Starting phenix.real_space_refine on Sat Aug 23 14:52:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io8_35611/08_2025/8io8_35611.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io8_35611/08_2025/8io8_35611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8io8_35611/08_2025/8io8_35611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io8_35611/08_2025/8io8_35611.map" model { file = "/net/cci-nas-00/data/ceres_data/8io8_35611/08_2025/8io8_35611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io8_35611/08_2025/8io8_35611.cif" } resolution = 2.17 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= 0.005 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 7962 2.51 5 N 2258 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12596 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Chain: "B" Number of atoms: 6240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.29, per 1000 atoms: 0.26 Number of scatterers: 12596 At special positions: 0 Unit cell: (100.86, 109.06, 99.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 10 15.00 Mg 2 11.99 O 2332 8.00 N 2258 7.00 C 7962 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: 1.07 Conformation dependent library (CDL) restraints added in 510.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 52.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.560A pdb=" N ALA A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 63 through 82 removed outlier: 3.521A pdb=" N HIS A 73 " --> pdb=" O PHE A 69 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.709A pdb=" N LEU A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 118 through 129 removed outlier: 4.119A pdb=" N PHE A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.520A pdb=" N THR A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 247 through 275 removed outlier: 4.627A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.539A pdb=" N SER A 312 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 337 through 342 removed outlier: 5.976A pdb=" N GLU A 340 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 4.003A pdb=" N ILE A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.673A pdb=" N ARG A 363 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 removed outlier: 6.177A pdb=" N GLY A 373 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 402 through 416 Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.630A pdb=" N ASP A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 494 through 498 removed outlier: 4.340A pdb=" N HIS A 497 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 498 " --> pdb=" O PHE A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 498' Processing helix chain 'A' and resid 499 through 516 Processing helix chain 'A' and resid 547 through 554 removed outlier: 4.021A pdb=" N ASP A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 680 through 688 Processing helix chain 'A' and resid 701 through 709 removed outlier: 4.339A pdb=" N ILE A 705 " --> pdb=" O TYR A 701 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 755 through 758 removed outlier: 3.634A pdb=" N ARG A 758 " --> pdb=" O PRO A 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 758' Processing helix chain 'A' and resid 761 through 783 Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'B' and resid 14 through 38 removed outlier: 3.597A pdb=" N ALA B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 63 through 82 removed outlier: 3.517A pdb=" N HIS B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 105 removed outlier: 3.703A pdb=" N LEU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.098A pdb=" N PHE B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.628A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 247 through 275 removed outlier: 4.597A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.560A pdb=" N SER B 312 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 337 through 342 removed outlier: 5.956A pdb=" N GLU B 340 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.971A pdb=" N ILE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.739A pdb=" N ARG B 363 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 376 removed outlier: 6.214A pdb=" N GLY B 373 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 402 through 416 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.616A pdb=" N ASP B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 494 through 498 removed outlier: 4.382A pdb=" N HIS B 497 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 498 " --> pdb=" O PHE B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 494 through 498' Processing helix chain 'B' and resid 