Starting phenix.real_space_refine on Wed Mar 4 17:50:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhl_24465/03_2026/7rhl_24465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhl_24465/03_2026/7rhl_24465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rhl_24465/03_2026/7rhl_24465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhl_24465/03_2026/7rhl_24465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rhl_24465/03_2026/7rhl_24465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhl_24465/03_2026/7rhl_24465.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 10005 2.51 5 N 2527 2.21 5 O 2757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15371 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3883 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 474} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3661 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 441} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3916 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3911 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 3.78, per 1000 atoms: 0.25 Number of scatterers: 15371 At special positions: 0 Unit cell: (97.672, 100.198, 160.822, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 2757 8.00 N 2527 7.00 C 10005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 701.5 milliseconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3652 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 70.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.538A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.079A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.851A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 221 Processing helix chain 'C' and resid 232 through 243 Processing helix chain 'C' and resid 243 through 253 removed outlier: 4.069A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 removed outlier: 4.903A pdb=" N ASP C 257 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 258 " --> pdb=" O PRO C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 258' Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.656A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 360 Processing helix chain 'C' and resid 371 through 424 removed outlier: 4.896A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 458 through 476 removed outlier: 5.781A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 578 through 587 removed outlier: 4.487A pdb=" N GLU C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'C' and resid 626 through 663 Processing helix chain 'B' and resid 653 through 680 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.921A pdb=" N TRP B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'B' and resid 724 through 735 Processing helix chain 'B' and resid 735 through 746 removed outlier: 3.835A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Proline residue: B 764 - end of helix removed outlier: 3.596A pdb=" N LYS B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 Processing helix chain 'B' and resid 786 through 817 Processing helix chain 'B' and resid 832 through 844 Processing helix chain 'B' and resid 854 through 887 Processing helix chain 'B' and resid 887 through 907 Processing helix chain 'B' and resid 910 through 929 Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 941 through 959 removed outlier: 6.392A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 978 Processing helix chain 'B' and resid 1029 through 1034 Processing helix chain 'B' and resid 1059 through 1067 Processing helix chain 'B' and resid 1069 through 1084 removed outlier: 3.606A pdb=" N LEU B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1130 Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.560A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.107A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.782A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 232 through 243 Processing helix chain 'A' and resid 243 through 253 removed outlier: 4.102A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 4.829A pdb=" N ASP A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 258' Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.994A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.785A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 424 removed outlier: 4.639A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 458 through 476 removed outlier: 6.417A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 588 through 607 Processing helix chain 'A' and resid 626 through 661 removed outlier: 3.849A pdb=" N SER A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.512A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 4.934A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.842A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.541A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 253 removed outlier: 4.075A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 261 removed outlier: 