Starting phenix.real_space_refine on Fri Jun 13 18:10:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhl_24465/06_2025/7rhl_24465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhl_24465/06_2025/7rhl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rhl_24465/06_2025/7rhl_24465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhl_24465/06_2025/7rhl_24465.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhl_24465/06_2025/7rhl_24465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhl_24465/06_2025/7rhl_24465.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 9.56, per 1000 atoms: 0.62 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: 3.86 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.58 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: 5.28 Time building geometry restraints manager: 4.58 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.560 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP D 442 HIS 0.013 0.002 HIS C 422 PHE 0.020 0.002 PHE C 298 TYR 0.019 0.001 TYR D 306 ARG 0.007 0.000 ARG D 433 Details of bonding type rmsd hydrogen bonds : bond 0.12824 ( 1077) hydrogen bonds : angle 4.92527 ( 3105) covalent geometry : bond 0.00315 (15713) covalent geometry : angle 0.56035 (21308) *********************** 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 : 1.619 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: 0.2794 time to fit residues: 85.6698 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 : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 173 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.115474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.094223 restraints weight = 22079.975| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.15 r_work: 0.2951 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15713 Z= 0.134 Angle : 0.461 6.275 21308 Z= 0.252 Chirality : 0.038 0.179 2407 Planarity : 0.003 0.043 2659 Dihedral : 3.645 20.431 2127 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.43 % Allowed : 3.78 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.19), residues: 1914 helix: 2.10 (0.14), residues: 1297 sheet: 1.02 (0.71), residues: 43 loop : 0.52 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 168 HIS 0.005 0.001 HIS B1049 PHE 0.019 0.001 PHE C 298 TYR 0.014 0.001 TYR C 351 ARG 0.003 0.000 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 1077) hydrogen bonds : angle 3.96070 ( 3105) covalent geometry : bond 0.00291 (15713) covalent geometry : angle 0.46055 (21308) *********************** 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 189 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 1.762 Fit side-chains REVERT: C 193 GLN cc_start: 0.9037 (tp40) cc_final: 0.8783 (tp40) REVERT: C 245 GLN cc_start: 0.8182 (tp40) cc_final: 0.7823 (tp-100) REVERT: B 736 ARG cc_start: 0.6458 (ptp90) cc_final: 0.6003 (ptm160) REVERT: B 1071 GLU cc_start: 0.7245 (mp0) cc_final: 0.6930 (mt-10) REVERT: D 265 TRP cc_start: 0.7607 (m100) cc_final: 0.7334 (m100) outliers start: 7 outliers final: 6 residues processed: 187 average time/residue: 0.2739 time to fit residues: 77.0078 Evaluate side-chains 178 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 18 optimal weight: 0.1980 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 127 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095956 restraints weight = 21945.964| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.22 r_work: 0.2973 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15713 Z= 0.097 Angle : 0.421 9.332 21308 Z= 0.226 Chirality : 0.037 0.168 2407 Planarity : 0.003 0.033 2659 Dihedral : 3.481 19.716 2127 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.37 % Allowed : 5.21 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.19), residues: 1914 helix: 2.42 (0.14), residues: 1298 sheet: 0.73 (0.66), residues: 43 loop : 0.52 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 168 HIS 0.003 0.001 HIS B 690 PHE 0.016 0.001 PHE A 423 TYR 0.013 0.001 TYR B 815 ARG 0.002 0.000 ARG C 433 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 1077) hydrogen bonds : angle 3.68287 ( 3105) covalent geometry : bond 0.00198 (15713) covalent geometry : angle 0.42060 (21308) *********************** 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 191 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 185 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: C 193 GLN cc_start: 0.8980 (tp40) cc_final: 0.8232 (tp-100) REVERT: C 245 GLN cc_start: 0.8210 (tp40) cc_final: 0.7833 (tp-100) REVERT: B 736 ARG cc_start: 0.6410 (ptp90) cc_final: 0.5927 (ptm160) REVERT: B 746 LEU cc_start: 0.6254 (pp) cc_final: 0.5458 (tp) REVERT: B 1071 GLU cc_start: 0.7138 (mp0) cc_final: 0.6856 (mt-10) REVERT: A 443 THR cc_start: 0.8422 (m) cc_final: 0.8201 (t) REVERT: A 601 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7455 (mm110) REVERT: D 265 TRP cc_start: 0.7610 (m100) cc_final: 0.7379 (m100) REVERT: D 351 TYR cc_start: 0.8673 (t80) cc_final: 0.8360 (t80) REVERT: D 439 ASP cc_start: 0.7691 (m-30) cc_final: 0.7414 (m-30) outliers start: 6 outliers final: 5 residues processed: 187 average time/residue: 0.3288 time to fit residues: 90.7680 Evaluate side-chains 178 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain D residue 399 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 145 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 152 optimal weight: 0.0870 chunk 181 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095101 restraints weight = 21748.688| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.24 r_work: 0.2953 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15713 Z= 0.104 Angle : 0.423 7.205 21308 Z= 0.227 Chirality : 0.037 0.164 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.451 18.471 2127 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.56 % Allowed : 6.14 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.19), residues: 1914 helix: 2.54 (0.14), residues: 1300 sheet: 0.73 (0.67), residues: 43 loop : 0.55 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 168 HIS 0.004 0.001 HIS B1049 PHE 0.018 0.001 PHE C 298 TYR 0.013 0.001 TYR B 810 ARG 0.002 0.000 ARG D 424 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 1077) hydrogen bonds : angle 3.60669 ( 3105) covalent geometry : bond 0.00224 (15713) covalent geometry : angle 0.42331 (21308) *********************** 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 190 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 1.664 Fit side-chains revert: symmetry clash REVERT: C 193 GLN cc_start: 0.8985 (tp40) cc_final: 0.8265 (tp-100) REVERT: C 245 GLN cc_start: 0.8179 (tp40) cc_final: 0.7793 (tp-100) REVERT: B 736 ARG cc_start: 0.6406 (ptp90) cc_final: 0.5899 (ptm160) REVERT: B 746 LEU cc_start: 0.6243 (pp) cc_final: 0.5392 (tp) REVERT: B 1071 GLU cc_start: 0.7136 (mp0) cc_final: 0.6873 (mt-10) REVERT: A 256 THR cc_start: 0.8163 (p) cc_final: 0.7710 (p) outliers start: 9 outliers final: 7 residues processed: 185 average time/residue: 0.2706 time to fit residues: 75.3252 Evaluate side-chains 181 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1031 ILE 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 399 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 174 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.093174 restraints weight = 22107.982| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.21 r_work: 0.2940 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1440 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= 0.137 Angle : 0.457 7.222 21308 Z= 0.243 Chirality : 0.039 0.224 2407 Planarity : 0.003 0.029 2659 Dihedral : 3.563 17.815 2127 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.62 % Allowed : 7.20 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.19), residues: 1914 helix: 2.53 (0.14), residues: 1300 sheet: 0.64 (0.69), residues: 44 loop : 0.50 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 168 HIS 0.006 0.001 HIS B1049 PHE 0.021 0.001 PHE C 298 TYR 0.015 0.001 TYR C 351 ARG 0.003 0.000 ARG B 793 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 1077) hydrogen bonds : angle 3.66928 ( 3105) covalent geometry : bond 0.00308 (15713) covalent geometry : angle 0.45708 (21308) *********************** 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 185 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 1.696 Fit side-chains REVERT: C 193 GLN cc_start: 