Starting phenix.real_space_refine on Thu Nov 20 02:40:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bcj_7081/11_2025/6bcj_7081.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bcj_7081/11_2025/6bcj_7081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bcj_7081/11_2025/6bcj_7081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bcj_7081/11_2025/6bcj_7081.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bcj_7081/11_2025/6bcj_7081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bcj_7081/11_2025/6bcj_7081.map" } resolution = 3.14 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Na 4 4.78 5 C 19260 2.51 5 N 5216 2.21 5 O 5252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29868 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "C" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "D" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' NA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.86, per 1000 atoms: 0.23 Number of scatterers: 29868 At special positions: 0 Unit cell: (150.87, 150.87, 163.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 Na 4 11.00 O 5252 8.00 N 5216 7.00 C 19260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.03 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.03 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.03 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " distance=2.03 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: 2.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6992 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 68.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.992A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.706A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE B 202 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.622A pdb=" N GLN B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.749A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 344 through 358 removed outlier: 3.544A pdb=" N LEU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 362 removed outlier: 3.763A pdb=" N LEU B 362 " --> pdb=" O LYS B 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.783A pdb=" N ILE B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 406 through 416 removed outlier: 4.246A pdb=" N ALA B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.691A pdb=" N VAL B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 removed outlier: 3.720A pdb=" N TYR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 4.113A pdb=" N ASN B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 484 " --> pdb=" O GLN B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.612A pdb=" N LEU B 562 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.565A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 removed outlier: 3.839A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 668 " --> pdb=" O ARG B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 663 through 668' Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 704 removed outlier: 3.571A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 704' Processing helix chain 'B' and resid 766 through 772 Processing helix chain 'B' and resid 774 through 799 Processing helix chain 'B' and resid 807 through 830 Processing helix chain 'B' and resid 849 through 858 removed outlier: 3.889A pdb=" N ASP B 858 " --> pdb=" O LEU B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR B 880 " --> pdb=" O GLY B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 900 removed outlier: 3.537A pdb=" N GLY B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B 892 " --> pdb=" O ARG B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 920 removed outlier: 4.648A pdb=" N LYS B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 948 removed outlier: 3.815A pdb=" N VAL B 926 " --> pdb=" O MET B 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 943 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG B 965 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Proline residue: B 966 - end of helix Processing helix chain 'B' and resid 980 through 984 Processing helix chain 'B' and resid 1012 through 1029 removed outlier: 3.967A pdb=" N VAL B1016 " --> pdb=" O ALA B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1089 Processing helix chain 'B' and resid 1113 through 1141 Processing helix chain 'B' and resid 1142 through 1162 Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.992A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.705A pdb=" N SER A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET A 200 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 202 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.622A pdb=" N GLN A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.749A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 344 through 358 removed outlier: 3.545A pdb=" N LEU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 362 removed outlier: 3.763A pdb=" N LEU A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 362' Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.782A pdb=" N ILE A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 406 through 416 removed outlier: 4.245A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.691A pdb=" N VAL A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.720A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.112A pdb=" N ASN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 484 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.613A pdb=" N LEU A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.564A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.839A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 668' Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.570A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 704' Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 774 through 799 Processing helix chain 'A' and resid 807 through 830 Processing helix chain 'A' and resid 849 through 858 removed outlier: 3.889A pdb=" N ASP A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 900 removed outlier: 3.537A pdb=" N GLY A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 920 removed outlier: 4.649A pdb=" N LYS A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 removed outlier: 3.816A pdb=" N VAL A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG A 965 " --> pdb=" O ARG A 961 " (cutoff:3.500A) Proline residue: A 966 - end of helix Processing helix chain 'A' and resid 980 through 984 Processing helix chain 'A' and resid 1012 through 1029 removed outlier: 3.968A pdb=" N VAL A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1089 Processing helix chain 'A' and resid 1113 through 1141 Processing helix chain 'A' and resid 1142 through 1162 Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.992A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 163 through 178 removed outlier: 3.705A pdb=" N SER C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 202 