Starting phenix.real_space_refine on Tue May 27 19:03:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bcj_7081/05_2025/6bcj_7081.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bcj_7081/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6bcj_7081/05_2025/6bcj_7081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bcj_7081/05_2025/6bcj_7081.map" model { file = "/net/cci-nas-00/data/ceres_data/6bcj_7081/05_2025/6bcj_7081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bcj_7081/05_2025/6bcj_7081.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.04, per 1000 atoms: 0.54 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: 5.86 Conformation dependent library (CDL) restraints added in 3.4 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: 3.02 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: 11.31 Time building geometry restraints manager: 7.06 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: 2.090 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: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 59.930 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.064 0.003 TRP B 816 HIS 0.008 0.002 HIS B 166 PHE 0.035 0.004 PHE D 81 TYR 0.021 0.003 TYR A 339 ARG 0.009 0.001 ARG D1058 Details of bonding type rmsd hydrogen bonds : bond 0.21679 ( 1698) hydrogen bonds : angle 7.71663 ( 5034) SS BOND : bond 0.00105 ( 4) SS BOND : angle 1.14881 ( 8) covalent geometry : bond 0.00825 (30528) covalent geometry : angle 0.96779 (41372) *********************** 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 : 3.379 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: 0.4916 time to fit residues: 420.6537 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 : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 337 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN B 782 ASN B1010 GLN B1013 ASN B1080 HIS A 633 ASN ** A 669 GLN ** 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 261 GLN D 633 ASN D 782 ASN D1010 GLN D1013 ASN D1080 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.170630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136435 restraints weight = 40411.928| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.54 r_work: 0.3112 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30532 Z= 0.154 Angle : 0.593 10.576 41380 Z= 0.307 Chirality : 0.038 0.166 4676 Planarity : 0.005 0.054 5208 Dihedral : 4.614 22.273 4092 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.16 % Allowed : 7.25 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.12), residues: 3672 helix: -0.38 (0.10), residues: 2384 sheet: -1.23 (0.30), residues: 216 loop : -2.64 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 214 HIS 0.005 0.001 HIS D 166 PHE 0.022 0.002 PHE C 793 TYR 0.016 0.001 TYR C 964 ARG 0.006 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 1698) hydrogen bonds : angle 4.16615 ( 5034) SS BOND : bond 0.00007 ( 4) SS BOND : angle 0.60244 ( 8) covalent geometry : bond 0.00340 (30528) covalent geometry : angle 0.59266 (41372) *********************** 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 406 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 369 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 PHE cc_start: 0.8026 (m-80) cc_final: 0.7816 (m-80) REVERT: B 241 TYR cc_start: 0.6942 (m-80) cc_final: 0.6650 (m-80) REVERT: B 454 HIS cc_start: 0.7929 (t70) cc_final: 0.7524 (t-90) REVERT: B 849 ARG cc_start: 0.5580 (mtt180) cc_final: 0.4884 (ptm160) REVERT: A 356 MET cc_start: 0.6878 (mmm) cc_final: 0.6579 (mmm) REVERT: A 454 HIS cc_start: 0.7925 (t70) cc_final: 0.7543 (t-90) REVERT: A 849 ARG cc_start: 0.5644 (mtt180) cc_final: 0.4917 (ptm160) REVERT: A 1141 ASP cc_start: 0.8808 (m-30) cc_final: 0.8436 (t0) REVERT: C 224 PHE cc_start: 0.8169 (m-80) cc_final: 0.7953 (m-80) REVERT: C 252 LEU cc_start: 0.8005 (tp) cc_final: 0.7508 (mp) REVERT: C 356 MET cc_start: 0.6772 (mmm) cc_final: 0.6434 (mmm) REVERT: C 454 HIS cc_start: 0.7932 (t70) cc_final: 0.7624 (t-90) REVERT: C 849 ARG cc_start: 0.5597 (mtt180) cc_final: 0.4874 (ptm160) REVERT: C 1141 ASP cc_start: 0.8770 (m-30) cc_final: 0.8443 (t0) REVERT: D 224 PHE cc_start: 0.8111 (m-80) cc_final: 0.7881 (m-80) REVERT: D 241 TYR cc_start: 0.6894 (m-80) cc_final: 0.6623 (m-80) REVERT: D 252 LEU cc_start: 