3.796A pdb=" N LEU D 258 " --> pdb=" O PRO D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.828A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.897A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 Processing helix chain 'D' and resid 404 through 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.804A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 476 removed outlier: 5.922A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 588 through 606 Processing helix chain 'D' and resid 626 through 663 removed outlier: 3.777A pdb=" N ILE D 644 " --> pdb=" O ARG D 640 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 645 " --> pdb=" O PHE D 641 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'C' and resid 496 through 500 Processing sheet with id=AA3, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.291A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS C 507 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 536 " --> pdb=" O VAL C 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.891A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 720 " --> pdb=" O ARG B 717 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.495A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 988 through 990 removed outlier: 6.346A pdb=" N TYR B 988 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B1048 " --> pdb=" O TYR B 988 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY B1011 " --> pdb=" O VAL B1018 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL B1018 " --> pdb=" O GLY B1011 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.739A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.667A pdb=" N ILE A 565 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 524 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 537 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 526 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.997A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.209A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS D 507 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4820 1.34 - 1.46: 3855 1.46 - 1.58: 6900 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 15713 Sorted by residual: bond pdb=" CB VAL A 492 " pdb=" CG1 VAL A 492 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CB THR B 842 " pdb=" CG2 THR B 842 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.51e+00 bond pdb=" CB ASN D 559 " pdb=" CG ASN D 559 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CA ASN D 559 " pdb=" CB ASN D 559 " ideal model delta sigma weight residual 1.530 1.551 -0.020 1.69e-02 3.50e+03 1.44e+00 bond pdb=" C ARG C 277 " pdb=" O ARG C 277 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.33e-02 5.65e+03 1.19e+00 ... (remaining 15708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 21038 2.05 - 4.10: 239 4.10 - 6.15: 21 6.15 - 8.19: 9 8.19 - 10.24: 1 Bond angle restraints: 21308 Sorted by residual: angle pdb=" N PRO B1106 " pdb=" CA PRO B1106 " pdb=" CB PRO B1106 " ideal model delta sigma weight residual 103.00 110.35 -7.35 1.10e+00 8.26e-01 4.47e+01 angle pdb=" CB MET A 604 " pdb=" CG MET A 604 " pdb=" SD MET A 604 " ideal model delta sigma weight residual 112.70 122.94 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C GLY D 558 " pdb=" N ASN D 559 " pdb=" CA ASN D 559 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" CB LYS D 455 " pdb=" CG LYS D 455 " pdb=" CD LYS D 455 " ideal model delta sigma weight residual 111.30 119.09 -7.79 2.30e+00 1.89e-01 1.15e+01 angle pdb=" N TYR B 865 " pdb=" CA TYR B 865 " pdb=" C TYR B 865 " ideal model delta sigma weight residual 111.69 107.95 3.74 1.23e+00 6.61e-01 9.25e+00 ... (remaining 21303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8454 17.94 - 35.88: 725 35.88 - 53.82: 104 53.82 - 71.76: 30 71.76 - 89.70: 9 Dihedral angle restraints: 9322 sinusoidal: 3634 harmonic: 5688 Sorted by residual: dihedral pdb=" CA ARG B 997 " pdb=" C ARG B 997 " pdb=" N GLU B 998 " pdb=" CA GLU B 998 " ideal model delta harmonic sigma weight residual -180.00 -156.20 -23.80 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA THR D 181 " pdb=" C THR D 181 " pdb=" N MET D 182 " pdb=" CA MET D 182 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA VAL A 469 " pdb=" C VAL A 469 " pdb=" N HIS A 470 " pdb=" CA HIS A 470 " ideal model delta harmonic sigma weight residual 180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 9319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1884 0.047 - 0.093: 430 0.093 - 0.140: 88 0.140 - 0.186: 3 0.186 - 0.233: 2 Chirality restraints: 2407 Sorted by residual: chirality pdb=" CA PRO B1106 " pdb=" N PRO B1106 " pdb=" C PRO B1106 " pdb=" CB PRO B1106 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN D 559 " pdb=" N ASN D 559 " pdb=" C ASN D 559 " pdb=" CB ASN D 559 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CB VAL D 350 " pdb=" CA VAL D 350 " pdb=" CG1 VAL D 350 " pdb=" CG2 VAL D 