499 through 516 Processing helix chain 'B' and resid 547 through 554 removed outlier: 4.020A pdb=" N ASP B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 635 through 653 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 701 through 709 removed outlier: 4.295A pdb=" N ILE B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS B 706 " --> pdb=" O PRO B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 731 through 739 Processing helix chain 'B' and resid 742 through 754 Processing helix chain 'B' and resid 755 through 758 removed outlier: 3.578A pdb=" N ARG B 758 " --> pdb=" O PRO B 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 758' Processing helix chain 'B' and resid 761 through 783 Processing helix chain 'B' and resid 786 through 791 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.237A pdb=" N ASN A 84 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA A 173 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 86 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL A 175 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 88 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLY A 177 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 170 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU A 205 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 172 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A 207 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N CYS A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS A 209 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 176 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU A 239 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL A 288 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 241 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ARG A 290 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 243 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 466 removed outlier: 8.316A pdb=" N MET A 465 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 422 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY A 487 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N LEU A 529 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 489 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 531 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR A 491 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 442 through 443 removed outlier: 5.347A pdb=" N LYS A 442 " --> pdb=" O SER A 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.649A pdb=" N VAL A 629 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL A 661 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 631 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 663 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER A 633 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 630 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASN A 697 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA A 632 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.279A pdb=" N ASN B 84 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA B 173 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 86 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL B 175 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 88 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLY B 177 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU B 239 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 288 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE B 241 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ARG B 290 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 243 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 300 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 397 through 400 removed outlier: 4.670A pdb=" N SER B 397 " --> pdb=" O GLN B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 466 removed outlier: 8.273A pdb=" N MET B 465 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 422 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY B 487 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU B 529 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE B 489 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER B 531 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR B 491 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 442 through 443 removed outlier: 5.337A pdb=" N LYS B 442 " --> pdb=" O SER B 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 613 through 615 removed outlier: 6.670A pdb=" N VAL B 629 " --> pdb=" O ARG B 659 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL B 661 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE B 631 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL B 663 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER B 633 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 630 " --> pdb=" O ILE B 695 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN B 697 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA B 632 " --> pdb=" O ASN B 697 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1488 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: 2.06 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2097 1.31 - 1.43: 3632 1.43 - 1.56: 7158 1.56 - 1.68: 16 1.68 - 1.81: 49 Bond restraints: 12952 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.695 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.609 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C LEU B 640 " pdb=" O LEU B 640 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.17e-02 7.31e+03 2.02e+01 bond pdb=" C LEU A 640 " pdb=" O LEU A 640 " ideal model delta sigma weight residual 1.237 1.184 0.052 1.17e-02 7.31e+03 2.01e+01 ... (remaining 12947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 17545 3.18 - 6.35: 120 6.35 - 9.53: 20 9.53 - 12.70: 2 12.70 - 15.88: 1 Bond angle restraints: 17688 Sorted by residual: angle pdb=" N LYS A 556 " pdb=" CA LYS A 556 " pdb=" C LYS A 556 " ideal model delta sigma weight residual 110.28 100.00 10.28 1.48e+00 4.57e-01 4.82e+01 angle pdb=" N ARG B 753 " pdb=" CA ARG B 753 " pdb=" C ARG B 753 " ideal model delta sigma weight residual 111.36 117.57 -6.21 1.09e+00 8.42e-01 3.25e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 111.07 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O3A TPP A 802 " pdb=" PB TPP A 802 " pdb=" O3B TPP A 802 " ideal model delta sigma weight residual 104.26 111.17 -6.91 1.33e+00 5.64e-01 2.69e+01 angle pdb=" N ALA B 558 " pdb=" CA ALA B 558 " pdb=" C ALA B 558 " ideal model delta sigma weight residual 113.01 107.02 5.99 1.20e+00 6.94e-01 2.49e+01 ... (remaining 17683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 7176 17.64 - 35.28: 368 35.28 - 52.91: 74 52.91 - 70.55: 13 70.55 - 88.19: 7 Dihedral angle restraints: 7638 sinusoidal: 3096 harmonic: 4542 Sorted by residual: dihedral pdb=" CA GLY A 294 " pdb=" C GLY A 294 " pdb=" N TRP A 295 " pdb=" CA TRP A 295 " ideal model delta harmonic sigma weight residual 180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLY B 294 " pdb=" C GLY B 294 " pdb=" N TRP B 295 " pdb=" CA TRP B 295 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU A 85 " pdb=" C LEU A 85 " pdb=" N ILE A 86 " pdb=" CA ILE A 86 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 7635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1499 0.054 - 0.108: 321 0.108 - 0.162: 58 0.162 - 0.216: 10 0.216 - 0.270: 4 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA THR A 554 " pdb=" N THR A 554 " pdb=" C THR A 554 " pdb=" CB THR A 554 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA THR B 554 " pdb=" N THR B 554 " pdb=" C THR B 554 " pdb=" CB THR B 554 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1889 not shown) Planarity restraints: 2318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 786 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO B 787 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 787 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 787 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 536 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ARG A 536 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG A 536 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A 537 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 276 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C GLY A 276 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY A 276 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 277 " 0.010 2.00e-02 2.50e+03 ... (remaining 2315 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 122 2.59 - 3.16: 10610 3.16 - 3.74: 20674 3.74 - 4.32: 31356 4.32 - 4.90: 49929 Nonbonded interactions: 112691 Sorted by model distance: nonbonded pdb=" OD1 ASP B 178 " pdb="MG MG B 803 " model vdw 2.008 2.170 nonbonded pdb=" O TYR B 213 " pdb="MG MG B 803 " model vdw 2.017 2.170 nonbonded pdb=" O3B TPP B 802 " pdb="MG MG B 803 " model vdw 2.028 2.170 nonbonded pdb=" OD1 ASP A 178 " pdb="MG MG A 803 " model vdw 2.056 2.170 nonbonded pdb=" O1A TPP A 802 " pdb="MG MG A 803 " model vdw 2.072 2.170 ... (remaining 112686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.300 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 : 0.006 0.146 12952 Z= 0.302 Angle : 0.672 15.878 17688 Z= 0.341 Chirality : 0.049 0.270 1892 Planarity : 0.004 0.054 2318 Dihedral : 11.485 88.191 4714 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.08 % Allowed : 2.56 % Favored : 97.36 % 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 aren not related in a simple way. whole: 0.23 (0.21), residues: 1572 helix: 0.53 (0.19), residues: 700 sheet: 0.96 (0.38), residues: 184 loop : -0.36 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 398 TYR 0.012 0.001 TYR B 87 PHE 0.009 0.002 PHE B 129 TRP 0.010 0.001 TRP A 61 HIS 0.005 0.001 HIS A 699 Details of bonding type rmsd covalent geometry : bond 0.00613 (12952) covalent geometry : angle 0.67234 (17688) hydrogen bonds : bond 0.20134 ( 551) hydrogen bonds : angle 6.00980 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.457 Fit side-chains REVERT: A 217 ASN cc_start: 0.8706 (m-40) cc_final: 0.8396 (m110) REVERT: A 729 ILE cc_start: 0.8814 (mm) cc_final: 0.8269 (tp) REVERT: B 217 ASN cc_start: 0.8649 (m-40) cc_final: 0.8369 (m110) REVERT: B 514 LYS cc_start: 0.8853 (tttt) cc_final: 0.8578 (ttmt) outliers start: 1 outliers final: 2 residues processed: 127 average time/residue: 0.8297 time to fit residues: 112.5619 Evaluate side-chains 94 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 128 GLN B 730 ASN B 781 GLN B 791 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.087109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.068253 restraints weight = 19538.681| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.16 r_work: 0.2744 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12952 Z= 0.109 Angle : 0.511 10.313 17688 Z= 0.256 Chirality : 0.043 0.166 1892 Planarity : 0.004 0.048 2318 Dihedral : 7.777 91.608 1808 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.75 % Allowed : 6.49 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.21), residues: 1572 helix: 1.30 (0.19), residues: 714 sheet: 1.15 (0.39), residues: 176 loop : -0.25 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 682 TYR 0.010 0.001 TYR B 108 PHE 0.006 0.001 PHE B 125 TRP 0.005 0.001 TRP A 61 HIS 0.007 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00230 (12952) covalent geometry : angle 0.51055 (17688) hydrogen bonds : bond 0.03933 ( 551) hydrogen bonds : angle 4.07421 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.372 Fit side-chains REVERT: A 217 ASN cc_start: 0.8747 (m-40) cc_final: 0.8543 (m-40) REVERT: A 681 ASP cc_start: 0.8316 (m-30) cc_final: 0.8088 (m-30) REVERT: A 721 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7919 (mmt-90) REVERT: A 729 ILE cc_start: 0.8734 (mm) cc_final: 0.8134 (tp) REVERT: B 82 ASP cc_start: 0.8951 (t0) cc_final: 0.8642 (t70) REVERT: B 149 GLU cc_start: 0.7898 (pt0) cc_final: 0.7434 (pm20) REVERT: B 217 ASN cc_start: 0.8688 (m-40) cc_final: 0.8374 (m-40) REVERT: B 514 LYS cc_start: 0.9123 (tttt) cc_final: 0.8745 (ttmt) outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.7564 time to fit residues: 82.1372 Evaluate side-chains 86 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 110 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 139 optimal weight: 0.0770 chunk 60 optimal weight: 6.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS B 740 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.088688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.069901 restraints weight = 19754.667| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.16 r_work: 0.2775 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12952 Z= 0.093 Angle : 0.472 11.028 17688 Z= 0.232 Chirality : 0.042 0.179 1892 Planarity : 0.004 0.045 2318 Dihedral : 7.237 82.113 1808 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.75 % Allowed : 7.24 % Favored : 92.01 % 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 aren not related in a simple way. whole: 1.17 (0.22), residues: 1572 helix: 1.68 (0.19), residues: 724 sheet: 0.94 (0.39), residues: 180 loop : -0.21 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 223 TYR 0.009 0.001 TYR B 480 PHE 0.007 0.001 PHE B 125 TRP 0.006 0.001 TRP A 444 HIS 0.004 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00208 (12952) covalent geometry : angle 0.47220 (17688) hydrogen bonds : bond 0.03148 ( 551) hydrogen bonds : angle 3.69848 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.590 Fit side-chains REVERT: A 681 ASP cc_start: 0.8266 (m-30) cc_final: 0.8042 (m-30) REVERT: A 721 ARG cc_start: 0.8233 (mmt-90) cc_final: 0.7900 (mmt-90) REVERT: A 729 ILE cc_start: 0.8794 (mm) cc_final: 0.8274 (tp) REVERT: B 82 ASP cc_start: 0.8930 (t0) cc_final: 0.8644 (t70) REVERT: B 149 GLU cc_start: 0.7864 (pt0) cc_final: 0.7412 (pm20) REVERT: B 217 ASN cc_start: 0.8650 (m-40) cc_final: 