Starting phenix.real_space_refine on Tue Aug 26 08:19:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g04_50910/08_2025/9g04_50910.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g04_50910/08_2025/9g04_50910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g04_50910/08_2025/9g04_50910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g04_50910/08_2025/9g04_50910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g04_50910/08_2025/9g04_50910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g04_50910/08_2025/9g04_50910.map" } resolution = 2.7 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= 0.009 sd= 0.233 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 S 72 5.16 5 C 10842 2.51 5 N 2760 2.21 5 O 3225 1.98 5 H 16839 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 33738 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 16755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 16755 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 28, 'TRANS': 976} Chain breaks: 2 Chain: "B" Number of atoms: 16983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 16983 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 28, 'TRANS': 989} Chain breaks: 2 Time building chain proxies: 6.87, per 1000 atoms: 0.20 Number of scatterers: 33738 At special positions: 0 Unit cell: (119.124, 143.452, 114.09, 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 72 16.00 O 3225 8.00 N 2760 7.00 C 10842 6.00 H 16839 1.00 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: 3.17 Conformation dependent library (CDL) restraints added in 904.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 20 sheets defined 50.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.548A pdb=" N CYS A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 76 through 93 removed outlier: 3.713A pdb=" N ARG A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 215 through 229 removed outlier: 4.315A pdb=" N ILE A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 257 Processing helix chain 'A' and resid 259 through 279 removed outlier: 3.915A pdb=" N GLU A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 299 Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.565A pdb=" N ASP A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 400 through 418 Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 490 through 506 removed outlier: 3.593A pdb=" N PHE A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 529 removed outlier: 4.166A pdb=" N VAL A 528 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.506A pdb=" N SER A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 removed outlier: 4.305A pdb=" N VAL A 617 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 669 removed outlier: 3.555A pdb=" N ILE A 666 " --> pdb=" O ASN A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 701 Processing helix chain 'A' and resid 784 through 789 Processing helix chain 'A' and resid 789 through 801 removed outlier: 3.640A pdb=" N GLU A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 847 Proline residue: A 835 - end of helix Processing helix chain 'A' and resid 869 through 895 removed outlier: 4.119A pdb=" N ILE A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 876 " --> pdb=" O ASN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 917 Processing helix chain 'A' and resid 919 through 927 removed outlier: 3.825A pdb=" N VAL A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A 925 " --> pdb=" O ALA A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 952 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 963 through 974 Processing helix chain 'A' and resid 976 through 990 removed outlier: 3.636A pdb=" N ILE A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1013 removed outlier: 4.051A pdb=" N ILE A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1033 Processing helix chain 'A' and resid 1034 through 1036 No H-bonds generated for 'chain 'A' and resid 1034 through 1036' Processing helix chain 'B' and resid 20 through 27 Processing helix chain 'B' and resid 38 through 45 removed outlier: 3.565A pdb=" N CYS B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 57 through 69 Processing helix chain 'B' and resid 76 through 93 removed outlier: 3.643A pdb=" N SER B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 144 removed outlier: 3.528A pdb=" N ASN B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.607A pdb=" N ILE B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 229 removed outlier: 4.052A pdb=" N ILE B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 259 through 279 removed outlier: 3.511A pdb=" N ASP B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.046A pdb=" N SER B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.645A pdb=" N GLN B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 400 through 418 Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.654A pdb=" N ASN B 459 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 490 through 506 removed outlier: 3.579A pdb=" N PHE B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 removed outlier: 4.089A pdb=" N VAL B 528 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.600A pdb=" N ARG B 552 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 587 through 591 removed outlier: 3.503A pdb=" N THR B 590 " --> pdb=" O ASN B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.552A pdb=" N SER B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 603 " --> pdb=" O ASN B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 618 removed outlier: 4.343A pdb=" N VAL B 617 " --> pdb=" O VAL B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 669 Processing helix chain 'B' and resid 687 through 701 Processing helix chain 'B' and resid 779 through 781 No H-bonds generated for 'chain 'B' and resid 779 through 781' Processing helix chain 'B' and resid 782 through 789 Processing helix chain 'B' and resid 789 through 801 Processing helix chain 'B' and resid 826 through 847 Proline residue: B 835 - end of helix Processing helix chain 'B' and resid 870 through 894 removed outlier: 3.549A pdb=" N LYS B 876 " --> pdb=" O ASN B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 917 Processing helix chain 'B' and resid 919 through 928 removed outlier: 4.084A pdb=" N VAL B 924 " --> pdb=" O TYR B 920 