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.622A pdb=" N GLN C 261 " --> pdb=" O TYR C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.749A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 344 through 358 removed outlier: 3.543A pdb=" N LEU C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 362 removed outlier: 3.762A pdb=" N LEU C 362 " --> pdb=" O LYS C 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 359 through 362' Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.782A pdb=" N ILE C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 406 through 416 removed outlier: 4.245A pdb=" N ALA C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 removed outlier: 3.691A pdb=" N VAL C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.721A pdb=" N TYR C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 removed outlier: 4.113A pdb=" N ASN C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 484 " --> pdb=" O GLN C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 removed outlier: 3.612A pdb=" N LEU C 562 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.565A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 removed outlier: 3.839A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 668 " --> pdb=" O ARG C 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 663 through 668' Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 704 removed outlier: 3.571A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 700 through 704' Processing helix chain 'C' and resid 766 through 772 Processing helix chain 'C' and resid 774 through 799 Processing helix chain 'C' and resid 807 through 830 Processing helix chain 'C' and resid 849 through 858 removed outlier: 3.890A pdb=" N ASP C 858 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR C 880 " --> pdb=" O GLY C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 900 removed outlier: 3.538A pdb=" N GLY C 887 " --> pdb=" O LEU C 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 892 " --> pdb=" O ARG C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 920 removed outlier: 4.648A pdb=" N LYS C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 948 removed outlier: 3.816A pdb=" N VAL C 926 " --> pdb=" O MET C 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 943 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 948 " --> pdb=" O THR C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG C 965 " --> pdb=" O ARG C 961 " (cutoff:3.500A) Proline residue: C 966 - end of helix Processing helix chain 'C' and resid 980 through 984 Processing helix chain 'C' and resid 1012 through 1029 removed outlier: 3.968A pdb=" N VAL C1016 " --> pdb=" O ALA C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C1056 " --> pdb=" O LEU C1052 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1089 Processing helix chain 'C' and resid 1113 through 1141 Processing helix chain 'C' and resid 1142 through 1162 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.991A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.706A pdb=" N SER D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET D 200 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 202 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.623A pdb=" N GLN D 261 " --> pdb=" O TYR D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.750A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.545A pdb=" N LEU D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 362 removed outlier: 3.763A pdb=" N LEU D 362 " --> pdb=" O LYS D 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 362' Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.782A pdb=" N ILE D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 406 through 416 removed outlier: 4.245A pdb=" N ALA D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 removed outlier: 3.692A pdb=" N VAL D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 465 removed outlier: 3.721A pdb=" N TYR D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 4.112A pdb=" N ASN D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 484 " --> pdb=" O GLN D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 removed outlier: 3.612A pdb=" N LEU D 562 " --> pdb=" O PRO D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.565A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 removed outlier: 3.838A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 668 " --> pdb=" O ARG D 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 663 through 668' Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 704 removed outlier: 3.571A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 700 through 704' Processing helix chain 'D' and resid 766 through 772 Processing helix chain 'D' and resid 774 through 799 Processing helix chain 'D' and resid 807 through 830 Processing helix chain 'D' and resid 849 through 858 removed outlier: 3.890A pdb=" N ASP D 858 " --> pdb=" O LEU D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR D 880 " --> pdb=" O GLY D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 900 removed outlier: 3.537A pdb=" N GLY D 887 " --> pdb=" O LEU D 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS D 892 " --> pdb=" O ARG D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE D 906 " --> pdb=" O LEU D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 920 removed outlier: 4.648A pdb=" N LYS D 915 " --> pdb=" O GLN D 911 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 919 " --> pdb=" O LYS D 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 948 removed outlier: 3.816A pdb=" N VAL D 926 " --> pdb=" O MET D 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 948 " --> pdb=" O THR D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG D 965 " --> pdb=" O ARG D 961 " (cutoff:3.500A) Proline residue: D 966 - end of helix Processing helix chain 'D' and resid 980 through 984 Processing helix chain 'D' and resid 1012 through 1029 removed outlier: 3.968A pdb=" N VAL D1016 " --> pdb=" O ALA D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D1056 " --> pdb=" O LEU D1052 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1089 Processing helix chain 'D' and resid 1113 through 1141 Processing helix chain 'D' and resid 1142 through 1162 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 210 through 211 removed outlier: 6.835A pdb=" N ALA B 210 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP B 78 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 92 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 186 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE B 234 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY B 188 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 236 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 190 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE B 154 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL B 189 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR B 156 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL B 119 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 277 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER B 121 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 302 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR B 365 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 301 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 985 through 987 removed outlier: 3.947A pdb=" N ILE B 985 " --> pdb=" O HIS B 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 987 " --> pdb=" O TRP B 996 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP B 996 " --> pdb=" O GLY B 987 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA5, first strand: chain 'A' and resid 210 through 211 removed outlier: 6.833A pdb=" N ALA A 210 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP A 78 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 92 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA A 186 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE A 234 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY A 188 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 236 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA A 190 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A 154 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL A 189 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 156 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 119 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU A 277 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER A 121 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 302 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR A 365 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 301 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 987 removed outlier: 3.948A pdb=" N ILE A 985 " --> pdb=" O HIS A 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 987 " --> pdb=" O TRP A 996 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP A 996 " --> pdb=" O GLY A 987 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 210 through 211 removed outlier: 6.834A pdb=" N ALA C 210 " --> pdb=" O TYR C 76 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP C 78 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 92 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA C 186 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N PHE C 234 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY C 188 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 236 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA C 190 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE C 154 " --> pdb=" O MET C 187 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL C 189 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR C 156 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 119 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 277 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER C 121 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 302 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR C 365 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 301 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 985 through 987 removed outlier: 3.948A pdb=" N ILE C 985 " --> pdb=" O HIS C 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 987 " --> pdb=" O TRP C 996 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP C 996 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 210 through 211 removed outlier: 6.834A pdb=" N ALA D 210 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP D 78 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 92 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA D 186 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N PHE D 234 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY D 188 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 236 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA D 190 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE D 154 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL D 189 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR D 156 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL D 119 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU D 277 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER D 121 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 302 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR D 365 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU D 301 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 985 through 987 removed outlier: 3.946A pdb=" N ILE D 985 " --> pdb=" O HIS D 998 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 987 " --> pdb=" O TRP D 996 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP D 996 " --> pdb=" O GLY D 987 " (cutoff:3.500A) 1698 hydrogen bonds defined for protein. 5034 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: 6.02 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8037 1.33 - 1.46: 6828 1.46 - 1.58: 15459 1.58 - 1.70: 0 1.70 - 1.83: 204 Bond restraints: 30528 Sorted by residual: bond pdb=" CB VAL C 776 " pdb=" CG1 VAL C 776 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" CB VAL A 776 " pdb=" CG1 VAL A 776 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" C PHE C 340 " pdb=" N PRO C 341 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.36e+00 bond pdb=" C PHE A 340 " pdb=" N PRO A 341 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.36e+00 bond pdb=" CB VAL B 776 " pdb=" CG1 VAL B 776 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 30523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 39788 2.16 - 4.33: 1334 4.33 - 6.49: 160 6.49 - 8.66: 58 8.66 - 10.82: 32 Bond angle restraints: 41372 Sorted by residual: angle pdb=" N PRO B1073 " pdb=" CA PRO B1073 " pdb=" C PRO B1073 " ideal model delta sigma weight residual 110.70 117.10 -6.40 1.22e+00 6.72e-01 2.75e+01 angle pdb=" N PRO D1073 " pdb=" CA PRO D1073 " pdb=" C PRO D1073 " ideal model delta sigma weight residual 110.70 117.08 -6.38 1.22e+00 6.72e-01 2.73e+01 angle pdb=" N PRO A1073 " pdb=" CA PRO A1073 " pdb=" C PRO A1073 " ideal model delta sigma weight residual 110.70 117.08 -6.38 1.22e+00 6.72e-01 2.73e+01 angle pdb=" N PRO C1073 " pdb=" CA PRO C1073 " pdb=" C PRO C1073 " ideal model delta sigma weight residual 110.70 117.05 -6.35 1.22e+00 6.72e-01 2.71e+01 angle pdb=" CB ARG C 965 " pdb=" CG ARG C 965 " pdb=" CD ARG C 965 " ideal model delta sigma weight residual 111.30 100.48 10.82 2.30e+00 1.89e-01 2.21e+01 ... (remaining 41367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 17373 16.49 - 32.98: 619 32.98 - 49.46: 96 49.46 - 65.95: 8 65.95 - 82.44: 20 Dihedral angle restraints: 18116 sinusoidal: 7320 harmonic: 10796 Sorted by residual: dihedral pdb=" CB CYS B 989 " pdb=" SG CYS B 989 " pdb=" SG CYS B1007 " pdb=" CB CYS B1007 " ideal model delta sinusoidal sigma weight residual -86.00 -168.44 82.44 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS A 989 " pdb=" SG CYS A 989 " pdb=" SG CYS A1007 " pdb=" CB CYS A1007 " ideal model delta sinusoidal sigma weight residual -86.00 -168.43 82.43 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS C 989 " pdb=" SG CYS C 989 " pdb=" SG CYS C1007 " pdb=" CB CYS C1007 " ideal model delta sinusoidal sigma weight residual -86.00 -168.42 82.42 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 18113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2983 0.048 - 0.096: 1377 0.096 - 0.143: 273 0.143 - 0.191: 39 0.191 - 0.239: 4 Chirality restraints: 4676 Sorted by residual: chirality pdb=" CB ILE B 279 " pdb=" CA ILE B 279 " pdb=" CG1 ILE B 279 " pdb=" CG2 ILE B 279 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE C 279 " pdb=" CA ILE C 279 " pdb=" CG1 ILE C 279 " pdb=" CG2 ILE C 279 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4673 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 816 " -0.030 2.00e-02 2.50e+03 2.41e-02 1.46e+01 pdb=" CG TRP B 816 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 816 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 816 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 816 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 816 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 816 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 816 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.030 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 816 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 816 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP D 816 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 816 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 816 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 816 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 816 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 816 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 816 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 816 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 816 " 0.008 2.00e-02 2.50e+03 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8780 2.82 - 3.34: 26099 3.34 - 3.86: 46204 3.86 - 4.38: 53211 4.38 - 4.90: 93129 Nonbonded interactions: 227423 Sorted by model distance: nonbonded pdb=" O LEU D 948 " pdb=" CD1 LEU D 948 " model vdw 2.301 3.460 nonbonded pdb=" O LEU B 948 " pdb=" CD1 LEU B 948 " model vdw 2.303 3.460 nonbonded pdb=" O LEU A 948 " pdb=" CD1 LEU A 948 " model vdw 2.306 3.460 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.331 3.040 nonbonded pdb=" O ARG D 354 " pdb=" OG1 THR D 357 " model vdw 2.332 3.040 ... (remaining 227418 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 12 through 1162) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.010 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.940 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 30532 Z= 0.341 Angle : 0.968 10.821 41380 Z= 0.531 Chirality : 0.053 0.239 4676 Planarity : 0.007 0.071 5208 Dihedral : 9.603 77.213 11112 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.38 % Allowed : 1.88 % Favored : 97.75 % 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: -4.83 (0.09), residues: 3672 helix: -3.23 (0.06), residues: 2348 sheet: -1.40 (0.29), residues: 216 loop : -3.00 (0.15), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1058 TYR 0.021 0.003 TYR A 339 PHE 0.035 0.004 PHE D 81 TRP 0.064 0.003 TRP B 816 HIS 0.008 0.002 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00825 (30528) covalent geometry : angle 0.96779 (41372) SS BOND : bond 0.00105 ( 4) SS BOND : angle 1.14881 ( 8) hydrogen bonds : bond 0.21679 ( 1698) hydrogen bonds : angle 7.71663 ( 5034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 566 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.8106 (tp) cc_final: 0.7878 (mt) REVERT: B 252 LEU cc_start: 0.7854 (tp) cc_final: 0.7441 (tp) REVERT: B 454 HIS cc_start: 0.7438 (t70) cc_final: 0.7153 (t-90) REVERT: B 849 ARG cc_start: 0.5820 (mtt180) cc_final: 0.4987 (ptm160) REVERT: B 1140 ARG cc_start: 0.8009 (ttt90) cc_final: 0.7772 (ttp-110) REVERT: B 1143 ASP cc_start: 0.8159 (m-30) cc_final: 0.7924 (m-30) REVERT: A 94 LEU cc_start: 0.8219 (tp) cc_final: 0.7985 (mt) REVERT: A 169 VAL cc_start: 0.7636 (t) cc_final: 0.7397 (m) REVERT: A 252 LEU cc_start: 0.7942 (tp) cc_final: 0.7513 (tp) REVERT: A 454 HIS cc_start: 0.7377 (t70) cc_final: 0.7064 (t-90) REVERT: A 849 ARG cc_start: 0.5881 (mtt180) cc_final: 0.5047 (ptm160) REVERT: A 1140 ARG cc_start: 0.8063 (ttt90) cc_final: 0.7824 (ttp-110) REVERT: A 1141 ASP cc_start: 0.8018 (m-30) cc_final: 0.7727 (m-30) REVERT: A 1143 ASP cc_start: 0.8157 (m-30) cc_final: 0.7905 (m-30) REVERT: C 94 LEU cc_start: 0.8140 (tp) cc_final: 0.7919 (mt) REVERT: C 411 GLN cc_start: 0.8141 (tt0) cc_final: 0.7912 (tp40) REVERT: C 454 HIS cc_start: 0.7485 (t70) cc_final: 0.7192 (t-90) REVERT: C 849 ARG cc_start: 0.5760 (mtt180) cc_final: 0.4934 (ptm160) REVERT: C 1140 ARG cc_start: 0.8066 (ttt90) cc_final: 0.7823 (ttp-110) REVERT: C 1141 ASP cc_start: 0.7982 (m-30) cc_final: 0.7681 (m-30) REVERT: C 1143 ASP cc_start: 0.8159 (m-30) cc_final: 0.7908 (m-30) REVERT: D 94 LEU cc_start: 0.8104 (tp) cc_final: 0.7894 (mt) REVERT: D 411 GLN cc_start: 0.8162 (tt0) cc_final: 0.7925 (tp40) REVERT: D 454 HIS cc_start: 0.7486 (t70) cc_final: 0.7206 (t-90) REVERT: D 849 ARG cc_start: 0.5783 (mtt180) cc_final: 0.4960 (ptm160) REVERT: D 1141 ASP cc_start: 0.7993 (m-30) cc_final: 0.7689 (m-30) REVERT: D 1143 ASP cc_start: 0.8165 (m-30) cc_final: 0.7912 (m-30) outliers start: 12 outliers final: 0 residues processed: 578 average time/residue: 0.2429 time to fit residues: 207.4588 Evaluate side-chains 301 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN B 782 ASN B1010 GLN B1013 ASN B1080 HIS ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN A1010 GLN A1013 ASN A1080 HIS C 633 ASN C 782 ASN C1010 GLN C1013 ASN C1080 HIS D 633 ASN D 782 ASN D1010 GLN D1013 ASN D1080 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.173006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138954 restraints weight = 40832.719| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.57 r_work: 0.3152 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 30532 Z= 0.120 Angle : 0.552 10.400 41380 Z= 0.286 Chirality : 0.037 0.161 4676 Planarity : 0.005 0.047 5208 Dihedral : 4.485 22.032 4092 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.16 % Allowed : 6.72 % Favored : 92.12 % 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: -1.63 (0.12), residues: 3672 helix: -0.33 (0.10), residues: 2392 sheet: -1.23 (0.29), residues: 216 loop : -2.60 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 109 TYR 0.017 0.001 TYR C 964 PHE 0.018 0.002 PHE B 250 TRP 0.019 0.001 TRP B 214 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00244 (30528) covalent geometry : angle 0.55159 (41372) SS BOND : bond 0.00051 ( 4) SS BOND : angle 0.50565 ( 8) hydrogen bonds : bond 0.04844 ( 