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 2404 not shown) Planarity restraints: 2659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 864 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ASN B 864 " -0.069 2.00e-02 2.50e+03 pdb=" O ASN B 864 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR B 865 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO B 764 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 179 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C ASN C 179 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN C 179 " 0.010 2.00e-02 2.50e+03 pdb=" N TRP C 180 " 0.009 2.00e-02 2.50e+03 ... (remaining 2656 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1750 2.75 - 3.29: 15611 3.29 - 3.83: 28015 3.83 - 4.36: 31590 4.36 - 4.90: 53995 Nonbonded interactions: 130961 Sorted by model distance: nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.217 3.040 nonbonded pdb=" O LEU C 169 " pdb=" OG1 THR C 173 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASN B 776 " pdb=" OH TYR B 789 " model vdw 2.237 3.040 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR B 684 " pdb=" OD1 ASN B 687 " model vdw 2.276 3.040 ... (remaining 130956 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 156 through 605 or resid 625 through 661)) selection = (chain 'C' and resid 156 through 661) selection = (chain 'D' and (resid 156 through 605 or resid 625 through 661)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.003 0.050 15713 Z= 0.143 Angle : 0.560 10.242 21308 Z= 0.304 Chirality : 0.041 0.233 2407 Planarity : 0.004 0.059 2659 Dihedral : 13.966 89.703 5670 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.18), residues: 1914 helix: 1.45 (0.13), residues: 1290 sheet: 1.69 (0.75), residues: 43 loop : 0.48 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 433 TYR 0.019 0.001 TYR D 306 PHE 0.020 0.002 PHE C 298 TRP 0.016 0.002 TRP D 442 HIS 0.013 0.002 HIS C 422 Details of bonding type rmsd covalent geometry : bond 0.00315 (15713) covalent geometry : angle 0.56035 (21308) hydrogen bonds : bond 0.12824 ( 1077) hydrogen bonds : angle 4.92527 ( 3105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.657 Fit side-chains REVERT: C 604 MET cc_start: 0.6920 (mtt) cc_final: 0.6595 (mtt) REVERT: B 736 ARG cc_start: 0.6355 (ptp90) cc_final: 0.6140 (ptm160) REVERT: B 780 GLU cc_start: 0.6424 (mt-10) cc_final: 0.6055 (pt0) REVERT: B 1071 GLU cc_start: 0.6635 (mp0) cc_final: 0.6301 (mp0) REVERT: A 196 TYR cc_start: 0.8581 (m-80) cc_final: 0.8334 (m-80) REVERT: A 204 ASP cc_start: 0.7982 (m-30) cc_final: 0.7619 (m-30) REVERT: A 601 GLN cc_start: 0.7332 (mm110) cc_final: 0.7118 (mm-40) REVERT: D 351 TYR cc_start: 0.8483 (t80) cc_final: 0.8025 (t80) REVERT: D 422 HIS cc_start: 0.7379 (m170) cc_final: 0.7148 (m170) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1241 time to fit residues: 38.4704 Evaluate side-chains 170 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 ASN C 444 ASN C 601 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 ASN D 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.096470 restraints weight = 21889.838| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.21 r_work: 0.2994 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15713 Z= 0.106 Angle : 0.437 6.731 21308 Z= 0.238 Chirality : 0.038 0.176 2407 Planarity : 0.003 0.040 2659 Dihedral : 3.572 20.578 2127 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.25 % Allowed : 3.85 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.19), residues: 1914 helix: 2.16 (0.14), residues: 1295 sheet: 1.16 (0.71), residues: 43 loop : 0.53 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 287 TYR 0.013 0.001 TYR D 306 PHE 0.017 0.001 PHE C 298 TRP 0.014 0.001 TRP C 168 HIS 0.003 0.001 HIS B 690 Details of bonding type rmsd covalent geometry : bond 0.00219 (15713) covalent geometry : angle 0.43739 (21308) hydrogen bonds : bond 0.03789 ( 1077) hydrogen bonds : angle 3.88377 ( 3105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 183 time to evaluate : 0.593 Fit side-chains REVERT: C 193 GLN cc_start: 0.9021 (tp40) cc_final: 0.8809 (tp40) REVERT: C 245 GLN cc_start: 0.8209 (tp40) cc_final: 0.8000 (tp-100) REVERT: B 736 ARG cc_start: 0.6394 (ptp90) cc_final: 0.5898 (ptm160) REVERT: B 1071 GLU cc_start: 0.7163 (mp0) cc_final: 0.6857 (mt-10) REVERT: D 351 TYR cc_start: 0.8746 (t80) cc_final: 0.8295 (t80) outliers start: 4 outliers final: 3 residues processed: 187 average time/residue: 0.1287 time to fit residues: 36.1760 Evaluate side-chains 171 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain D residue 366 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 90 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 52 optimal weight: 0.0970 chunk 102 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 ASN B 864 ASN A 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093026 restraints weight = 22228.269| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.22 