0.8037 (tp) cc_final: 0.7557 (mp) REVERT: D 411 GLN cc_start: 0.8138 (tt0) cc_final: 0.7780 (tp-100) REVERT: D 454 HIS cc_start: 0.7892 (t70) cc_final: 0.7585 (t-90) REVERT: D 849 ARG cc_start: 0.5667 (mtt180) cc_final: 0.4925 (ptm160) REVERT: D 1141 ASP cc_start: 0.8822 (m-30) cc_final: 0.8418 (t0) outliers start: 37 outliers final: 23 residues processed: 394 average time/residue: 0.4927 time to fit residues: 295.9790 Evaluate side-chains 300 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 277 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 GLN 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 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 825 LEU Chi-restraints excluded: chain A residue 1013 ASN 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 825 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 825 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 253 optimal weight: 7.9990 chunk 171 optimal weight: 0.0970 chunk 352 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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** A 261 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129373 restraints weight = 40531.472| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.92 r_work: 0.3046 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30532 Z= 0.162 Angle : 0.573 10.002 41380 Z= 0.295 Chirality : 0.039 0.174 4676 Planarity : 0.004 0.045 5208 Dihedral : 4.300 19.700 4092 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.06 % Allowed : 8.59 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 3672 helix: 0.84 (0.10), residues: 2364 sheet: -0.90 (0.31), residues: 208 loop : -2.59 (0.16), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1054 HIS 0.004 0.001 HIS D 166 PHE 0.022 0.002 PHE B 793 TYR 0.015 0.001 TYR B 339 ARG 0.006 0.001 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.05422 ( 1698) hydrogen bonds : angle 3.82025 ( 5034) SS BOND : bond 0.00052 ( 4) SS BOND : angle 0.55636 ( 8) covalent geometry : bond 0.00381 (30528) covalent geometry : angle 0.57302 (41372) *********************** 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 365 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 299 time to evaluate : 3.391 Fit side-chains REVERT: B 241 TYR cc_start: 0.6927 (m-80) cc_final: 0.6708 (m-80) REVERT: B 252 LEU cc_start: 0.7896 (tt) cc_final: 0.7555 (tp) REVERT: B 454 HIS cc_start: 0.7944 (t70) cc_final: 0.7473 (t-90) REVERT: B 574 MET cc_start: 0.9170 (mmm) cc_final: 0.8930 (mtt) REVERT: B 849 ARG cc_start: 0.5530 (mtt180) cc_final: 0.4891 (ptm160) REVERT: B 937 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8679 (mp) REVERT: B 948 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8771 (pp) REVERT: A 169 VAL cc_start: 0.7712 (t) cc_final: 0.7329 (m) REVERT: A 224 PHE cc_start: 0.7975 (m-80) cc_final: 0.7611 (m-80) REVERT: A 252 LEU cc_start: 0.7880 (tt) cc_final: 0.7538 (tp) REVERT: A 454 HIS cc_start: 0.7947 (t70) cc_final: 0.7477 (t-90) REVERT: A 574 MET cc_start: 0.9166 (mmm) cc_final: 0.8935 (mtt) REVERT: A 849 ARG cc_start: 0.5475 (mtt180) cc_final: 0.4856 (ptm160) REVERT: A 937 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8684 (mp) REVERT: A 948 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8752 (pp) REVERT: C 241 TYR cc_start: 0.7123 (m-80) cc_final: 0.6908 (m-80) REVERT: C 252 LEU cc_start: 0.8099 (tp) cc_final: 0.7627 (mp) REVERT: C 288 ARG cc_start: 0.7224 (mtp180) cc_final: 0.7016 (mtm180) REVERT: C 454 HIS cc_start: 0.7956 (t70) cc_final: 0.7671 (t-90) REVERT: C 574 MET cc_start: 0.9150 (mmm) cc_final: 0.8914 (mtt) REVERT: C 849 ARG cc_start: 0.5492 (mtt180) cc_final: 0.4856 (ptm160) REVERT: C 937 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8684 (mp) REVERT: D 241 TYR cc_start: 0.6918 (m-80) cc_final: 0.6715 (m-80) REVERT: D 252 LEU cc_start: 0.8073 (tp) cc_final: 0.7605 (mp) REVERT: D 288 ARG cc_start: 0.7158 (mtp180) cc_final: 0.6953 (mtm180) REVERT: D 411 GLN cc_start: 0.8038 (tt0) cc_final: 0.7667 (tp-100) REVERT: D 454 HIS cc_start: 0.7967 (t70) cc_final: 0.7684 (t-90) REVERT: D 574 MET cc_start: 0.9162 (mmm) cc_final: 0.8920 (mtt) REVERT: D 699 CYS cc_start: 0.8113 (t) cc_final: 0.7867 (t) REVERT: D 849 ARG cc_start: 0.5462 (mtt180) cc_final: 0.4845 (ptm160) REVERT: D 937 