1698) hydrogen bonds : angle 4.05877 ( 5034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 388 time to evaluate : 1.174 Fit side-chains REVERT: B 454 HIS cc_start: 0.7842 (t70) cc_final: 0.7441 (t-90) REVERT: B 614 ASP cc_start: 0.8568 (t70) cc_final: 0.8328 (t0) REVERT: B 849 ARG cc_start: 0.5646 (mtt180) cc_final: 0.4940 (ptm160) REVERT: A 169 VAL cc_start: 0.7879 (t) cc_final: 0.7514 (m) REVERT: A 197 ASN cc_start: 0.7789 (t0) cc_final: 0.7427 (t0) REVERT: A 356 MET cc_start: 0.6930 (mmm) cc_final: 0.6694 (mmm) REVERT: A 454 HIS cc_start: 0.7824 (t70) cc_final: 0.7435 (t-90) REVERT: A 614 ASP cc_start: 0.8575 (t70) cc_final: 0.8349 (t0) REVERT: A 849 ARG cc_start: 0.5623 (mtt180) cc_final: 0.4943 (ptm160) REVERT: A 1141 ASP cc_start: 0.8812 (m-30) cc_final: 0.8429 (t0) REVERT: C 252 LEU cc_start: 0.8036 (tp) cc_final: 0.7567 (mp) REVERT: C 356 MET cc_start: 0.6829 (mmm) cc_final: 0.6557 (mmm) REVERT: C 411 GLN cc_start: 0.8118 (tt0) cc_final: 0.7813 (tp-100) REVERT: C 454 HIS cc_start: 0.7883 (t70) cc_final: 0.7475 (t-90) REVERT: C 614 ASP cc_start: 0.8502 (t70) cc_final: 0.8287 (t0) REVERT: C 849 ARG cc_start: 0.5593 (mtt180) cc_final: 0.4905 (ptm160) REVERT: C 1141 ASP cc_start: 0.8773 (m-30) cc_final: 0.8459 (t0) REVERT: D 252 LEU cc_start: 0.8027 (tp) cc_final: 0.7566 (mp) REVERT: D 411 GLN cc_start: 0.8134 (tt0) cc_final: 0.7864 (tp-100) REVERT: D 454 HIS cc_start: 0.7826 (t70) cc_final: 0.7417 (t-90) REVERT: D 614 ASP cc_start: 0.8573 (t70) cc_final: 0.8343 (t0) REVERT: D 849 ARG cc_start: 0.5579 (mtt180) cc_final: 0.4898 (ptm160) REVERT: D 1141 ASP cc_start: 0.8811 (m-30) cc_final: 0.8412 (t0) outliers start: 37 outliers final: 18 residues processed: 414 average time/residue: 0.2344 time to fit residues: 144.9147 Evaluate side-chains 309 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 291 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 1013 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 267 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 344 optimal weight: 7.9990 chunk 329 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 342 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN A 633 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN C 261 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D 261 GLN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.171671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137683 restraints weight = 40765.246| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.61 r_work: 0.3146 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30532 Z= 0.127 Angle : 0.528 8.584 41380 Z= 0.272 Chirality : 0.037 0.161 4676 Planarity : 0.004 0.041 5208 Dihedral : 4.111 19.303 4092 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.84 % Allowed : 8.22 % Favored : 89.94 % 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: -0.25 (0.13), residues: 3672 helix: 0.93 (0.10), residues: 2392 sheet: -1.11 (0.31), residues: 216 loop : -2.50 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.014 0.001 TYR D 964 PHE 0.018 0.002 PHE C 793 TRP 0.013 0.001 TRP A 214 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00284 (30528) covalent geometry : angle 0.52754 (41372) SS BOND : bond 0.00042 ( 4) SS BOND : angle 0.42990 ( 8) hydrogen bonds : bond 0.04773 ( 1698) hydrogen bonds : angle 3.68601 ( 5034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 320 time to evaluate : 1.073 Fit side-chains REVERT: B 224 PHE cc_start: 0.7939 (m-80) cc_final: 0.7557 (m-80) REVERT: B 252 LEU cc_start: 0.7919 (tt) cc_final: 0.7567 (tp) REVERT: B 454 HIS cc_start: 0.7718 (t70) cc_final: 0.7326 (t-90) REVERT: B 574 MET cc_start: 0.9140 (mmm) cc_final: 0.8867 (mtt) REVERT: B 614 ASP cc_start: 0.8375 (t70) cc_final: 0.8148 (t0) REVERT: B 635 GLU cc_start: 0.8110 (mp0) cc_final: 0.7877 (mp0) REVERT: B 849 ARG cc_start: 0.5657 (mtt180) cc_final: 0.4966 (ptm160) REVERT: A 224 PHE cc_start: 0.8051 (m-80) cc_final: 0.7656 (m-80) REVERT: A 252 LEU cc_start: 0.7915 (tt) cc_final: 0.7561 (tp) REVERT: A 454 HIS cc_start: 0.7811 (t70) cc_final: 0.7407 (t-90) REVERT: A 574 MET cc_start: 0.9156 (mmm) cc_final: 0.8890 (mtt) REVERT: A 635 GLU cc_start: 0.8090 (mp0) cc_final: 0.7863 (mp0) REVERT: A 849 ARG cc_start: 0.5550 (mtt180) cc_final: 0.4928 (ptm160) REVERT: A 948 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8631 (pp) REVERT: C 224 PHE cc_start: 0.7954 (m-80) cc_final: 0.7574 (m-80) REVERT: C 252 LEU cc_start: 0.8102 (tp) cc_final: 0.7655 (mp) REVERT: C 411 GLN cc_start: 0.8092 (tt0) cc_final: 0.7779 (tp-100) REVERT: C 454 HIS cc_start: 0.7809 (t70) cc_final: 0.7402 (t-90) REVERT: C 574 MET cc_start: 0.9141 (mmm) cc_final: 0.8881 (mtt) REVERT: C 635 GLU cc_start: 0.8104 (mp0) cc_final: 0.7881 (mp0) REVERT: C 849 ARG cc_start: 0.5603 (mtt180) cc_final: 0.4923 (ptm160) REVERT: D 224 PHE cc_start: 0.7860 (m-80) cc_final: 0.7464 (m-80) REVERT: D 252 LEU cc_start: 0.8113 (tp) cc_final: 0.7674 (mp) REVERT: D 411 GLN cc_start: 0.8054 (tt0) cc_final: 0.7763 (tp-100) REVERT: D 454 HIS cc_start: 0.7815 (t70) cc_final: 0.7412 (t-90) REVERT: D 574 MET cc_start: 0.9153 (mmm) cc_final: 0.8880 (mtt) REVERT: D 635 GLU cc_start: 0.8131 (mp0) cc_final: 0.7912 (mp0) REVERT: D 699 CYS cc_start: 0.7950 (t) cc_final: 0.7689 (t) REVERT: D 849 ARG cc_start: 0.5592 (mtt180) cc_final: 0.4916 (ptm160) outliers start: 59 outliers final: 26 residues processed: 363 average time/residue: 0.1973 time to fit residues: 112.4965 Evaluate side-chains 291 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 181 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 360 optimal weight: 3.9990 chunk 344 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 264 optimal weight: 0.0020 chunk 130 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 862 GLN B1013 ASN A 862 GLN A1013 ASN C 862 GLN C1013 ASN D 862 GLN D1013 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140478 restraints weight = 40316.975| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.59 r_work: 0.3188 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30532 Z= 0.099 Angle : 0.491 14.855 41380 Z= 0.252 Chirality : 0.036 0.161 4676 Planarity : 0.004 0.039 5208 Dihedral : 3.869 17.914 4092 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.59 % Allowed : 9.03 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.14), residues: 3672 helix: 1.53 (0.11), residues: 2396 sheet: -1.33 (0.29), residues: 236 loop : -2.34 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.012 0.001 TYR B 964 PHE 0.012 0.001 PHE B 627 TRP 0.009 0.001 TRP D1123 HIS 0.003 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00205 (30528) covalent geometry : angle 0.49079 (41372) SS BOND : bond 0.00006 ( 4) SS BOND : angle 0.28389 ( 8) hydrogen bonds : bond 0.03875 ( 1698) hydrogen bonds : angle 3.43253 ( 5034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 PHE cc_start: 0.8175 (m-80) cc_final: 0.7842 (m-80) REVERT: B 454 HIS cc_start: 0.7744 (t70) cc_final: 0.7358 (t-90) REVERT: B 849 ARG cc_start: 0.5613 (mtt180) cc_final: 0.5031 (ptm160) REVERT: A 169 VAL cc_start: 0.7759 (t) cc_final: 0.7413 (m) REVERT: A 224 PHE cc_start: 0.8229 (m-80) cc_final: 0.7916 (m-80) REVERT: A 400 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 454 HIS cc_start: 0.7743 (t70) cc_final: 0.7364 (t-90) REVERT: A 849 ARG cc_start: 0.5467 (mtt180) cc_final: 0.4931 (ptm160) REVERT: C 224 PHE cc_start: 0.8215 (m-80) cc_final: 0.7878 (m-80) REVERT: C 252 LEU cc_start: 0.8141 (tp) cc_final: 0.7690 (mp) REVERT: C 400 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8582 (mp) REVERT: C 454 HIS cc_start: 0.7752 (t70) cc_final: 0.7358 (t-90) REVERT: C 699 CYS cc_start: 0.7906 (t) cc_final: 0.7639 (t) REVERT: C 849 ARG cc_start: 0.5455 (mtt180) cc_final: 0.4903 (ptm160) REVERT: D 224 PHE cc_start: 0.8180 (m-80) cc_final: 0.7817 (m-80) REVERT: D 252 LEU cc_start: 0.8134 (tp) cc_final: 0.7694 (mp) REVERT: D 454 HIS cc_start: 0.7692 (t70) cc_final: 0.7300 (t-90) REVERT: D 699 CYS cc_start: 0.7885 (t) cc_final: 0.7631 (t) REVERT: D 849 ARG cc_start: 0.5430 (mtt180) cc_final: 0.4895 (ptm160) outliers start: 51 outliers final: 31 residues processed: 348 average time/residue: 0.2101 time to fit residues: 113.6422 Evaluate side-chains 295 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 48 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 129 optimal weight: 0.4980 chunk 118 optimal weight: 40.0000 chunk 232 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 330 optimal weight: 0.0070 chunk 137 optimal weight: 5.9990 chunk 354 optimal weight: 0.4980 chunk 237 optimal weight: 0.0170 overall best weight: 1.0038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN A1013 ASN C 197 ASN C1013 ASN D1013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.173209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139398 restraints weight = 40631.706| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.48 r_work: 0.3164 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30532 Z= 0.103 Angle : 0.486 12.481 41380 Z= 0.249 Chirality : 0.036 0.155 4676 Planarity : 0.003 0.038 5208 Dihedral : 3.745 17.556 4092 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.81 % Allowed : 9.72 % Favored : 88.47 % 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: 0.82 (0.14), residues: 3672 helix: 1.86 (0.11), residues: 2404 sheet: -1.21 (0.30), residues: 236 loop : -2.30 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 109 TYR 0.012 0.001 TYR C 339 PHE 0.012 0.001 PHE B 627 TRP 0.009 0.001 TRP B 214 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00223 (30528) covalent geometry : angle 0.48600 (41372) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.26563 ( 8) hydrogen bonds : bond 0.03947 ( 1698) hydrogen bonds : angle 3.33308 ( 5034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 1.018 Fit side-chains REVERT: B 285 MET cc_start: 0.6252 (mmm) cc_final: 0.5856 (mmp) REVERT: B 400 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8459 (mp) REVERT: B 454 HIS cc_start: 0.7741 (t70) cc_final: 0.7345 (t-90) REVERT: B 574 MET cc_start: 0.9140 (mtt) cc_final: 0.8909 (mtt) REVERT: B 699 CYS cc_start: 0.7656 (t) cc_final: 0.7372 (t) REVERT: B 849 ARG cc_start: 0.5059 (mtt180) cc_final: 0.4714 (ptm160) REVERT: B 851 ARG cc_start: 0.4779 (mtt180) cc_final: 0.4447 (mtp-110) REVERT: A 169 VAL cc_start: 0.7734 (t) cc_final: 0.7451 (m) REVERT: A 400 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 454 HIS cc_start: 0.7734 (t70) cc_final: 0.7346 (t-90) REVERT: A 849 ARG cc_start: 0.5091 (mtt180) cc_final: 0.4712 (ptm160) REVERT: A 948 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8510 (pp) REVERT: C 252 LEU cc_start: 0.8075 (tp) cc_final: 0.7655 (mp) REVERT: C 285 MET cc_start: 0.6388 (mmm) cc_final: 0.6029 (mmp) REVERT: C 400 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8461 (mp) REVERT: C 454 HIS cc_start: 0.7717 (t70) cc_final: 0.7333 (t-90) REVERT: C 699 CYS cc_start: 0.7689 (t) cc_final: 0.7405 (t) REVERT: C 849 ARG cc_start: 0.5100 (mtt180) cc_final: 0.4726 (ptm160) REVERT: D 241 TYR cc_start: 0.7087 (m-80) cc_final: 0.6796 (m-80) REVERT: D 252 LEU cc_start: 0.8062 (tp) cc_final: 0.7656 (mp) REVERT: D 400 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8463 (mp) REVERT: D 454 HIS cc_start: 0.7742 (t70) cc_final: 0.7341 (t-90) REVERT: D 699 CYS cc_start: 0.7713 (t) cc_final: 0.7422 (t) REVERT: D 849 ARG cc_start: 0.5074 (mtt180) cc_final: 0.4712 (ptm160) outliers start: 58 outliers final: 40 residues processed: 332 average time/residue: 0.2119 time to fit residues: 108.9155 Evaluate side-chains 311 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 303 optimal weight: 20.0000 chunk 323 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 235 optimal weight: 0.3980 chunk 214 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN A 261 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN C1013 ASN D1013 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.169216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.128725 restraints weight = 39970.553| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.00 r_work: 0.3236 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30532 Z= 0.131 Angle : 0.514 11.661 41380 Z= 0.263 Chirality : 0.037 0.150 4676 Planarity : 0.004 0.040 5208 Dihedral : 3.776 18.241 4092 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.88 % Allowed : 9.78 % Favored : 88.34 % 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: 0.95 (0.14), residues: 3672 helix: 1.96 (0.11), residues: 2404 sheet: -1.10 (0.31), residues: 236 loop : -2.28 (0.16), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.012 0.001 TYR B 964 PHE 0.018 0.001 PHE C 906 TRP 0.010 0.001 TRP C 680 HIS 0.003 0.001 HIS B1127 Details of bonding type rmsd covalent geometry : bond 0.00300 (30528) covalent geometry : angle 0.51441 (41372) SS BOND : bond 0.00045 ( 4) SS BOND : angle 0.33168 ( 8) hydrogen bonds : bond 0.04536 ( 1698) hydrogen bonds : angle 3.37942 ( 5034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 270 time to evaluate : 0.957 Fit side-chains REVERT: B 400 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 454 HIS cc_start: 0.7496 (t70) cc_final: 0.7228 (t-90) REVERT: B 574 MET cc_start: 0.9027 (mtt) cc_final: 0.8817 (mtt) REVERT: A 169 VAL cc_start: 0.8100 (t) cc_final: 0.7865 (m) REVERT: A 400 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 454 HIS cc_start: 0.7526 (t70) cc_final: 0.7273 (t-90) REVERT: A 574 MET cc_start: 0.9033 (mtt) cc_final: 0.8828 (mtt) REVERT: A 948 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8585 (pp) REVERT: C 252 LEU cc_start: 0.8082 (tp) cc_final: 0.7755 (mp) REVERT: C 400 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8520 (mp) REVERT: C 454 HIS cc_start: 0.7535 (t70) cc_final: 0.7262 (t-90) REVERT: C 574 MET cc_start: 0.9002 (mtt) cc_final: 0.8792 (mtt) REVERT: C 948 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8329 (pp) REVERT: D 252 