r_work: 0.2921 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15713 Z= 0.143 Angle : 0.470 10.751 21308 Z= 0.252 Chirality : 0.039 0.172 2407 Planarity : 0.003 0.036 2659 Dihedral : 3.624 18.872 2127 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.56 % Allowed : 5.15 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.19), residues: 1914 helix: 2.32 (0.14), residues: 1300 sheet: 0.66 (0.67), residues: 43 loop : 0.47 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 271 TYR 0.017 0.001 TYR C 351 PHE 0.021 0.001 PHE C 298 TRP 0.016 0.001 TRP C 168 HIS 0.006 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00321 (15713) covalent geometry : angle 0.46978 (21308) hydrogen bonds : bond 0.03870 ( 1077) hydrogen bonds : angle 3.79574 ( 3105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.548 Fit side-chains REVERT: C 193 GLN cc_start: 0.8978 (tp40) cc_final: 0.8221 (tp-100) REVERT: C 245 GLN cc_start: 0.8176 (tp40) cc_final: 0.7961 (tp-100) REVERT: C 381 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8724 (t70) REVERT: B 736 ARG cc_start: 0.6463 (ptp90) cc_final: 0.5963 (ptm160) REVERT: B 746 LEU cc_start: 0.6280 (pp) cc_final: 0.5519 (tp) REVERT: B 1071 GLU cc_start: 0.7133 (mp0) cc_final: 0.6856 (mt-10) REVERT: A 256 THR cc_start: 0.8168 (p) cc_final: 0.7728 (p) outliers start: 9 outliers final: 6 residues processed: 183 average time/residue: 0.1323 time to fit residues: 36.1346 Evaluate side-chains 175 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 366 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 174 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.090053 restraints weight = 22103.058| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.21 r_work: 0.2872 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15713 Z= 0.216 Angle : 0.533 7.290 21308 Z= 0.286 Chirality : 0.041 0.210 2407 Planarity : 0.004 0.033 2659 Dihedral : 3.901 18.384 2127 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.99 % Allowed : 6.51 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.19), residues: 1914 helix: 2.15 (0.14), residues: 1300 sheet: 0.40 (0.69), residues: 44 loop : 0.29 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 424 TYR 0.020 0.002 TYR C 351 PHE 0.025 0.002 PHE C 298 TRP 0.019 0.002 TRP C 168 HIS 0.010 0.002 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00501 (15713) covalent geometry : angle 0.53271 (21308) hydrogen bonds : bond 0.04192 ( 1077) hydrogen bonds : angle 3.96618 ( 3105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.634 Fit side-chains REVERT: C 193 GLN cc_start: 0.8985 (tp40) cc_final: 0.8195 (tp-100) REVERT: C 245 GLN cc_start: 0.8119 (tp40) cc_final: 0.7906 (tp-100) REVERT: C 381 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8728 (t70) REVERT: C 498 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8371 (mm-40) REVERT: B 736 ARG cc_start: 0.6417 (ptp90) cc_final: 0.5905 (ptm160) REVERT: B 746 LEU cc_start: 0.6394 (pp) cc_final: 0.5595 (tp) REVERT: A 256 THR cc_start: 0.8195 (p) cc_final: 0.7720 (p) REVERT: A 424 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8008 (mmt180) outliers start: 16 outliers final: 10 residues processed: 187 average time/residue: 0.1291 time to fit residues: 36.1773 Evaluate side-chains 178 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 85 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN B 689 HIS D 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.090059 restraints weight = 22119.937| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.21 r_work: 0.2883 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15713 Z= 0.197 Angle : 0.513 7.882 21308 Z= 0.275 Chirality : 0.041 0.216 2407 Planarity : 0.004 0.053 2659 Dihedral : 3.921 18.512 2127 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.12 % Allowed : 7.75 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.19), residues: 1914 helix: 2.11 (0.14), residues: 1297 sheet: 0.39 (0.71), residues: 44 loop : 0.19 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 271 TYR 0.018 0.002 TYR B 810 PHE 0.030 0.002 PHE A 423 TRP 0.021 0.002 TRP C 168 HIS 0.008 0.002 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00455 (15713) covalent geometry : angle 0.51301 (21308) hydrogen bonds : bond 0.04089 ( 1077) hydrogen bonds : angle 3.96415 ( 3105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.656 Fit side-chains REVERT: B 736 ARG cc_start: 0.6437 (ptp90) cc_final: 0.5941 (ptm160) REVERT: B 746 LEU cc_start: 0.6377 (pp) cc_final: 0.5626 (tp) REVERT: A 424 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8094 (mmt180) REVERT: A 556 LYS cc_start: 0.6934 (mmtm) cc_final: 0.6338 (mttt) outliers start: 18 outliers final: 12 residues processed: 183 average time/residue: 0.1200 time to fit residues: 33.3109 Evaluate side-chains 176 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 157 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.091755 restraints weight = 