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8689 (mp) REVERT: D 948 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8769 (pp) REVERT: D 1141 ASP cc_start: 0.8760 (m-30) cc_final: 0.8556 (t0) outliers start: 66 outliers final: 27 residues processed: 345 average time/residue: 0.4220 time to fit residues: 229.7753 Evaluate side-chains 298 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 3.417 ------------------------------------------------------------------------------- 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 872 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1161 LEU 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 872 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 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 408 ASP Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1161 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 648 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1161 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 350 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 324 optimal weight: 2.9990 chunk 325 optimal weight: 7.9990 chunk 363 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 299 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B1013 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN C1013 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4012 r_free = 0.4012 target = 0.169785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135217 restraints weight = 40416.965| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.49 r_work: 0.3106 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 30532 Z= 0.139 Angle : 0.534 9.402 41380 Z= 0.275 Chirality : 0.038 0.176 4676 Planarity : 0.004 0.042 5208 Dihedral : 4.102 19.161 4092 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.56 % Allowed : 8.62 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3672 helix: 1.39 (0.11), residues: 2364 sheet: -0.95 (0.31), residues: 216 loop : -2.45 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 214 HIS 0.003 0.001 HIS A1127 PHE 0.017 0.002 PHE A 793 TYR 0.014 0.001 TYR B 339 ARG 0.004 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04838 ( 1698) hydrogen bonds : angle 3.61907 ( 5034) SS BOND : bond 0.00033 ( 4) SS BOND : angle 0.43405 ( 8) covalent geometry : bond 0.00321 (30528) covalent geometry : angle 0.53414 (41372) *********************** 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 363 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 281 time to evaluate : 3.295 Fit side-chains REVERT: B 224 PHE cc_start: 0.7989 (m-80) cc_final: 0.7612 (m-80) REVERT: B 241 TYR cc_start: 0.6875 (m-80) cc_final: 0.6668 (m-80) REVERT: B 400 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 454 HIS cc_start: 0.7905 (t70) cc_final: 0.7445 (t-90) REVERT: B 849 ARG cc_start: 0.5608 (mtt180) cc_final: 0.4974 (ptm160) REVERT: B 937 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 948 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8712 (pp) REVERT: A 169 VAL cc_start: 0.7810 (t) cc_final: 0.7345 (m) REVERT: A 224 PHE cc_start: 0.8294 (m-80) cc_final: 0.7991 (m-80) REVERT: A 241 TYR cc_start: 0.7072 (m-80) cc_final: 0.6852 (m-80) REVERT: A 400 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8503 (mp) REVERT: A 454 HIS cc_start: 0.7869 (t70) cc_final: 0.7410 (t-90) REVERT: A 849 ARG cc_start: 0.5378 (mtt180) cc_final: 0.4823 (ptm160) REVERT: A 937 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 948 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8710 (pp) REVERT: A 1141 ASP cc_start: 0.8162 (t0) cc_final: 0.7923 (t0) REVERT: C 224 PHE cc_start: 0.8014 (m-80) cc_final: 0.7632 (m-80) REVERT: C 252 LEU cc_start: 0.8101 (tp) cc_final: 0.7653 (mp) REVERT: C 285 MET cc_start: 0.6124 (mmp) cc_final: 0.5329 (mmt) REVERT: C 288 ARG cc_start: 0.7218 (mtp180) cc_final: 0.6689 (mtm180) REVERT: C 400 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8499 (mp) REVERT: C 415 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: C 454 HIS cc_start: 0.7867 (t70) cc_final: 0.7632 (t-90) REVERT: C 849 ARG cc_start: 0.5611 (mtt180) cc_final: 0.4971 (ptm160) REVERT: C 937 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8678 (mp) REVERT: C 948 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8406 (pp) REVERT: C 1141 