LEU cc_start: 0.8114 (tp) cc_final: 0.7786 (mp) REVERT: D 400 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8521 (mp) REVERT: D 454 HIS cc_start: 0.7569 (t70) cc_final: 0.7292 (t-90) REVERT: D 574 MET cc_start: 0.9025 (mtt) cc_final: 0.8815 (mtt) outliers start: 60 outliers final: 41 residues processed: 317 average time/residue: 0.2029 time to fit residues: 101.8302 Evaluate side-chains 303 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 3 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 278 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 326 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN B 862 GLN B1013 ASN A 862 GLN A1013 ASN C 862 GLN C1013 ASN D 862 GLN D1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.166170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130156 restraints weight = 40287.255| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.53 r_work: 0.3144 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 30532 Z= 0.240 Angle : 0.640 12.358 41380 Z= 0.324 Chirality : 0.042 0.148 4676 Planarity : 0.004 0.045 5208 Dihedral : 4.180 19.085 4092 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.28 % Allowed : 9.59 % Favored : 88.12 % 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: 0.58 (0.14), residues: 3672 helix: 1.69 (0.11), residues: 2368 sheet: -0.65 (0.31), residues: 216 loop : -2.45 (0.16), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 109 TYR 0.013 0.002 TYR A 230 PHE 0.031 0.002 PHE C 906 TRP 0.014 0.002 TRP C 680 HIS 0.006 0.002 HIS B1127 Details of bonding type rmsd covalent geometry : bond 0.00587 (30528) covalent geometry : angle 0.64030 (41372) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.65900 ( 8) hydrogen bonds : bond 0.06082 ( 1698) hydrogen bonds : angle 3.69475 ( 5034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 258 time to evaluate : 1.199 Fit side-chains REVERT: B 252 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7603 (tt) REVERT: B 285 MET cc_start: 0.6562 (mmp) cc_final: 0.6356 (mmp) REVERT: B 400 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8560 (mp) REVERT: B 454 HIS cc_start: 0.7873 (t70) cc_final: 0.7476 (t-90) REVERT: B 937 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8759 (mp) REVERT: B 1141 ASP cc_start: 0.8671 (t0) cc_final: 0.8145 (t0) REVERT: A 252 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 400 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 851 ARG cc_start: 0.4960 (mtt180) cc_final: 0.4730 (mtp-110) REVERT: A 937 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8758 (mp) REVERT: A 948 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8777 (pp) REVERT: A 1141 ASP cc_start: 0.8527 (t0) cc_final: 0.7975 (t0) REVERT: C 252 LEU cc_start: 0.8122 (tp) cc_final: 0.7628 (mp) REVERT: C 400 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 454 HIS cc_start: 0.7844 (t70) cc_final: 0.7418 (t-90) REVERT: C 937 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8755 (mp) REVERT: C 948 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8518 (pp) REVERT: D 252 LEU cc_start: 0.8132 (tp) cc_final: 0.7643 (mp) REVERT: D 400 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8572 (mp) REVERT: D 454 HIS cc_start: 0.7867 (t70) cc_final: 0.7432 (t-90) REVERT: D 937 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8761 (mp) outliers start: 73 outliers final: 43 residues processed: 320 average time/residue: 0.1996 time to fit residues: 100.7238 Evaluate side-chains 298 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1064 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1071 LEU Chi-restraints excluded: chain C residue 1144 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1144 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 153 optimal weight: 0.7980 chunk 282 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 358 optimal weight: 0.0970 chunk 218 optimal weight: 7.9990 chunk 339 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 326 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN A 480 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN D 480 GLN D1013 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.170315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.134533 restraints weight = 40450.321| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.64 r_work: 0.3204 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30532 Z= 0.105 Angle : 0.498 10.418 41380 Z= 0.259 Chirality : 0.037 0.194 4676 Planarity : 0.004 0.041 5208 Dihedral : 3.832 18.395 4092 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.50 % Allowed : 10.28 % Favored : 88.22 % 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: 1.06 (0.14), residues: 3672 helix: 2.07 (0.11), residues: 2380 sheet: -0.59 (0.32), residues: 216 loop : -2.32 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 109 TYR 0.012 0.001 TYR A 964 PHE 0.013 0.001 PHE A 415 TRP 0.012 0.001 TRP D1123 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00221 (30528) covalent geometry : angle 0.49847 (41372) SS BOND : bond 0.00014 ( 4) SS BOND : angle 0.26717 ( 8) hydrogen bonds : bond 0.04104 ( 1698) hydrogen bonds : angle 3.38927 ( 5034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 1.175 Fit side-chains REVERT: B 94 LEU cc_start: 0.8386 (mt) cc_final: 0.8098 (pt) REVERT: B 400 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8483 (mp) REVERT: B 454 HIS cc_start: 0.7844 (t70) cc_final: 0.7423 (t-90) REVERT: B 923 MET cc_start: 0.8809 (mmm) cc_final: 0.8582 (mmm) REVERT: A 169 VAL cc_start: 0.7867 (t) cc_final: 0.7361 (m) REVERT: A 252 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7530 (tt) REVERT: A 400 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 454 HIS cc_start: 0.7895 (t70) cc_final: 0.7476 (t-90) REVERT: A 923 MET cc_start: 0.8809 (mmm) cc_final: 0.8597 (mmm) REVERT: A 948 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8513 (pp) REVERT: C 94 LEU cc_start: 0.8401 (mt) cc_final: 0.8102 (pt) REVERT: C 252 LEU cc_start: 0.8054 (tp) cc_final: 0.7573 (mp) REVERT: C 400 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8486 (mp) REVERT: C 454 HIS cc_start: 0.7840 (t70) cc_final: 0.7395 (t-90) REVERT: C 948 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8362 (pp) REVERT: D 94 LEU cc_start: 0.8379 (mt) cc_final: 0.8098 (pt) REVERT: D 252 LEU cc_start: 0.8114 (tp) cc_final: 0.7631 (mp) REVERT: D 400 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8473 (mp) REVERT: D 454 HIS cc_start: 0.7882 (t70) cc_final: 0.7425 (t-90) REVERT: D 923 MET cc_start: 0.8806 (mmm) cc_final: 0.8578 (mmm) outliers start: 48 outliers final: 34 residues processed: 325 average time/residue: 0.1930 time to fit residues: 100.7210 Evaluate side-chains 297 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1071 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 239 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 290 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 201 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 311 optimal weight: 8.9990 chunk 319 optimal weight: 20.