21917.020| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.21 r_work: 0.2898 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15713 Z= 0.132 Angle : 0.462 7.937 21308 Z= 0.247 Chirality : 0.039 0.223 2407 Planarity : 0.003 0.032 2659 Dihedral : 3.745 18.918 2127 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.81 % Allowed : 8.37 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.19), residues: 1914 helix: 2.35 (0.14), residues: 1288 sheet: 0.36 (0.71), residues: 44 loop : 0.29 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 424 TYR 0.016 0.001 TYR B 810 PHE 0.022 0.001 PHE A 423 TRP 0.020 0.001 TRP C 168 HIS 0.005 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00297 (15713) covalent geometry : angle 0.46185 (21308) hydrogen bonds : bond 0.03726 ( 1077) hydrogen bonds : angle 3.81042 ( 3105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.650 Fit side-chains REVERT: B 736 ARG cc_start: 0.6435 (ptp90) cc_final: 0.5931 (ptm160) REVERT: B 746 LEU cc_start: 0.6348 (pp) cc_final: 0.5564 (tp) REVERT: B 879 MET cc_start: 0.8716 (tpp) cc_final: 0.8415 (tpt) REVERT: B 1071 GLU cc_start: 0.7167 (mp0) cc_final: 0.6879 (mp0) REVERT: A 556 LYS cc_start: 0.6879 (mmtm) cc_final: 0.6296 (mttt) outliers start: 13 outliers final: 9 residues processed: 178 average time/residue: 0.1232 time to fit residues: 33.1165 Evaluate side-chains 174 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 122 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN C 245 GLN B 953 ASN D 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096104 restraints weight = 21817.177| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.30 r_work: 0.2937 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15713 Z= 0.097 Angle : 0.427 7.958 21308 Z= 0.227 Chirality : 0.038 0.217 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.513 19.040 2127 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.81 % Allowed : 8.75 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.19), residues: 1914 helix: 2.54 (0.14), residues: 1289 sheet: 0.32 (0.69), residues: 49 loop : 0.40 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 424 TYR 0.013 0.001 TYR B 810 PHE 0.015 0.001 PHE C 298 TRP 0.018 0.001 TRP C 168 HIS 0.003 0.001 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00202 (15713) covalent geometry : angle 0.42734 (21308) hydrogen bonds : bond 0.03319 ( 1077) hydrogen bonds : angle 3.60564 ( 3105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.525 Fit side-chains REVERT: B 695 ASP cc_start: 0.6696 (m-30) cc_final: 0.6177 (m-30) REVERT: B 736 ARG cc_start: 0.6383 (ptp90) cc_final: 0.5927 (ptm160) REVERT: B 746 LEU cc_start: 0.6249 (pp) cc_final: 0.5430 (tp) REVERT: B 879 MET cc_start: 0.8707 (tpp) cc_final: 0.8413 (tpt) REVERT: B 1071 GLU cc_start: 0.7181 (mp0) cc_final: 0.6905 (mt-10) REVERT: A 265 TRP cc_start: 0.8026 (m100) cc_final: 0.7756 (m100) REVERT: A 556 LYS cc_start: 0.6743 (mmtm) cc_final: 0.6142 (mtpt) REVERT: D 177 MET cc_start: 0.8274 (mtp) cc_final: 0.8043 (mtp) REVERT: D 351 TYR cc_start: 0.8883 (t80) cc_final: 0.8380 (t80) REVERT: D 439 ASP cc_start: 0.7694 (m-30) cc_final: 0.7344 (m-30) outliers start: 13 outliers final: 8 residues processed: 185 average time/residue: 0.1175 time to fit residues: 33.1023 Evaluate side-chains 175 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 78 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 141 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN C 266 ASN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN D 422 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.089558 restraints weight = 22082.109| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.21 r_work: 0.2881 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15713 Z= 0.245 Angle : 0.558 7.853 21308 Z= 0.296 Chirality : 0.043 0.237 2407 Planarity : 0.004 0.038 2659 Dihedral : 3.914 18.535 2127 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.99 % Allowed : 9.18 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.19), residues: 1914 helix: 2.19 (0.14), residues: 1298 sheet: 0.56 (0.76), residues: 44 loop : 0.20 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 271 TYR 0.021 0.002 TYR C 351 PHE 0.025 0.002 PHE C 298 TRP 0.017 0.002 TRP C 168 HIS 0.009 0.002 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00573 (15713) covalent geometry : angle 0.55796 (21308) hydrogen bonds : bond 0.04240 ( 1077) hydrogen bonds : angle 3.96015 ( 3105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.688 Fit side-chains REVERT: C 498 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8416 (mm-40) REVERT: B 736 ARG cc_start: 0.6477 (ptp90) cc_final: 0.5996 (ptm160) REVERT: B 746 LEU cc_start: 0.6384 (pp) cc_final: 0.5634 (tp) REVERT: B 879 MET cc_start: 0.8757 (tpp) cc_final: 0.8403 (tpt) REVERT: B 1071 GLU cc_start: 0.7169 (mp0) cc_final: 0.6873 (mp0) REVERT: A 265 TRP cc_start: 0.8032 (m100) cc_final: 0.7779 (m100) REVERT: D 220 ARG cc_start: 0.8000 (mmt90) cc_final: 