ASP cc_start: 0.8236 (t0) cc_final: 0.8002 (t0) REVERT: D 224 PHE cc_start: 0.7982 (m-80) cc_final: 0.7591 (m-80) REVERT: D 241 TYR cc_start: 0.6904 (m-80) cc_final: 0.6698 (m-80) REVERT: D 252 LEU cc_start: 0.8090 (tp) cc_final: 0.7641 (mp) REVERT: D 285 MET cc_start: 0.6206 (mmp) cc_final: 0.5876 (mmt) REVERT: D 400 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8483 (mp) REVERT: D 454 HIS cc_start: 0.7846 (t70) cc_final: 0.7610 (t-90) REVERT: D 849 ARG cc_start: 0.5404 (mtt180) cc_final: 0.4841 (ptm160) REVERT: D 937 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8689 (mp) REVERT: D 948 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8714 (pp) outliers start: 82 outliers final: 45 residues processed: 348 average time/residue: 0.4301 time to fit residues: 235.7343 Evaluate side-chains 315 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 257 time to evaluate : 3.507 ------------------------------------------------------------------------------- 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 437 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 948 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 437 ASP 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 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 C residue 102 THR 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 415 PHE Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 473 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 872 LEU 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 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 473 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 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 173 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 287 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B1013 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 GLN A1013 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN C1013 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4000 r_free = 0.4000 target = 0.168830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134476 restraints weight = 40254.276| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.52 r_work: 0.3087 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30532 Z= 0.156 Angle : 0.550 9.845 41380 Z= 0.283 Chirality : 0.039 0.178 4676 Planarity : 0.004 0.043 5208 Dihedral : 4.057 19.160 4092 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.34 % Allowed : 9.56 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3672 helix: 1.64 (0.11), residues: 2364 sheet: -1.28 (0.30), residues: 236 loop : -2.33 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 680 HIS 0.004 0.001 HIS A1127 PHE 0.016 0.002 PHE B 793 TYR 0.013 0.001 TYR C 339 ARG 0.003 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.05034 ( 1698) hydrogen bonds : angle 3.59637 ( 5034) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.44284 ( 8) covalent geometry : bond 0.00368 (30528) covalent geometry : angle 0.54966 (41372) *********************** 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 347 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 272 time to evaluate : 3.348 Fit side-chains REVERT: B 285 MET cc_start: 0.6411 (mmm) cc_final: 0.5860 (mmp) REVERT: B 400 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 454 HIS cc_start: 0.7939 (t70) cc_final: 0.7653 (t-90) REVERT: B 574 MET cc_start: 0.9175 (mtt) cc_final: 0.8968 (mtt) REVERT: B 849 ARG cc_start: 0.5405 (mtt180) cc_final: 0.4858 (ptm160) REVERT: B 851 ARG cc_start: 0.4918 (mtt180) cc_final: 0.4614 (mtp-110) REVERT: B 937 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8724 (mp) REVERT: B 948 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8748 (pp) REVERT: A 400 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 454 HIS cc_start: 0.7922 (t70) cc_final: 0.7472 (t-90) REVERT: A 574 MET cc_start: 0.9181 (mtt) cc_final: 0.8975 (mtt) REVERT: A 683 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 849 ARG cc_start: 0.5493 (mtt180) cc_final: 0.4898 (ptm160) REVERT: A 937 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 948 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8750 (pp) REVERT: A 1141 ASP cc_start: 0.8469 (t0) cc_final: 0.8037 (t0) REVERT: C 252 LEU cc_start: 0.8082 (tp) cc_final: 0.7606 (mp) REVERT: C 285 MET cc_start: 0.6179 (mmp) cc_final: 0.5939 (mmt) REVERT: C 400 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8526 (mp) REVERT: C 454 HIS cc_start: 0.7877 (t70) cc_final: 0.7644 (t-90) REVERT: C 574 MET cc_start: 0.9177 (mtt) cc_final: 0.8971 (mtt) REVERT: C 849 ARG cc_start: 0.5502 (mtt180) cc_final: 0.4888 (ptm160) REVERT: C 937 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8722 (mp) REVERT: C 948 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8422 (pp) REVERT: C 1141 ASP cc_start: 0.8485 (t0) cc_final: 0.8057 (t0) REVERT: D 252 LEU cc_start: 0.8079 (tp) cc_final: 0.7597 (mp) REVERT: D 400 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8520 (mp) REVERT: D 454 HIS cc_start: 0.7854 (t70) cc_final: 0.7625 (t-90) REVERT: D 574 MET cc_start: 0.9192 (mtt) cc_final: 0.8985 (mtt) REVERT: D 849 ARG cc_start: 0.5484 (mtt180) cc_final: 0.4883 (ptm160) REVERT: D 937 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8727 (mp) REVERT: D 948 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8757 (pp) REVERT: D 1141 ASP cc_start: 0.8235 (t0) cc_final: 0.8014 (t0) outliers start: 75 outliers final: 46 residues processed: 326 average time/residue: 0.4290 time to fit residues: 221.6628 Evaluate side-chains 316 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 201 LEU 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 437 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE 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 948 LEU 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 437 ASP Chi-restraints excluded: chain A residue 473 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 872 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 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 437 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 872 LEU 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 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 437 ASP 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 872 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 111 optimal weight: 20.0000 chunk 337 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 318 optimal weight: 0.9980 chunk 327 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN A 633 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 GLN A1013 ASN C 633 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D 633 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.169517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135732 restraints weight = 40315.674| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.62 r_work: 0.3104 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30532 Z= 0.135 Angle : 0.520 9.500 41380 Z= 0.268 Chirality : 0.038 0.178 4676 Planarity : 0.004 0.042 5208 Dihedral : 3.945 19.017 4092 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.56 % Allowed : 9.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3672 helix: 1.84 (0.11), residues: 2372 sheet: -1.21 (0.31), residues: 236 loop : -2.29 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 680 HIS 0.004 0.001 HIS B1127 PHE 0.014 0.001 PHE D 793 TYR 0.012 0.001 TYR D 339 ARG 0.003 0.000 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 1698) hydrogen bonds : angle 3.50532 ( 5034) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.38139 ( 8) covalent geometry : bond 0.00313 (30528) covalent geometry : angle 0.52010 (41372) *********************** 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 385 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 303 time to evaluate : 3.343 Fit side-chains REVERT: B 94 LEU cc_start: 0.8353 (mt) cc_final: 0.8097 (pt) REVERT: B 285 MET cc_start: 0.6400 (mmm) cc_final: 0.5885 (mmp) REVERT: B 400 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8539 (mp) REVERT: B 454 HIS cc_start: 0.7940 (t70) cc_final: 0.7463 (t-90) REVERT: B 849 ARG cc_start: 0.5470 (mtt180) cc_final: 0.4940 (ptm160) REVERT: B 851 ARG cc_start: 0.4943 (mtt180) cc_final: 0.4620 (mtp-110) REVERT: B 937 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 948 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8700 (pp) REVERT: B 1141 ASP cc_start: 0.8818 (t0) cc_final: 0.8255 (t0) REVERT: A 94 LEU cc_start: 0.8387 (mt) cc_final: 0.8139 (pt) REVERT: A 169 VAL cc_start: 0.7858 (t) cc_final: 