0.8963 (tp40) cc_final: 0.8201 (tp-100) REVERT: C 430 MET cc_start: 0.8677 (tpp) cc_final: 0.8430 (tpt) REVERT: B 736 ARG cc_start: 0.6445 (ptp90) cc_final: 0.5947 (ptm160) REVERT: B 746 LEU cc_start: 0.6292 (pp) cc_final: 0.5439 (tp) REVERT: B 1071 GLU cc_start: 0.7105 (mp0) cc_final: 0.6854 (mt-10) REVERT: A 256 THR cc_start: 0.8184 (p) cc_final: 0.7702 (p) outliers start: 10 outliers final: 8 residues processed: 181 average time/residue: 0.2624 time to fit residues: 71.6559 Evaluate side-chains 178 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1031 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 160 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.093340 restraints weight = 22064.555| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.22 r_work: 0.2926 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15713 Z= 0.124 Angle : 0.452 7.871 21308 Z= 0.241 Chirality : 0.038 0.221 2407 Planarity : 0.003 0.035 2659 Dihedral : 3.550 18.094 2127 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.74 % Allowed : 7.88 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.19), residues: 1914 helix: 2.54 (0.14), residues: 1300 sheet: 0.60 (0.70), residues: 44 loop : 0.49 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 168 HIS 0.005 0.001 HIS B1049 PHE 0.019 0.001 PHE C 298 TYR 0.015 0.001 TYR B 810 ARG 0.002 0.000 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1077) hydrogen bonds : angle 3.63871 ( 3105) covalent geometry : bond 0.00275 (15713) covalent geometry : angle 0.45235 (21308) *********************** 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: 12 poor density : 171 time to evaluate : 1.743 Fit side-chains REVERT: C 193 GLN cc_start: 0.8937 (tp40) cc_final: 0.8183 (tp-100) REVERT: C 245 GLN cc_start: 0.8148 (tp40) cc_final: 0.7915 (tp-100) REVERT: C 430 MET cc_start: 0.8711 (tpp) cc_final: 0.8455 (tpt) REVERT: B 736 ARG cc_start: 0.6404 (ptp90) cc_final: 0.5902 (ptm160) REVERT: B 746 LEU cc_start: 0.6242 (pp) cc_final: 0.5439 (tp) REVERT: B 879 MET cc_start: 0.8698 (tpp) cc_final: 0.8403 (tpt) REVERT: B 1071 GLU cc_start: 0.7094 (mp0) cc_final: 0.6846 (mt-10) REVERT: A 256 THR cc_start: 0.8156 (p) cc_final: 0.7638 (p) REVERT: A 443 THR cc_start: 0.8458 (m) cc_final: 0.8031 (t) REVERT: A 445 LYS cc_start: 0.7366 (mppt) cc_final: 0.7076 (mmtm) outliers start: 12 outliers final: 11 residues processed: 177 average time/residue: 0.3168 time to fit residues: 84.5882 Evaluate side-chains 176 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain B residue 693 LEU 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 305 MET 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 399 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 187 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 10 optimal weight: 0.0870 chunk 183 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 89 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.3164 ------------------------------------------------------------------------------- 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** B 805 ASN B 864 ASN D 163 ASN D 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.091264 restraints weight = 22133.435| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.25 r_work: 0.2894 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15713 Z= 0.165 Angle : 0.491 8.005 21308 Z= 0.261 Chirality : 0.040 0.233 2407 Planarity : 0.003 0.029 2659 Dihedral : 3.704 17.793 2127 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.93 % Allowed : 8.37 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.19), residues: 1914 helix: 2.44 (0.14), residues: 1300 sheet: 0.61 (0.74), residues: 44 loop : 0.39 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 168 HIS 0.007 0.001 HIS B1049 PHE 0.033 0.002 PHE A 423 TYR 0.017 0.002 TYR A 349 ARG 0.003 0.000 ARG D 271 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 1077) hydrogen bonds : angle 3.76333 ( 3105) covalent geometry : bond 0.00377 (15713) covalent geometry : angle 0.49081 (21308) *********************** 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 186 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 2.292 Fit side-chains REVERT: C 193 GLN cc_start: 