0.7610 (tpp80) outliers start: 16 outliers final: 12 residues processed: 176 average time/residue: 0.1271 time to fit residues: 33.7476 Evaluate side-chains 171 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 89 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN D 243 ASN D 422 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.091053 restraints weight = 22024.697| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.22 r_work: 0.2898 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15713 Z= 0.150 Angle : 0.490 8.878 21308 Z= 0.259 Chirality : 0.039 0.226 2407 Planarity : 0.003 0.029 2659 Dihedral : 3.800 18.283 2127 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.87 % Allowed : 9.31 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.19), residues: 1914 helix: 2.32 (0.14), residues: 1288 sheet: 0.55 (0.75), residues: 44 loop : 0.23 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 271 TYR 0.016 0.002 TYR B 810 PHE 0.020 0.001 PHE C 298 TRP 0.019 0.001 TRP C 168 HIS 0.006 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00341 (15713) covalent geometry : angle 0.48990 (21308) hydrogen bonds : bond 0.03839 ( 1077) hydrogen bonds : angle 3.84145 ( 3105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.593 Fit side-chains REVERT: C 498 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8351 (mm-40) REVERT: B 736 ARG cc_start: 0.6456 (ptp90) cc_final: 0.5985 (ptm160) REVERT: B 746 LEU cc_start: 0.6332 (pp) cc_final: 0.5549 (tp) REVERT: B 879 MET cc_start: 0.8715 (tpp) cc_final: 0.8373 (tpt) REVERT: B 1071 GLU cc_start: 0.7142 (mp0) cc_final: 0.6856 (mp0) REVERT: A 265 TRP cc_start: 0.8010 (m100) cc_final: 0.7762 (m100) REVERT: A 286 GLN cc_start: 0.7570 (tm-30) cc_final: 0.7258 (tp40) REVERT: D 177 MET cc_start: 0.8305 (mtp) cc_final: 0.8051 (mtp) REVERT: D 220 ARG cc_start: 0.7941 (mmt90) cc_final: 0.7582 (tpp80) outliers start: 14 outliers final: 12 residues processed: 177 average time/residue: 0.1267 time to fit residues: 33.7102 Evaluate side-chains 172 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 182 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN D 243 ASN D 422 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.092067 restraints weight = 22018.304| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.21 r_work: 0.2916 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15713 Z= 0.130 Angle : 0.474 8.525 21308 Z= 0.249 Chirality : 0.039 0.237 2407 Planarity : 0.003 0.029 2659 Dihedral : 3.695 18.237 2127 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.81 % Allowed : 9.37 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.19), residues: 1914 helix: 2.40 (0.14), residues: 1289 sheet: 0.31 (0.70), residues: 49 loop : 0.30 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 271 TYR 0.016 0.001 TYR B 810 PHE 0.018 0.001 PHE C 298 TRP 0.020 0.001 TRP C 168 HIS 0.005 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00292 (15713) covalent geometry : angle 0.47363 (21308) hydrogen bonds : bond 0.03660 ( 1077) hydrogen bonds : angle 3.75183 ( 3105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.550 Fit side-chains REVERT: C 498 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8322 (mm-40) REVERT: B 736 ARG cc_start: 0.6464 (ptp90) cc_final: 0.6012 (ptm160) REVERT: B 746 LEU cc_start: 0.6317 (pp) cc_final: 0.5516 (tp) REVERT: B 879 MET cc_start: 0.8754 (tpp) cc_final: 0.8401 (tpt) REVERT: B 1071 GLU cc_start: 0.7167 (mp0) cc_final: 0.6883 (mp0) REVERT: A 265 TRP cc_start: 0.8011 (m100) cc_final: 0.7776 (m100) REVERT: A 286 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7225 (tp40) REVERT: D 177 MET cc_start: 0.8276 (mtp) cc_final: 0.8047 (mtp) outliers start: 13 outliers final: 12 residues processed: 175 average time/residue: 0.1267 time to fit residues: 33.5165 Evaluate side-chains 177 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN D 243 ASN D 422 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.093719 restraints weight = 21809.768| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.24 r_work: 0.2937 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15713 Z= 0.103 Angle : 0.454 10.189 21308 Z= 0.237 Chirality : 0.038 0.232 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.575 22.957 2127 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.68 % Allowed : 9.74 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.19), residues: 1914 helix: 2.53 (0.14), residues: 1289 sheet: 0.34 (0.70), residues: 49 loop : 0.36 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 424 TYR 0.014 0.001 TYR B 810 PHE 0.015 0.001 PHE C 298 TRP 0.020 0.001 TRP C 168 HIS 0.004 0.001 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00221 (15713) covalent geometry : angle 0.45433 (21308) hydrogen bonds : bond 0.03394 ( 1077) hydrogen bonds : angle 3.63272 ( 3105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3629.35 seconds wall clock time: 63 minutes 0.44 seconds (3780.44 seconds total)