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU B 925 " --> pdb=" O ALA B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 942 removed outlier: 3.549A pdb=" N LYS B 941 " --> pdb=" O GLU B 938 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 942 " --> pdb=" O ASP B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 951 Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 963 through 974 Processing helix chain 'B' and resid 976 through 990 removed outlier: 3.624A pdb=" N ILE B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1013 removed outlier: 4.022A pdb=" N ILE B 999 " --> pdb=" O THR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1025 Processing helix chain 'B' and resid 1026 through 1033 Processing helix chain 'B' and resid 1034 through 1036 No H-bonds generated for 'chain 'B' and resid 1034 through 1036' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 12.578A pdb=" N SER A 445 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N GLY A 473 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N GLU A 447 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N ASN A 471 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN A 449 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N VAL A 633 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR A 466 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET A 635 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE A 468 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 627 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 116 removed outlier: 6.810A pdb=" N VAL A 113 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER A 115 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ARG A 314 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N PHE A 105 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS A 316 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 127 Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 365 removed outlier: 13.638A pdb=" N PHE A 567 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N LEU A 580 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA A 569 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 512 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR A 581 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS A 514 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N TYR A 537 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A 513 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N MET A 539 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU A 515 " --> pdb=" O MET A 539 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU A 541 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER A 517 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 624 Processing sheet with id=AA8, first strand: chain 'A' and resid 720 through 722 removed outlier: 4.179A pdb=" N VAL A 720 " --> pdb=" O TYR A 727 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AB1, first strand: chain 'A' and resid 806 through 813 removed outlier: 3.917A pdb=" N LYS A 806 " --> pdb=" O ASN A 824 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 5 through 7 removed outlier: 12.623A pdb=" N SER B 445 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N GLY B 473 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N GLU B 447 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N ASN B 471 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN B 449 " --> pdb=" O GLY B 469 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL B 633 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR B 466 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N MET B 635 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE B 468 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 627 " --> pdb=" O ILE B 634 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 113 through 116 removed outlier: 6.884A pdb=" N VAL B 113 " --> pdb=" O LYS B 316 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER B 115 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N ARG B 314 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N PHE B 105 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS B 316 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 318 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 127 Processing sheet with id=AB5, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB6, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB7, first strand: chain 'B' and resid 364 through 365 removed outlier: 13.603A pdb=" N PHE B 567 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N LEU B 580 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA B 569 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 512 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR B 581 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS B 514 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N TYR B 537 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 513 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N MET B 539 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU B 515 " --> pdb=" O MET B 539 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 541 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER B 517 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 623 through 624 Processing sheet with id=AB9, first strand: chain 'B' and resid 720 through 722 removed outlier: 4.111A pdb=" N VAL B 720 " --> pdb=" O TYR B 727 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 764 through 765 Processing sheet with id=AC2, first strand: chain 'B' and resid 806 through 813 removed outlier: 3.922A pdb=" N LYS B 806 " --> pdb=" O ASN B 824 " (cutoff:3.500A) 826 hydrogen bonds defined for protein. 