0.8319 (m-40) REVERT: B 514 LYS cc_start: 0.9134 (tttt) cc_final: 0.8780 (ttmt) REVERT: B 516 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8598 (mp0) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 0.7589 time to fit residues: 81.5233 Evaluate side-chains 89 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 135 optimal weight: 0.9980 chunk 139 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.088887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.069892 restraints weight = 19451.418| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.20 r_work: 0.2770 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12952 Z= 0.091 Angle : 0.463 11.400 17688 Z= 0.227 Chirality : 0.041 0.174 1892 Planarity : 0.004 0.042 2318 Dihedral : 7.124 89.343 1806 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.21 % Allowed : 6.86 % Favored : 91.93 % 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 aren not related in a simple way. whole: 1.31 (0.22), residues: 1572 helix: 1.83 (0.19), residues: 724 sheet: 0.94 (0.39), residues: 180 loop : -0.18 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 682 TYR 0.008 0.001 TYR A 480 PHE 0.007 0.001 PHE A 125 TRP 0.006 0.001 TRP B 509 HIS 0.004 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00204 (12952) covalent geometry : angle 0.46307 (17688) hydrogen bonds : bond 0.02923 ( 551) hydrogen bonds : angle 3.59441 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.466 Fit side-chains REVERT: A 681 ASP cc_start: 0.8174 (m-30) cc_final: 0.7951 (m-30) REVERT: A 729 ILE cc_start: 0.8812 (mm) cc_final: 0.8279 (tp) REVERT: B 82 ASP cc_start: 0.8961 (t0) cc_final: 0.8632 (t70) REVERT: B 217 ASN cc_start: 0.8633 (m-40) cc_final: 0.8261 (m-40) REVERT: B 514 LYS cc_start: 0.9135 (tttt) cc_final: 0.8773 (ttmt) REVERT: B 516 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8620 (mp0) outliers start: 16 outliers final: 6 residues processed: 99 average time/residue: 0.6911 time to fit residues: 73.5797 Evaluate side-chains 91 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 791 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.087583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.068567 restraints weight = 19659.635| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.20 r_work: 0.2743 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12952 Z= 0.114 Angle : 0.480 12.341 17688 Z= 0.234 Chirality : 0.042 0.179 1892 Planarity : 0.004 0.040 2318 Dihedral : 7.065 88.282 1802 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.98 % Allowed : 7.62 % Favored : 91.40 % 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 aren not related in a simple way. whole: 1.35 (0.22), residues: 1572 helix: 1.85 (0.19), residues: 724 sheet: 1.08 (0.39), residues: 176 loop : -0.17 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 711 TYR 0.008 0.001 TYR B 108 PHE 0.007 0.001 PHE A 233 TRP 0.005 0.001 TRP B 24 HIS 0.004 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00264 (12952) covalent geometry : angle 0.47964 (17688) hydrogen bonds : bond 0.03122 ( 551) hydrogen bonds : angle 3.60237 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.492 Fit side-chains REVERT: A 681 ASP cc_start: 0.8206 (m-30) cc_final: 0.7955 (m-30) REVERT: A 713 HIS cc_start: 0.8749 (m170) cc_final: 0.8510 (m-70) REVERT: A 729 ILE cc_start: 0.8800 (mm) cc_final: 0.8252 (tp) REVERT: B 82 ASP cc_start: 0.8964 (t0) cc_final: 0.8658 (t70) REVERT: B 217 ASN cc_start: 0.8641 (m-40) cc_final: 0.8246 (m-40) REVERT: B 514 LYS cc_start: 0.9102 (tttt) cc_final: 0.8733 (ttmt) REVERT: B 516 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8604 (mp0) outliers start: 13 outliers final: 5 residues processed: 90 average time/residue: 0.7069 time to fit residues: 68.5744 Evaluate side-chains 85 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 100 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.0040 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.090245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.071327 restraints weight = 19517.973| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.20 r_work: 0.2803 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12952 Z= 0.079 Angle : 0.452 12.092 17688 Z= 0.219 Chirality : 0.041 0.171 1892 Planarity : 0.004 0.040 2318 Dihedral : 6.904 89.530 1802 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.83 % Allowed : 7.84 % Favored : 91.33 % 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 aren not related in a simple way. whole: 1.47 (0.22), residues: 1572 helix: 2.01 (0.20), residues: 712 sheet: 1.02 (0.39), residues: 182 loop : -0.11 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 