0.8945 (tp40) cc_final: 0.8187 (tp-100) REVERT: C 245 GLN cc_start: 0.8124 (tp40) cc_final: 0.7905 (tp-100) REVERT: C 430 MET cc_start: 0.8764 (tpp) cc_final: 0.8488 (tpt) REVERT: B 736 ARG cc_start: 0.6427 (ptp90) cc_final: 0.5941 (ptm160) REVERT: B 746 LEU cc_start: 0.6404 (pp) cc_final: 0.5602 (tp) REVERT: B 879 MET cc_start: 0.8786 (tpp) cc_final: 0.8442 (tpt) REVERT: B 1071 GLU cc_start: 0.7155 (mp0) cc_final: 0.6896 (mp0) outliers start: 15 outliers final: 10 residues processed: 180 average time/residue: 0.3827 time to fit residues: 105.5260 Evaluate side-chains 175 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 3.135 ------------------------------------------------------------------------------- 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 A residue 156 VAL Chi-restraints excluded: chain A residue 305 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 138 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- 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 D 422 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.090321 restraints weight = 22047.906| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.24 r_work: 0.2881 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15713 Z= 0.186 Angle : 0.512 8.319 21308 Z= 0.272 Chirality : 0.040 0.225 2407 Planarity : 0.003 0.030 2659 Dihedral : 3.828 17.697 2127 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.81 % Allowed : 8.62 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.19), residues: 1914 helix: 2.35 (0.14), residues: 1289 sheet: 0.56 (0.76), residues: 44 loop : 0.33 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 168 HIS 0.008 0.001 HIS B1049 PHE 0.023 0.002 PHE A 423 TYR 0.018 0.002 TYR D 349 ARG 0.003 0.000 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 1077) hydrogen bonds : angle 3.85608 ( 3105) covalent geometry : bond 0.00428 (15713) covalent geometry : angle 0.51235 (21308) *********************** 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 180 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.944 Fit side-chains REVERT: C 193 GLN cc_start: 0.8928 (tp40) cc_final: 0.8401 (tp40) REVERT: C 430 MET cc_start: 0.8746 (tpp) cc_final: 0.8475 (tpt) REVERT: C 498 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8399 (mm-40) REVERT: B 736 ARG cc_start: 0.6442 (ptp90) cc_final: 0.5949 (ptm160) REVERT: B 746 LEU cc_start: 0.6439 (pp) cc_final: 0.5663 (tp) REVERT: B 879 MET cc_start: 0.8796 (tpp) cc_final: 0.8449 (tpt) outliers start: 13 outliers final: 10 residues processed: 176 average time/residue: 0.3091 time to fit residues: 83.0241 Evaluate side-chains 175 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 305 MET 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 399 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 134 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 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 = 0.3353 r_free = 0.3353 target = 0.114141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.092188 restraints weight = 21937.567| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.20 r_work: 0.2919 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15713 Z= 0.131 Angle : 0.468 8.607 21308 Z= 0.248 Chirality : 0.039 0.224 2407 Planarity : 0.003 0.029 2659 Dihedral : 3.707 18.462 2127 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.68 % Allowed : 8.93 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.19), residues: 1914 helix: 2.47 (0.14), residues: 1288 sheet: 0.48 (0.75), residues: 44 loop : 0.38 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 168 HIS 0.006 0.001 HIS B1049 PHE 0.024 0.001 PHE A 423 TYR 0.016 0.001 TYR B 810 ARG 0.002 0.000 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 1077) hydrogen bonds : angle 3.75764 ( 3105) covalent geometry : bond 0.00296 (15713) covalent geometry : angle 0.46780 (21308) *********************** 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: 11 poor density : 169 time to evaluate : 2.930 Fit side-chains REVERT: C 193 GLN cc_start: 0.8912 (tp40) cc_final: 0.8403 (tp40) REVERT: C 430 MET cc_start: 0.8734 (tpp) cc_final: 0.8456 (tpt) REVERT: C 498 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8288 (mm-40) REVERT: B 736 ARG cc_start: 0.6403 (ptp90) cc_final: 0.5932 (ptm160) REVERT: B 746 LEU cc_start: 0.6378 (pp) cc_final: 0.5590 (tp) REVERT: B 879 MET cc_start: 0.8771 (tpp) cc_final: 0.8426 (tpt) REVERT: B 1071 GLU cc_start: 0.7197 (mp0) cc_final: 0.6908 (mp0) REVERT: A 443 THR cc_start: 0.8472 (m) cc_final: 0.8142 (t) REVERT: A 445 LYS cc_start: 0.7375 (mppt) cc_final: 0.7154 (mmtm) REVERT: D 177 MET cc_start: 0.8299 (mtp) cc_final: 0.8030 (mtp) outliers start: 11 outliers final: 9 residues processed: 175 average time/residue: 0.3185 time to fit residues: 84.2533 Evaluate side-chains 172 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 305 MET 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 399 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 180 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 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 = 0.3359 r_free = 0.3359 target = 0.114383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.093025 restraints weight = 22237.334| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.17 r_work: 0.2937 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15713 Z= 0.113 Angle : 0.452 8.582 21308 Z= 0.238 Chirality : 0.038 0.223 2407 Planarity : 0.003 0.029 2659 Dihedral : 3.606 18.630 2127 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.62 % Allowed : 9.00 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.19), residues: 1914 helix: 2.53 (0.14), residues: 1289 sheet: 0.21 (0.70), residues: 49 loop : 0.45 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 168 HIS 0.004 0.001 HIS B1049 PHE 0.022 0.001 PHE A 423 TYR 0.015 0.001 TYR B 810 ARG 0.003 0.000 ARG D 514 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1077) hydrogen bonds : angle 3.67240 ( 3105) covalent geometry : bond 0.00250 (15713) covalent geometry : angle 0.45157 (21308) ********************** 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 180 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 1.675 Fit side-chains REVERT: C 193 GLN cc_start: 0.8920 (tp40) cc_final: 0.8437 (tp40) REVERT: C 430 MET cc_start: 0.8703 (tpp) cc_final: 0.8418 (tpt) REVERT: B 736 ARG cc_start: 0.6349 (ptp90) cc_final: 0.5900 (ptm160) REVERT: B 746 LEU cc_start: 0.6275 (pp) cc_final: 0.5457 (tp) REVERT: B 879 MET cc_start: 0.8705 (tpp) cc_final: 0.8349 (tpt) REVERT: B 1071 GLU cc_start: 0.7195 (mp0) cc_final: 0.6919 (mp0) REVERT: A 265 TRP cc_start: 0.7997 (m100) cc_final: 0.7747 (m100) REVERT: A 443 THR cc_start: 0.8491 (m) cc_final: 0.8147 (t) REVERT: D 177 MET cc_start: 0.8290 (mtp) cc_final: 0.8066 (mtp) outliers start: 10 outliers final: 10 residues processed: 175 average time/residue: 0.2644 time to fit residues: 70.3006 Evaluate side-chains 171 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 305 MET 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 399 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 21 optimal weight: 0.0040 chunk 168 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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 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 = 0.3369 r_free = 0.3369 target = 0.115063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.094029 restraints weight = 22168.738| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.14 r_work: 0.2954 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15713 Z= 0.105 Angle : 0.449 8.683 21308 Z= 0.236 Chirality : 0.038 0.221 2407 Planarity : 0.003 0.029 2659 Dihedral : 3.534 18.844 2127 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.62 % Allowed : 9.31 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.19), residues: 1914 helix: 2.67 (0.14), residues: 1280 sheet: 0.18 (0.70), residues: 49 loop : 0.53 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 168 HIS 0.005 0.001 HIS D 422 PHE 0.025 0.001 PHE A 423 TYR 0.014 0.001 TYR B 810 ARG 0.004 0.000 ARG D 514 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 1077) hydrogen bonds : angle 3.60247 ( 3105) covalent geometry : bond 0.00226 (15713) covalent geometry : angle 0.44861 (21308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8227.94 seconds wall clock time: 147 minutes 11.51 seconds (8831.51 seconds total)