2316 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: 9.23 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16819 1.03 - 1.23: 71 1.23 - 1.42: 7220 1.42 - 1.62: 9831 1.62 - 1.81: 124 Bond restraints: 34065 Sorted by residual: bond pdb=" N ARG B 2 " pdb=" CA ARG B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ARG A 2 " pdb=" CA ARG A 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.67e+00 bond pdb=" N ARG B 2 " pdb=" H ARG B 2 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N ARG A 2 " pdb=" H ARG A 2 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" CG PRO A 815 " pdb=" CD PRO A 815 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.73e+00 ... (remaining 34060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.08: 61596 7.08 - 14.16: 4 14.16 - 21.24: 2 21.24 - 28.32: 9 28.32 - 35.40: 6 Bond angle restraints: 61617 Sorted by residual: angle pdb=" C GLU B 42 " pdb=" CA GLU B 42 " pdb=" HA GLU B 42 " ideal model delta sigma weight residual 109.00 73.60 35.40 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C ILE B 683 " pdb=" CA ILE B 683 " pdb=" HA ILE B 683 " ideal model delta sigma weight residual 109.00 73.85 35.15 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CB ILE B 683 " pdb=" CA ILE B 683 " pdb=" HA ILE B 683 " ideal model delta sigma weight residual 109.00 74.64 34.36 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N GLU B 42 " pdb=" CA GLU B 42 " pdb=" HA GLU B 42 " ideal model delta sigma weight residual 110.00 75.82 34.18 3.00e+00 1.11e-01 1.30e+02 angle pdb=" N ILE B 683 " pdb=" CA ILE B 683 " pdb=" HA ILE B 683 " ideal model delta sigma weight residual 110.00 76.46 33.54 3.00e+00 1.11e-01 1.25e+02 ... (remaining 61612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14768 17.91 - 35.82: 761 35.82 - 53.73: 224 53.73 - 71.64: 139 71.64 - 89.55: 24 Dihedral angle restraints: 15916 sinusoidal: 8690 harmonic: 7226 Sorted by residual: dihedral pdb=" CA ARG A 384 " pdb=" C ARG A 384 " pdb=" N PRO A 385 " pdb=" CA PRO A 385 " ideal model delta harmonic sigma weight residual -180.00 -149.21 -30.79 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA ASP A 814 " pdb=" C ASP A 814 " pdb=" N PRO A 815 " pdb=" CA PRO A 815 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA VAL B 813 " pdb=" C VAL B 813 " pdb=" N ASP B 814 " pdb=" CA ASP B 814 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 15913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.322: 2504 0.322 - 0.645: 1 0.645 - 0.967: 0 0.967 - 1.290: 0 1.290 - 1.612: 3 Chirality restraints: 2508 Sorted by residual: chirality pdb=" CB ILE A 213 " pdb=" CA ILE A 213 " pdb=" CG1 ILE A 213 " pdb=" CG2 ILE A 213 " both_signs ideal model delta sigma weight residual False 2.64 1.03 1.61 2.00e-01 2.50e+01 6.50e+01 chirality pdb=" CB ILE B 213 " pdb=" CA ILE B 213 " pdb=" CG1 ILE B 213 " pdb=" CG2 ILE B 213 " both_signs ideal model delta sigma weight residual False 2.64 1.12 1.53 2.00e-01 2.50e+01 5.84e+01 chirality pdb=" CB VAL A 281 " pdb=" CA VAL A 281 " pdb=" CG1 VAL A 281 " pdb=" CG2 VAL A 281 " both_signs ideal model delta sigma weight residual False -2.63 -1.27 -1.36 2.00e-01 2.50e+01 4.64e+01 ... (remaining 2505 not shown) Planarity restraints: 4933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 814 " -0.117 5.00e-02 4.00e+02 1.76e-01 4.97e+01 pdb=" N PRO A 815 " 0.305 5.00e-02 4.00e+02 pdb=" CA PRO A 815 " -0.105 5.00e-02 4.00e+02 pdb=" CD PRO A 815 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 552 " 0.059 9.50e-02 1.11e+02 4.19e-02 3.10e+01 pdb=" NE ARG B 552 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 552 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 552 " -0.066 2.00e-02 2.50e+03 pdb=" NH2 ARG B 552 " 0.040 2.00e-02 2.50e+03 pdb="HH11 ARG B 552 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 552 " 0.066 2.00e-02 2.50e+03 pdb="HH21 ARG B 552 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 552 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1023 " -0.223 9.50e-02 1.11e+02 7.95e-02 2.35e+01 pdb=" NE ARG A1023 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A1023 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A1023 " 0.048 2.00e-02 2.50e+03 pdb=" NH2 ARG A1023 " 0.036 2.00e-02 2.50e+03 pdb="HH11 ARG A1023 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A1023 " -0.037 2.00e-02 2.50e+03 pdb="HH21 ARG A1023 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1023 " -0.035 2.00e-02 2.50e+03 ... (remaining 4930 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1031 2.15 - 2.76: 63447 2.76 - 3.38: 90403 3.38 - 3.99: 117311 3.99 - 4.60: 187437 Nonbonded interactions: 459629 Sorted by model distance: nonbonded pdb=" O SER B 212 " pdb=" H GLU B 214 " model vdw 1.538 2.450 nonbonded pdb=" OE1 GLU A 51 " pdb=" H GLY A 282 " model vdw 1.543 2.450 nonbonded pdb=" OE1 GLU B 51 " pdb=" H GLY B 282 " model vdw 1.567 2.450 nonbonded pdb=" O LYS A 75 " pdb=" H ASP A 77 " model vdw 1.569 2.450 nonbonded pdb=" H ILE B 683 " pdb=" HA ILE B 683 " model vdw 1.573 1.816 ... (remaining 459624 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 2 through 1024 or (resid 1025 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name H or name H \ A )) or resid 1026 through 1037)) selection = (chain 'B' and (resid 2 through 927 or resid 947 through 1037)) } 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.430 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 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 : 0.005 0.064 17226 Z= 0.229 Angle : 0.775 19.088 23179 Z= 0.454 Chirality : 0.070 1.612 2508 Planarity : 0.010 0.176 2972 Dihedral : 13.248 89.553 6664 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.94 % Allowed : 3.58 % Favored : 95.47 % Rotamer: Outliers : 0.58 % Allowed : 3.30 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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 (0.16), residues: 2011 helix: -1.10 (0.14), residues: 918 sheet: 0.27 (0.31), residues: 264 loop : -0.92 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG B 404 TYR 0.021 0.004 TYR B 712 PHE 0.019 0.003 PHE B 464 TRP 0.015 0.003 TRP A 131 HIS 0.016 0.004 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00547 (17226) covalent geometry : angle 0.77515 (23179) hydrogen bonds : bond 0.22557 ( 814) hydrogen bonds : angle 6.98801 ( 2316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 391 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.8257 (tt0) cc_final: 0.7932 (tt0) REVERT: A 221 ASN cc_start: 0.8438 (t0) cc_final: 0.8210 (m110) REVERT: A 224 LYS cc_start: 0.8528 (mttt) cc_final: 0.7797 (ttpp) REVERT: A 492 LYS cc_start: 0.8566 (mttt) cc_final: 0.8259 (mmpt) REVERT: A 616 ASP cc_start: 0.8424 (t70) cc_final: 0.8193 (t0) REVERT: A 700 CYS cc_start: 0.6096 (t) cc_final: 0.5884 (t) REVERT: B 42 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7966 (tm-30) REVERT: B 111 