223 TYR 0.008 0.001 TYR B 480 PHE 0.008 0.001 PHE A 125 TRP 0.005 0.001 TRP B 703 HIS 0.004 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00176 (12952) covalent geometry : angle 0.45170 (17688) hydrogen bonds : bond 0.02580 ( 551) hydrogen bonds : angle 3.45860 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.405 Fit side-chains REVERT: A 713 HIS cc_start: 0.8737 (m170) cc_final: 0.8535 (m-70) REVERT: A 729 ILE cc_start: 0.8801 (mm) cc_final: 0.8272 (tp) REVERT: B 82 ASP cc_start: 0.8978 (t0) cc_final: 0.8650 (t70) REVERT: B 217 ASN cc_start: 0.8540 (m-40) cc_final: 0.8150 (m-40) REVERT: B 514 LYS cc_start: 0.9096 (tttt) cc_final: 0.8739 (ttmt) REVERT: B 515 ARG cc_start: 0.8566 (mtm110) cc_final: 0.8323 (mtm110) REVERT: B 516 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8477 (mp0) outliers start: 11 outliers final: 7 residues processed: 93 average time/residue: 0.6406 time to fit residues: 64.3328 Evaluate side-chains 90 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.066245 restraints weight = 19549.186| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.18 r_work: 0.2696 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12952 Z= 0.175 Angle : 0.531 14.171 17688 Z= 0.259 Chirality : 0.044 0.182 1892 Planarity : 0.004 0.039 2318 Dihedral : 7.233 85.870 1802 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.83 % Allowed : 8.30 % Favored : 90.87 % 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 aren not related in a simple way. whole: 1.27 (0.22), residues: 1572 helix: 1.78 (0.19), residues: 724 sheet: 1.03 (0.40), residues: 176 loop : -0.19 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 711 TYR 0.012 0.001 TYR B 108 PHE 0.013 0.001 PHE B 233 TRP 0.009 0.001 TRP B 794 HIS 0.006 0.001 HIS A 699 Details of bonding type rmsd covalent geometry : bond 0.00417 (12952) covalent geometry : angle 0.53057 (17688) hydrogen bonds : bond 0.03702 ( 551) hydrogen bonds : angle 3.74135 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.311 Fit side-chains REVERT: A 82 ASP cc_start: 0.8939 (t0) cc_final: 0.8650 (t70) REVERT: A 302 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8461 (mppt) REVERT: A 729 ILE cc_start: 0.8834 (mm) cc_final: 0.8193 (tp) REVERT: B 82 ASP cc_start: 0.8985 (t0) cc_final: 0.8662 (t70) REVERT: B 217 ASN cc_start: 0.8759 (m-40) cc_final: 0.8353 (m-40) REVERT: B 514 LYS cc_start: 0.9091 (tttt) cc_final: 0.8752 (ttmt) REVERT: B 516 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8578 (mp0) outliers start: 11 outliers final: 6 residues processed: 91 average time/residue: 0.6352 time to fit residues: 62.3614 Evaluate side-chains 90 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 132 optimal weight: 0.0060 chunk 102 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.087785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.068744 restraints weight = 19359.962| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.19 r_work: 0.2746 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12952 Z= 0.099 Angle : 0.484 14.176 17688 Z= 0.235 Chirality : 0.042 0.176 1892 Planarity : 0.004 0.041 2318 Dihedral : 7.030 85.999 1802 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.68 % Allowed : 8.37 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.22), residues: 1572 helix: 1.86 (0.19), residues: 724 sheet: 1.02 (0.40), residues: 176 loop : -0.19 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 758 TYR 0.009 0.001 TYR B 108 PHE 0.007 0.001 PHE A 125 TRP 0.006 0.001 TRP A 703 HIS 0.004 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00227 (12952) covalent geometry : angle 0.48380 (17688) hydrogen bonds : bond 0.02951 ( 551) hydrogen bonds : angle 3.56341 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.394 Fit side-chains REVERT: A 82 ASP cc_start: 0.8945 (t0) cc_final: 0.8662 (t70) REVERT: A 302 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8456 (mppt) REVERT: A 729 ILE cc_start: 0.8811 (mm) cc_final: 0.8263 (tp) REVERT: B 82 ASP cc_start: 0.8967 (t0) cc_final: 0.8625 (t70) REVERT: B 217 ASN cc_start: 0.8654 (m-40) cc_final: 0.8241 (m-40) REVERT: B 444 TRP cc_start: 0.8914 (t-100) cc_final: 0.8651 (t-100) REVERT: B 514 LYS cc_start: 0.9096 (tttt) cc_final: 0.8736 (ttmt) REVERT: B 515 ARG cc_start: 0.8580 (mtm110) cc_final: 0.8363 (mtm110) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.5912 time to fit residues: 57.8423 Evaluate side-chains 91 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 92 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.086511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.067514 restraints weight = 