp) REVERT: C 230 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8441 (tp30) REVERT: C 436 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: C 616 LYS cc_start: 0.9168 (tppp) cc_final: 0.8873 (mmmm) REVERT: C 617 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8703 (tpt-90) outliers start: 32 outliers final: 20 residues processed: 124 average time/residue: 0.6715 time to fit residues: 91.1119 Evaluate side-chains 130 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 411 VAL 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 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 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 56 LEU 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 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 547 ILE 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: 4.9990 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.064120 restraints weight = 23005.360| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.20 r_work: 0.2813 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1117 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= 0.214 Angle : 0.577 10.919 19990 Z= 0.309 Chirality : 0.045 0.154 2344 Planarity : 0.004 0.051 2567 Dihedral : 8.140 179.619 2088 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.14 % Allowed : 15.98 % Favored : 81.88 % 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 (0.20), residues: 1865 helix: 2.39 (0.18), residues: 738 sheet: 1.76 (0.25), residues: 436 loop : 0.32 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 661 TYR 0.021 0.002 TYR B 334 PHE 0.017 0.001 PHE C 340 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00478 (14741) covalent geometry : angle 0.57746 (19990) hydrogen bonds : bond 0.05887 ( 859) hydrogen bonds : angle 5.00882 ( 2427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7291.90 seconds wall clock time: 124 minutes 39.36 seconds (7479.36 seconds total)