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7188 (pt0) REVERT: B 122 LYS cc_start: 0.8562 (mmtt) cc_final: 0.7979 (tttm) REVERT: B 221 ASN cc_start: 0.8290 (t0) cc_final: 0.7985 (t0) REVERT: B 436 LYS cc_start: 0.8666 (tttt) cc_final: 0.8433 (ttmm) REVERT: B 492 LYS cc_start: 0.8557 (mttt) cc_final: 0.8141 (mmpt) REVERT: B 761 LYS cc_start: 0.8716 (ptmt) cc_final: 0.8300 (tttt) REVERT: B 922 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7168 (mmmm) REVERT: B 977 ARG cc_start: 0.7852 (ttt90) cc_final: 0.7419 (ttp80) outliers start: 11 outliers final: 1 residues processed: 398 average time/residue: 1.7742 time to fit residues: 772.9163 Evaluate side-chains 218 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain B residue 111 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.0470 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 686 ASN B 46 ASN B 251 ASN B 525 ASN B 686 ASN B 954 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096037 restraints weight = 62552.388| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.36 r_work: 0.3033 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17226 Z= 0.166 Angle : 0.672 15.991 23179 Z= 0.365 Chirality : 0.070 1.719 2508 Planarity : 0.006 0.167 2972 Dihedral : 5.785 56.104 2240 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.53 % Favored : 96.07 % Rotamer: Outliers : 2.20 % Allowed : 10.17 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.05 % 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: -0.15 (0.17), residues: 2011 helix: 0.70 (0.17), residues: 914 sheet: 0.10 (0.29), residues: 273 loop : -1.02 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1010 TYR 0.015 0.002 TYR B 78 PHE 0.017 0.002 PHE A 105 TRP 0.016 0.002 TRP A 131 HIS 0.009 0.002 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00384 (17226) covalent geometry : angle 0.67170 (23179) hydrogen bonds : bond 0.06739 ( 814) hydrogen bonds : angle 5.16416 ( 2316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.8261 (t0) cc_final: 0.7955 (m110) REVERT: A 224 LYS cc_start: 0.8047 (mttt) cc_final: 0.7168 (ttpp) REVERT: A 228 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: A 268 GLU cc_start: 0.8007 (tp30) cc_final: 0.7645 (tp30) REVERT: A 271 GLU cc_start: 0.8120 (tp30) cc_final: 0.7689 (tp30) REVERT: A 436 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8556 (tppt) REVERT: A 492 LYS cc_start: 0.8469 (mttt) cc_final: 0.8065 (mmpt) REVERT: A 616 ASP cc_start: 0.8731 (t70) cc_final: 0.8409 (t0) REVERT: A 688 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7324 (t70) REVERT: A 894 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: A 922 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7775 (mmtm) REVERT: B 25 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: B 111 GLU cc_start: 0.7530 (pm20) cc_final: 0.7063 (pm20) REVERT: B 122 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7773 (tttm) REVERT: B 196 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8106 (p0) REVERT: B 221 ASN cc_start: 0.7737 (t0) cc_final: 0.7520 (t0) REVERT: B 228 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: B 436 LYS cc_start: 0.8703 (tttt) cc_final: 0.8345 (ttmm) REVERT: B 492 LYS cc_start: 0.8230 (mttt) cc_final: 0.7759 (mmpt) REVERT: B 696 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7166 (mm) REVERT: B 761 LYS cc_start: 0.8566 (ptmt) cc_final: 0.8046 (tttp) REVERT: B 770 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8174 (mt-10) REVERT: B 922 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7676 (mmmm) REVERT: B 977 ARG cc_start: 0.7613 (ttt90) cc_final: 0.7164 (ttp80) outliers start: 42 outliers final: 12 residues processed: 254 average time/residue: 1.6830 time to fit residues: 471.7640 Evaluate side-chains 223 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 958 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 108 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 152 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 418 ASN B 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094667 restraints weight = 62591.118| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.34 r_work: 0.3016 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17226 Z= 0.166 Angle : 0.612 15.345 23179 Z= 0.331 Chirality : 0.070 1.731 2508 Planarity : 0.006 0.164 2972 Dihedral : 5.370 45.072 2237 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.58 % Favored : 96.02 % Rotamer: Outliers : 1.94 % Allowed : 10.85 % Favored : 87.21 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.05 % 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: 0.07 (0.18), residues: 2011 helix: 1.23 (0.17), residues: 914 sheet: -0.06 (0.29), residues: 281 loop : -1.28 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1010 TYR 0.014 0.002 TYR B 23 PHE 0.014 0.002 PHE B 105 TRP 0.014 0.002 TRP A 131 HIS 0.006 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00399 (17226) covalent geometry : angle 0.61210 (23179) hydrogen bonds : bond 0.06079 ( 814) hydrogen bonds : angle 4.91621 ( 2316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.7877 (mp0) cc_final: 0.7645 (mp0) REVERT: A 221 ASN cc_start: 0.8024 (t0) cc_final: 0.7810 (m110) REVERT: A 224 LYS cc_start: 0.7964 (mttt) cc_final: 0.7037 (ttpp) REVERT: A 228 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: A 268 GLU cc_start: 0.8155 (tp30) cc_final: 0.7785 (tp30) REVERT: A 271 GLU cc_start: 0.8111 (tp30) cc_final: 0.7731 (tp30) REVERT: A 492 LYS cc_start: 0.8496 (mttt) cc_final: 0.8068 (mmpt) REVERT: A 616 ASP cc_start: 0.8732 (t70) cc_final: 0.8403 (t0) REVERT: A 656 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: A 660 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: A 688 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7258 (t70) REVERT: A 715 GLU cc_start: 0.8094 (pt0) cc_final: 0.7870 (pt0) REVERT: A 894 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: A 912 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7061 (t80) REVERT: B 111 GLU cc_start: 0.7537 (pm20) cc_final: 0.7091 (pm20) REVERT: B 122 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7805 (tttm) REVERT: B 196 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8235 (p0) REVERT: B 225 GLN cc_start: 0.8100 (mm110) cc_final: 0.7806 (mm-40) REVERT: B 228 