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 862 GLN B1013 ASN A1013 ASN C 862 GLN C1013 ASN D1013 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.166216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128724 restraints weight = 40204.803| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.94 r_work: 0.3123 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 30532 Z= 0.228 Angle : 0.628 11.841 41380 Z= 0.319 Chirality : 0.042 0.190 4676 Planarity : 0.004 0.045 5208 Dihedral : 4.144 19.100 4092 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.47 % Allowed : 10.62 % Favored : 87.91 % 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: 0.70 (0.14), residues: 3672 helix: 1.74 (0.11), residues: 2384 sheet: -0.61 (0.31), residues: 216 loop : -2.35 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 109 TYR 0.013 0.002 TYR D 230 PHE 0.028 0.002 PHE B 906 TRP 0.014 0.002 TRP A 680 HIS 0.005 0.002 HIS C1127 Details of bonding type rmsd covalent geometry : bond 0.00555 (30528) covalent geometry : angle 0.62831 (41372) SS BOND : bond 0.00044 ( 4) SS BOND : angle 0.66360 ( 8) hydrogen bonds : bond 0.05950 ( 1698) hydrogen bonds : angle 3.69946 ( 5034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 1.181 Fit side-chains REVERT: B 252 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7662 (tt) REVERT: B 400 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 937 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8727 (mp) REVERT: B 1141 ASP cc_start: 0.8737 (t0) cc_final: 0.8214 (t0) REVERT: A 252 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7550 (tt) REVERT: A 400 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8534 (mp) REVERT: A 851 ARG cc_start: 0.4892 (mtt180) cc_final: 0.4613 (mtp-110) REVERT: A 937 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 948 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8771 (pp) REVERT: A 1141 ASP cc_start: 0.8632 (t0) cc_final: 0.8073 (t0) REVERT: C 252 LEU cc_start: 0.8161 (tp) cc_final: 0.7654 (mp) REVERT: C 400 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8548 (mp) REVERT: C 851 ARG cc_start: 0.4928 (mtt180) cc_final: 0.4635 (mtp85) REVERT: C 937 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8720 (mp) REVERT: C 948 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8553 (pp) REVERT: C 1141 ASP cc_start: 0.8701 (t0) cc_final: 0.8102 (t0) REVERT: D 252 LEU cc_start: 0.8166 (tp) cc_final: 0.7665 (mp) REVERT: D 400 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8521 (mp) REVERT: D 454 HIS cc_start: 0.7954 (t70) cc_final: 0.7716 (t-90) REVERT: D 851 ARG cc_start: 0.4918 (mtt180) cc_final: 0.4601 (mtp-110) REVERT: D 937 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8734 (mp) REVERT: D 1141 ASP cc_start: 0.8620 (t0) cc_final: 0.8044 (t0) outliers start: 47 outliers final: 32 residues processed: 297 average time/residue: 0.2064 time to fit residues: 95.2353 Evaluate side-chains 287 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 360 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 321 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 347 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.169977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133149 restraints weight = 40231.278| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.96 r_work: 0.3259 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30532 Z= 0.106 Angle : 0.497 10.207 41380 Z= 0.259 Chirality : 0.037 0.191 4676 Planarity : 0.004 0.040 5208 Dihedral : 3.889 18.420 4092 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.34 % Allowed : 10.75 % Favored : 87.91 % 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: 1.12 (0.14), residues: 3672 helix: 2.10 (0.11), residues: 2384 sheet: -0.60 (0.32), residues: 216 loop : -2.24 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.012 0.001 TYR C 964 PHE 0.014 0.001 PHE A 415 TRP 0.015 0.001 TRP D1014 HIS 0.005 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00224 (30528) covalent geometry : angle 0.49708 (41372) SS BOND : bond 0.00028 ( 4) SS BOND : angle 0.33167 ( 8) hydrogen bonds : bond 0.04150 ( 1698) hydrogen bonds : angle 3.42385 ( 5034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 1.025 Fit side-chains REVERT: B 400 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8490 (mp) REVERT: B 454 HIS cc_start: 0.7547 (t70) cc_final: 0.7243 (t-90) REVERT: B 1141 ASP cc_start: 0.8443 (t0) cc_final: 0.7960 (t0) REVERT: A 400 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8480 (mp) REVERT: A 923 MET cc_start: 0.8622 (mmm) cc_final: 0.8395 (mmm) REVERT: A 948 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8479 (pp) REVERT: A 1141 ASP cc_start: 0.8364 (t0) cc_final: 0.7831 (t0) REVERT: C 252 LEU cc_start: 0.8108 (tp) cc_final: 0.7753 (mp) REVERT: C 400 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8484 (mp) REVERT: C 454 HIS cc_start: 0.7557 (t70) cc_final: 0.7243 (t-90) REVERT: C 1141 ASP cc_start: 0.8415 (t0) cc_final: 0.7889 (t0) REVERT: D 252 LEU cc_start: 0.8120 (tp) cc_final: 0.7767 (mp) REVERT: D 400 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8516 (mp) REVERT: D 454 HIS cc_start: 0.7575 (t70) cc_final: 0.7255 (t-90) REVERT: D 1141 ASP cc_start: 0.8338 (t0) cc_final: 0.7806 (t0) outliers start: 43 outliers final: 31 residues processed: 303 average time/residue: 0.2031 time to fit residues: 96.0117 Evaluate side-chains 298 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 279 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 319 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 295 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN D 633 ASN D1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.163855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126001 restraints weight = 40637.614| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.00 r_work: 0.3062 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 30532 Z= 0.329 Angle : 0.739 12.575 41380 Z= 0.372 Chirality : 0.046 0.196 4676 Planarity : 0.005 0.047 5208 Dihedral : 4.453 20.001 4092 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.56 % Allowed : 10.81 % Favored : 87.62 % 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: 0.38 (0.13), residues: 3672 helix: 1.45 (0.10), residues: 2368 sheet: -0.70 (0.32), residues: 216 loop : -2.30 (0.16), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 965 TYR 0.021 0.002 TYR B 230 PHE 0.037 0.003 PHE B 906 TRP 0.017 0.002 TRP C 680 HIS 0.007 0.002 HIS C1127 Details of bonding type rmsd covalent geometry : bond 0.00808 (30528) covalent geometry : angle 0.73883 (41372) SS BOND : bond 0.00011 ( 4) SS BOND : angle 0.90479 ( 8) hydrogen bonds : bond 0.06943 ( 1698) hydrogen bonds : angle 3.91064 ( 5034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7780.12 seconds wall clock time: 133 minutes 22.54 seconds (8002.54 seconds total)