19605.774| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.19 r_work: 0.2723 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12952 Z= 0.133 Angle : 0.498 14.282 17688 Z= 0.242 Chirality : 0.043 0.177 1892 Planarity : 0.004 0.040 2318 Dihedral : 7.071 84.208 1802 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 0.53 % Allowed : 8.45 % Favored : 91.03 % 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 aren not related in a simple way. whole: 1.31 (0.22), residues: 1572 helix: 1.83 (0.19), residues: 724 sheet: 1.01 (0.40), residues: 176 loop : -0.19 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 711 TYR 0.010 0.001 TYR B 108 PHE 0.010 0.001 PHE B 233 TRP 0.006 0.001 TRP A 703 HIS 0.004 0.001 HIS A 699 Details of bonding type rmsd covalent geometry : bond 0.00312 (12952) covalent geometry : angle 0.49765 (17688) hydrogen bonds : bond 0.03232 ( 551) hydrogen bonds : angle 3.60527 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.299 Fit side-chains REVERT: A 82 ASP cc_start: 0.8945 (t0) cc_final: 0.8659 (t70) REVERT: A 302 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8463 (mppt) REVERT: A 729 ILE cc_start: 0.8825 (mm) cc_final: 0.8273 (tp) REVERT: B 82 ASP cc_start: 0.8988 (t0) cc_final: 0.8641 (t70) REVERT: B 217 ASN cc_start: 0.8702 (m-40) cc_final: 0.8294 (m-40) REVERT: B 444 TRP cc_start: 0.8931 (t-100) cc_final: 0.8708 (t-100) REVERT: B 514 LYS cc_start: 0.9110 (tttt) cc_final: 0.8755 (ttmt) REVERT: B 516 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8469 (mp0) outliers start: 7 outliers final: 6 residues processed: 89 average time/residue: 0.6751 time to fit residues: 64.8220 Evaluate side-chains 93 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 118 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 13 optimal weight: 0.0030 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.069028 restraints weight = 19608.229| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.20 r_work: 0.2754 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12952 Z= 0.095 Angle : 0.479 14.006 17688 Z= 0.232 Chirality : 0.042 0.165 1892 Planarity : 0.004 0.040 2318 Dihedral : 6.999 85.607 1802 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.86 % Favored : 97.01 % Rotamer: Outliers : 0.53 % Allowed : 8.60 % Favored : 90.87 % 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 aren not related in a simple way. whole: 1.39 (0.22), residues: 1572 helix: 1.96 (0.20), residues: 712 sheet: 0.86 (0.39), residues: 182 loop : -0.13 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 758 TYR 0.008 0.001 TYR B 108 PHE 0.007 0.001 PHE A 125 TRP 0.009 0.001 TRP A 703 HIS 0.004 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00215 (12952) covalent geometry : angle 0.47903 (17688) hydrogen bonds : bond 0.02871 ( 551) hydrogen bonds : angle 3.53165 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.495 Fit side-chains REVERT: A 82 ASP cc_start: 0.8950 (t0) cc_final: 0.8663 (t70) REVERT: A 302 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8466 (mppt) REVERT: B 82 ASP cc_start: 0.8967 (t0) cc_final: 0.8626 (t70) REVERT: B 217 ASN cc_start: 0.8653 (m-40) cc_final: 0.8242 (m-40) REVERT: B 444 TRP cc_start: 0.8915 (t-100) cc_final: 0.8665 (t-100) REVERT: B 514 LYS cc_start: 0.9097 (tttt) cc_final: 0.8748 (ttmt) outliers start: 7 outliers final: 8 residues processed: 88 average time/residue: 0.6286 time to fit residues: 59.6810 Evaluate side-chains 92 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 129 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.088310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.069334 restraints weight = 19434.057| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.19 r_work: 0.2759 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12952 Z= 0.093 Angle : 0.475 13.832 17688 Z= 0.230 Chirality : 0.042 0.163 1892 Planarity : 0.004 0.040 2318 Dihedral : 6.966 84.883 1802 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 0.53 % Allowed : 8.67 % Favored : 90.80 % 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 aren not related in a simple way. whole: 1.42 (0.22), residues: 1572 helix: 1.98 (0.20), residues: 712 sheet: 0.87 (0.39), residues: 182 loop : -0.12 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 711 TYR 0.008 0.001 TYR B 108 PHE 0.007 0.001 PHE A 125 TRP 0.010 0.001 TRP A 703 HIS 0.004 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00210 (12952) covalent geometry : angle 0.47532 (17688) hydrogen bonds : bond 0.02833 ( 551) hydrogen bonds : angle 3.51051 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4347.64 seconds wall clock time: 74 minutes 48.49 seconds (4488.49 seconds total)