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: B 436 LYS cc_start: 0.8685 (tttt) cc_final: 0.8330 (ttmm) REVERT: B 492 LYS cc_start: 0.8232 (mttt) cc_final: 0.7801 (mmpt) REVERT: B 585 MET cc_start: 0.9342 (mmt) cc_final: 0.8987 (mmt) REVERT: B 655 ASN cc_start: 0.7423 (t160) cc_final: 0.6703 (m-40) REVERT: B 688 ASP cc_start: 0.7634 (p0) cc_final: 0.7366 (t70) REVERT: B 761 LYS cc_start: 0.8567 (ptmt) cc_final: 0.8077 (tttp) REVERT: B 770 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 922 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7613 (mmmt) outliers start: 37 outliers final: 17 residues processed: 238 average time/residue: 1.7016 time to fit residues: 446.7329 Evaluate side-chains 219 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 958 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 132 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 170 optimal weight: 0.3980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 ASN B 251 ASN B 418 ASN B 655 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094527 restraints weight = 62550.214| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.34 r_work: 0.3017 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17226 Z= 0.157 Angle : 0.588 14.564 23179 Z= 0.316 Chirality : 0.068 1.689 2508 Planarity : 0.006 0.160 2972 Dihedral : 5.234 43.161 2237 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.78 % Favored : 95.82 % Rotamer: Outliers : 2.05 % Allowed : 11.90 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.05 % 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: 0.15 (0.18), residues: 2011 helix: 1.47 (0.17), residues: 911 sheet: -0.29 (0.29), residues: 284 loop : -1.36 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.013 0.001 TYR B 23 PHE 0.012 0.001 PHE A 105 TRP 0.011 0.001 TRP B 131 HIS 0.009 0.002 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00380 (17226) covalent geometry : angle 0.58818 (23179) hydrogen bonds : bond 0.05525 ( 814) hydrogen bonds : angle 4.80069 ( 2316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.8019 (t0) cc_final: 0.7766 (m110) REVERT: A 224 LYS cc_start: 0.7921 (mttt) cc_final: 0.7146 (tmtp) REVERT: A 228 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: A 268 GLU cc_start: 0.8180 (tp30) cc_final: 0.7804 (tp30) REVERT: A 271 GLU cc_start: 0.8128 (tp30) cc_final: 0.7733 (tp30) REVERT: A 492 LYS cc_start: 0.8487 (mttt) cc_final: 0.8061 (mmpt) REVERT: A 616 ASP cc_start: 0.8745 (t70) cc_final: 0.8409 (t0) REVERT: A 656 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 715 GLU cc_start: 0.8127 (pt0) cc_final: 0.7896 (pt0) REVERT: A 894 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: A 912 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.7027 (t80) REVERT: A 958 GLU cc_start: 0.7821 (tp30) cc_final: 0.7574 (tt0) REVERT: B 111 GLU cc_start: 0.7532 (pm20) cc_final: 0.7057 (pm20) REVERT: B 122 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7743 (tttm) REVERT: B 196 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8313 (p0) REVERT: B 225 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7812 (mm-40) REVERT: B 228 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: B 264 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7622 (t0) REVERT: B 436 LYS cc_start: 0.8679 (tttt) cc_final: 0.8332 (ttmm) REVERT: B 492 LYS cc_start: 0.8197 (mttt) cc_final: 0.7809 (mmpt) REVERT: B 524 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7681 (mtm-85) REVERT: B 585 MET cc_start: 0.9348 (mmt) cc_final: 0.9012 (mmt) REVERT: B 655 ASN cc_start: 0.7175 (t0) cc_final: 0.6779 (m110) REVERT: B 761 LYS cc_start: 0.8548 (ptmt) cc_final: 0.8040 (tptt) REVERT: B 770 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 869 GLU cc_start: 0.7763 (mp0) cc_final: 0.7428 (mp0) REVERT: B 922 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7628 (mmmt) outliers start: 39 outliers final: 19 residues processed: 232 average time/residue: 1.7613 time to fit residues: 449.9477 Evaluate side-chains 217 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 958 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 33 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 171 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095043 restraints weight = 62700.753| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.33 r_work: 0.2976 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17226 Z= 0.136 Angle : 0.565 14.581 23179 Z= 0.303 Chirality : 0.068 1.689 2508 Planarity : 0.005 0.156 2972 Dihedral : 5.131 42.320 2237 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.93 % Favored : 95.77 % Rotamer: Outliers : 2.10 % Allowed : 12.01 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.05 % 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 (0.18), residues: 2011 helix: 1.64 (0.17), residues: 916 sheet: -0.37 (0.28), residues: 284 loop : -1.41 (0.19), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 977 TYR 0.014 0.001 TYR B 23 PHE 0.011 0.001 PHE B 105 TRP 0.011 0.001 TRP B 131 HIS 0.005 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00325 (17226) covalent geometry : angle 0.56469 (23179) hydrogen bonds : bond 0.05120 ( 814) hydrogen bonds : angle 4.73955 ( 2316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7891 (t0) cc_final: 0.7616 (m110) REVERT: A 224 LYS cc_start: 0.7858 (mttt) cc_final: 0.7057 (tmtp) REVERT: A 228 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 268 GLU cc_start: 0.8211 (tp30) cc_final: 0.7849 (tp30) REVERT: A 271 GLU cc_start: 0.8114 (tp30) cc_final: 0.7729 (tp30) REVERT: A 492 LYS cc_start: 0.8466 (mttt) cc_final: 0.8043 (mmpt) REVERT: A 616 ASP cc_start: 0.8729 (t70) cc_final: 0.8395 (t0) REVERT: A 656 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: A 688 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7260 (t70) REVERT: A 715 GLU cc_start: 0.8199 (pt0) cc_final: 0.7951 (pt0) REVERT: A 894 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: A 912 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.7128 (t80) REVERT: A 958 GLU cc_start: 0.7796 (tp30) cc_final: 0.7541 (tt0) REVERT: B 111 GLU cc_start: 0.7500 (pm20) cc_final: 0.7074 (pm20) REVERT: B 122 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7700 (tttm) REVERT: B 225 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7770 (mm-40) REVERT: B 228 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: B 264 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7651 (t0) REVERT: B 314 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7715 (ttp-110) REVERT: B 409 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: B 436 LYS cc_start: 0.8660 (tttt) cc_final: 0.8305 (ttmm) REVERT: B 492 LYS cc_start: 0.8144 (mttt) cc_final: 0.7755 (mmpt) REVERT: B 585 MET cc_start: 0.9349 (mmt) cc_final: 0.9020 (mmt) REVERT: B 655 ASN cc_start: 0.6931 (t0) cc_final: 0.6600 (m110) REVERT: B 761 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8024 (tptt) REVERT: B 869 GLU cc_start: 0.7814 (mp0) cc_final: 0.7486 (mp0) REVERT: B 922 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7639 (mmmt) REVERT: B 1016 ARG cc_start: 0.7401 (mtp85) cc_final: 0.6979 (mmt-90) outliers start: 40 outliers final: 20 residues processed: 232 average time/residue: 1.6779 time to fit residues: 428.4321 Evaluate side-chains 225 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 958 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 ASN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092929 restraints weight = 62723.724| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.33 r_work: 0.2950 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17226 Z= 0.189 Angle : 0.601 14.649 23179 Z= 0.323 Chirality : 0.068 1.686 2508 Planarity : 0.006 0.156 2972 Dihedral : 5.228 42.208 2237 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.13 % Favored : 95.57 % Rotamer: Outliers : 2.31 % Allowed : 12.64 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.05 % 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: 0.12 (0.18), residues: 2011 helix: 1.57 (0.17), residues: 912 sheet: -0.38 (0.28), residues: 284 loop : -1.51 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 389 TYR 0.019 0.002 TYR A 697 PHE 0.013 0.002 PHE B 808 TRP 0.010 0.002 TRP B 131 HIS 0.007 0.002 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00466 (17226) covalent geometry : angle 0.60126 (23179) hydrogen bonds : bond 0.05857 ( 814) hydrogen bonds : angle 4.79522 ( 2316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.8047 (t0) cc_final: 0.7778 (m110) REVERT: A 224 LYS cc_start: 0.7952 (mttt) cc_final: 0.7115 (tmtp) REVERT: A 228 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: A 268 GLU cc_start: 0.8210 (tp30) cc_final: 0.7856 (tp30) REVERT: A 271 GLU cc_start: 0.8144 (tp30) cc_final: 0.7757 (tp30) REVERT: A 492 LYS cc_start: 0.8499 (mttt) cc_final: 0.8084 (mmpt) REVERT: A 616 ASP cc_start: 0.8749 (t70) cc_final: 0.8405 (t0) REVERT: A 688 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7268 (t70) REVERT: A 715 GLU cc_start: 0.8304 (pt0) cc_final: 0.8072 (pt0) REVERT: A 894 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: A 912 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.7083 (t80) REVERT: A 958 GLU cc_start: 0.7785 (tp30) cc_final: 0.7568 (tt0) REVERT: B 25 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: B 111 GLU cc_start: 0.7527 (pm20) cc_final: 0.7074 (pm20) REVERT: B 122 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7764 (tttm) REVERT: B 225 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7833 (mm-40) REVERT: B 228 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: B 264 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7611 (t0) REVERT: B 302 LYS cc_start: 0.7851 (mmpt) cc_final: 0.7625 (mppt) REVERT: B 314 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7787 (ttp-110) REVERT: B 436 LYS cc_start: 0.8710 (tttt) cc_final: 0.8354 (ttmm) REVERT: B 493 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7747 (mptt) REVERT: B 585 MET cc_start: 0.9357 (mmt) cc_final: 0.9021 (mmt) REVERT: B 655 ASN cc_start: 0.6942 (t0) cc_final: 0.6654 (m110) REVERT: B 761 LYS cc_start: 0.8588 (ptmt) cc_final: 0.8100 (tptt) REVERT: B 869 GLU cc_start: 0.7923 (mp0) cc_final: 0.7609 (mp0) REVERT: B 922 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7812 (mmmt) outliers start: 44 outliers final: 21 residues processed: 234 average time/residue: 1.5881 time to fit residues: 409.6511 Evaluate side-chains 223 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 958 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN B 251 ASN B 589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093525 restraints weight = 62680.767| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.34 r_work: 0.2955 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17226 Z= 0.160 Angle : 0.581 14.643 23179 Z= 0.310 Chirality : 0.068 1.683 2508 Planarity : 0.006 0.153 2972 Dihedral : 5.140 42.088 2237 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.93 % Favored : 95.77 % Rotamer: Outliers : 2.05 % Allowed : 13.37 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.05 % 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: 0.11 (0.18), residues: 2011 helix: 1.62 (0.17), residues: 918 sheet: -0.41 (0.28), residues: 283 loop : -1.61 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.013 0.001 TYR A 144 PHE 0.012 0.001 PHE B 105 TRP 0.009 0.001 TRP B 131 HIS 0.005 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00390 (17226) covalent geometry : angle 0.58063 (23179) hydrogen bonds : bond 0.05347 ( 814) hydrogen bonds : angle 4.74867 ( 2316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7996 (t0) cc_final: 0.7707 (m110) REVERT: A 224 LYS cc_start: 0.7927 (mttt) cc_final: 0.7087 (tmtp) REVERT: A 228 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: A 268 GLU cc_start: 0.8228 (tp30) cc_final: 0.7877 (tp30) REVERT: A 271 GLU cc_start: 0.8128 (tp30) cc_final: 0.7691 (tp30) REVERT: A 492 LYS cc_start: 0.8490 (mttt) cc_final: 0.8062 (mmpt) REVERT: A 616 ASP cc_start: 0.8746 (t70) cc_final: 0.8405 (t0) REVERT: A 688 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7231 (t70) REVERT: A 715 GLU cc_start: 0.8326 (pt0) cc_final: 0.8087 (pt0) REVERT: A 894 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: A 912 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7086 (t80) REVERT: A 958 GLU cc_start: 0.7743 (tp30) cc_final: 0.7516 (tt0) REVERT: B 25 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: B 111 GLU cc_start: 0.7516 (pm20) cc_final: 0.7097 (pm20) REVERT: B 122 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7715 (tttm) REVERT: B 225 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7821 (mm-40) REVERT: B 228 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: B 264 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7668 (t0) REVERT: B 302 LYS cc_start: 0.7827 (mmpt) cc_final: 0.7583 (mppt) REVERT: B 314 ARG cc_start: 0.8072 (ttp-170) cc_final: 0.7775 (ttp-110) REVERT: B 436 LYS cc_start: 0.8685 (tttt) cc_final: 0.8323 (ttmm) REVERT: B 493 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7689 (mptt) REVERT: B 585 MET cc_start: 0.9339 (mmt) cc_final: 0.9045 (mmt) REVERT: B 655 ASN cc_start: 0.6709 (t0) cc_final: 0.6491 (m110) REVERT: B 761 LYS cc_start: 0.8579 (ptmt) cc_final: 0.8085 (tptt) REVERT: B 869 GLU cc_start: 0.8007 (mp0) cc_final: 0.7637 (mp0) REVERT: B 922 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7768 (mmmt) outliers start: 39 outliers final: 22 residues processed: 225 average time/residue: 1.4805 time to fit residues: 366.5387 Evaluate side-chains 222 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 958 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 166 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 197 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 ASN B 251 ASN B 303 ASN B 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094767 restraints weight = 62508.195| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.34 r_work: 0.2975 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17226 Z= 0.129 Angle : 0.552 14.591 23179 Z= 0.294 Chirality : 0.067 1.684 2508 Planarity : 0.005 0.149 2972 Dihedral : 4.989 41.512 2237 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.88 % Favored : 95.82 % Rotamer: Outliers : 1.94 % Allowed : 13.58 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.05 % 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 (0.18), residues: 2011 helix: 1.76 (0.17), residues: 923 sheet: -0.42 (0.28), residues: 282 loop : -1.60 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.014 0.001 TYR B 23 PHE 0.011 0.001 PHE B 105 TRP 0.010 0.001 TRP B 131 HIS 0.005 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00309 (17226) covalent geometry : angle 0.55229 (23179) hydrogen bonds : bond 0.04773 ( 814) hydrogen bonds : angle 4.66345 ( 2316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7964 (t0) cc_final: 0.7708 (m110) REVERT: A 224 LYS cc_start: 0.7934 (mttt) cc_final: 0.7115 (tmtp) REVERT: A 228 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: A 268 GLU cc_start: 0.8202 (tp30) cc_final: 0.7862 (tp30) REVERT: A 271 GLU cc_start: 0.8089 (tp30) cc_final: 0.7678 (tp30) REVERT: A 455 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8187 (tppp) REVERT: A 492 LYS cc_start: 0.8463 (mttt) cc_final: 0.8038 (mmpt) REVERT: A 616 ASP cc_start: 0.8732 (t70) cc_final: 0.8399 (t0) REVERT: A 688 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7225 (t70) REVERT: A 715 GLU cc_start: 0.8274 (pt0) cc_final: 0.8026 (pt0) REVERT: A 894 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: A 912 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.7208 (t80) REVERT: B 25 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: B 111 GLU cc_start: 0.7523 (pm20) cc_final: 0.7094 (pm20) REVERT: B 122 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7657 (tttm) REVERT: B 126 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7186 (ptm160) REVERT: B 225 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7798 (mm-40) REVERT: B 228 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: B 302 LYS cc_start: 0.7810 (mmpt) cc_final: 0.7587 (mppt) REVERT: B 314 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7818 (ttp-110) REVERT: B 409 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: B 436 LYS cc_start: 0.8664 (tttt) cc_final: 0.8304 (ttmm) REVERT: B 493 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7664 (mptt) REVERT: B 585 MET cc_start: 0.9351 (mmt) cc_final: 0.9058 (mmt) REVERT: B 761 LYS cc_start: 0.8555 (ptmt) cc_final: 0.8062 (tptt) REVERT: B 869 GLU cc_start: 0.8011 (mp0) cc_final: 0.7603 (mp0) REVERT: B 922 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7717 (mtpt) REVERT: B 1016 ARG cc_start: 0.7374 (mtp85) cc_final: 0.6964 (mmt-90) outliers start: 37 outliers final: 19 residues processed: 230 average time/residue: 1.4712 time to fit residues: 371.7427 Evaluate side-chains 223 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 958 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 168 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN B 418 ASN B 655 ASN B 954 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094077 restraints weight = 62345.559| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.37 r_work: 0.2968 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17226 Z= 0.140 Angle : 0.558 14.647 23179 Z= 0.297 Chirality : 0.067 1.684 2508 Planarity : 0.005 0.147 2972 Dihedral : 4.984 41.426 2237 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.98 % Favored : 95.72 % Rotamer: Outliers : 1.89 % Allowed : 14.16 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.05 % 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: 0.26 (0.18), residues: 2011 helix: 1.82 (0.17), residues: 915 sheet: -0.41 (0.28), residues: 282 loop : -1.59 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.013 0.001 TYR A 675 PHE 0.011 0.001 PHE B 808 TRP 0.010 0.001 TRP B 131 HIS 0.006 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00340 (17226) covalent geometry : angle 0.55805 (23179) hydrogen bonds : bond 0.04913 ( 814) hydrogen bonds : angle 4.66207 ( 2316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7969 (t0) cc_final: 0.7707 (m110) REVERT: A 224 LYS cc_start: 0.7948 (mttt) cc_final: 0.7102 (tmtp) REVERT: A 228 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 268 GLU cc_start: 0.8214 (tp30) cc_final: 0.7880 (tp30) REVERT: A 271 GLU cc_start: 0.8058 (tp30) cc_final: 0.7650 (tp30) REVERT: A 455 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8221 (tppp) REVERT: A 492 LYS cc_start: 0.8478 (mttt) cc_final: 0.8057 (mmpt) REVERT: A 616 ASP cc_start: 0.8738 (t70) cc_final: 0.8404 (t0) REVERT: A 688 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7206 (t70) REVERT: A 715 GLU cc_start: 0.8261 (pt0) cc_final: 0.8009 (pt0) REVERT: A 894 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: A 912 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.7109 (t80) REVERT: B 25 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: B 111 GLU cc_start: 0.7512 (pm20) cc_final: 0.7065 (pm20) REVERT: B 122 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7663 (tttm) REVERT: B 126 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7175 (ptm160) REVERT: B 225 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7793 (mm-40) REVERT: B 228 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: B 302 LYS cc_start: 0.7850 (mmpt) cc_final: 0.7596 (mppt) REVERT: B 314 ARG cc_start: 0.8082 (ttp-170) cc_final: 0.7808 (ttp-110) REVERT: B 409 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: B 436 LYS cc_start: 0.8671 (tttt) cc_final: 0.8311 (ttmm) REVERT: B 493 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7666 (mptt) REVERT: B 506 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7422 (tt) REVERT: B 585 MET cc_start: 0.9350 (mmt) cc_final: 0.9052 (mmt) REVERT: B 761 LYS cc_start: 0.8554 (ptmt) cc_final: 0.8060 (tptt) REVERT: B 801 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: B 869 GLU cc_start: 0.8045 (mp0) cc_final: 0.7634 (mp0) REVERT: B 922 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7741 (mtpt) REVERT: B 1016 ARG cc_start: 0.7338 (mtp85) cc_final: 0.6924 (mmt-90) outliers start: 36 outliers final: 20 residues processed: 219 average time/residue: 1.4623 time to fit residues: 353.3683 Evaluate side-chains 223 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 958 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 99 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN B 418 ASN B 954 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094209 restraints weight = 62731.896| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.34 r_work: 0.2967 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17226 Z= 0.143 Angle : 0.589 26.065 23179 Z= 0.303 Chirality : 0.067 1.682 2508 Planarity : 0.006 0.197 2972 Dihedral : 5.013 41.484 2237 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.83 % Favored : 95.87 % Rotamer: Outliers : 1.89 % Allowed : 14.32 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.05 % 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: 0.25 (0.18), residues: 2011 helix: 1.82 (0.17), residues: 915 sheet: -0.41 (0.28), residues: 282 loop : -1.60 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1010 TYR 0.012 0.001 TYR B 23 PHE 0.011 0.001 PHE B 105 TRP 0.009 0.001 TRP B 131 HIS 0.006 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00349 (17226) covalent geometry : angle 0.58870 (23179) hydrogen bonds : bond 0.04937 ( 814) hydrogen bonds : angle 4.66936 ( 2316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 1025 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7972 (t0) cc_final: 0.7712 (m110) REVERT: A 224 LYS cc_start: 0.7942 (mttt) cc_final: 0.7126 (tmtp) REVERT: A 228 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: A 268 GLU cc_start: 0.8209 (tp30) cc_final: 0.7876 (tp30) REVERT: A 271 GLU cc_start: 0.8065 (tp30) cc_final: 0.7659 (tp30) REVERT: A 455 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8222 (tppp) REVERT: A 492 LYS cc_start: 0.8484 (mttt) cc_final: 0.8067 (mmpt) REVERT: A 616 ASP cc_start: 0.8736 (t70) cc_final: 0.8403 (t0) REVERT: A 688 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7229 (t70) REVERT: A 715 GLU cc_start: 0.8251 (pt0) cc_final: 0.7998 (pt0) REVERT: A 894 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: A 912 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7108 (t80) REVERT: B 25 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: B 111 GLU cc_start: 0.7508 (pm20) cc_final: 0.7065 (pm20) REVERT: B 122 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7677 (tttm) REVERT: B 126 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7183 (ptm160) REVERT: B 225 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7842 (mm-40) REVERT: B 228 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: B 302 LYS cc_start: 0.7857 (mmpt) cc_final: 0.7608 (mppt) REVERT: B 314 ARG cc_start: 0.8087 (ttp-170) cc_final: 0.7816 (ttp-110) REVERT: B 409 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: B 436 LYS cc_start: 0.8678 (tttt) cc_final: 0.8320 (ttmm) REVERT: B 493 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7677 (mptt) REVERT: B 506 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7479 (tt) REVERT: B 585 MET cc_start: 0.9348 (mmt) cc_final: 0.9047 (mmt) REVERT: B 761 LYS cc_start: 0.8558 (ptmt) cc_final: 0.8069 (tptt) REVERT: B 801 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: B 869 GLU cc_start: 0.8039 (mp0) cc_final: 0.7639 (mp0) REVERT: B 922 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7738 (mtpt) REVERT: B 1016 ARG cc_start: 0.7338 (mtp85) cc_final: 0.6924 (mmt-90) outliers start: 36 outliers final: 19 residues processed: 219 average time/residue: 1.7330 time to fit residues: 416.8312 Evaluate side-chains 224 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 958 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 176 optimal weight: 0.0670 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094692 restraints weight = 62474.487| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.33 r_work: 0.2973 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17226 Z= 0.130 Angle : 0.553 14.653 23179 Z= 0.294 Chirality : 0.067 1.682 2508 Planarity : 0.005 0.144 2972 Dihedral : 5.017 46.401 2237 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.23 % Favored : 95.57 % Rotamer: Outliers : 1.84 % Allowed : 14.32 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.05 % 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: 0.27 (0.18), residues: 2011 helix: 1.86 (0.17), residues: 920 sheet: -0.41 (0.28), residues: 282 loop : -1.64 (0.19), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 384 TYR 0.013 0.001 TYR B 23 PHE 0.010 0.001 PHE B 105 TRP 0.010 0.001 TRP B 131 HIS 0.006 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00312 (17226) covalent geometry : angle 0.55284 (23179) hydrogen bonds : bond 0.04718 ( 814) hydrogen bonds : angle 4.63914 ( 2316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12475.87 seconds wall clock time: 211 minutes 21.84 seconds (12681.84 seconds total)