0.7593 (m) REVERT: A 400 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 411 GLN cc_start: 0.8001 (tp40) cc_final: 0.7742 (tm-30) REVERT: A 415 PHE cc_start: 0.7024 (m-80) cc_final: 0.6739 (m-80) REVERT: A 635 GLU cc_start: 0.8049 (mp0) cc_final: 0.7794 (mp0) REVERT: A 849 ARG cc_start: 0.5443 (mtt180) cc_final: 0.4915 (ptm160) REVERT: A 851 ARG cc_start: 0.4894 (mtt180) cc_final: 0.4596 (mtp-110) REVERT: A 937 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8715 (mp) REVERT: A 948 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8697 (pp) REVERT: A 1141 ASP cc_start: 0.8549 (t0) cc_final: 0.8050 (t0) REVERT: C 252 LEU cc_start: 0.8129 (tp) cc_final: 0.7655 (mp) REVERT: C 400 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8542 (mp) REVERT: C 454 HIS cc_start: 0.7916 (t70) cc_final: 0.7698 (t-90) REVERT: C 849 ARG cc_start: 0.5422 (mtt180) cc_final: 0.4880 (ptm160) REVERT: C 851 ARG cc_start: 0.4964 (mtt180) cc_final: 0.4626 (mtp-110) REVERT: C 937 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8714 (mp) REVERT: C 948 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8427 (pp) REVERT: C 1141 ASP cc_start: 0.8544 (t0) cc_final: 0.8058 (t0) REVERT: D 252 LEU cc_start: 0.8168 (tp) cc_final: 0.7704 (mp) REVERT: D 400 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 454 HIS cc_start: 0.7893 (t70) cc_final: 0.7433 (t-90) REVERT: D 635 GLU cc_start: 0.8051 (mp0) cc_final: 0.7802 (mp0) REVERT: D 849 ARG cc_start: 0.5414 (mtt180) cc_final: 0.4882 (ptm160) REVERT: D 851 ARG cc_start: 0.4945 (mtt180) cc_final: 0.4624 (mtp-110) REVERT: D 937 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8716 (mp) REVERT: D 948 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (pp) REVERT: D 1141 ASP cc_start: 0.8382 (t0) cc_final: 0.8014 (t0) outliers start: 82 outliers final: 54 residues processed: 364 average time/residue: 0.4336 time to fit residues: 248.0331 Evaluate side-chains 336 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 270 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 201 LEU 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 407 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE 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 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 149 SER 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 437 ASP 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 872 LEU 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 102 THR 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 648 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 872 LEU 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 102 THR Chi-restraints excluded: chain D residue 149 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 872 LEU 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 948 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 362 optimal weight: 4.9990 chunk 291 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 345 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1013 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN C1013 ASN D1013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132409 restraints weight = 40317.138| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.49 r_work: 0.3062 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30532 Z= 0.200 Angle : 0.596 10.978 41380 Z= 0.304 Chirality : 0.041 0.193 4676 Planarity : 0.004 0.044 5208 Dihedral : 4.122 19.353 4092 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.56 % Allowed : 9.62 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3672 helix: 1.69 (0.11), residues: 2380 sheet: -0.70 (0.32), residues: 216 loop : -2.42 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 680 HIS 0.004 0.001 HIS A1127 PHE 0.021 0.002 PHE A 113 TYR 0.013 0.002 TYR B 339 ARG 0.005 0.001 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.05618 ( 1698) hydrogen bonds : angle 3.65467 ( 5034) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.58674 ( 8) covalent geometry : bond 0.00485 (30528) covalent geometry : angle 0.59622 (41372) *********************** 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 358 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 276 time to evaluate : 3.801 Fit side-chains REVERT: B 285 MET cc_start: 0.6392 (mmm) cc_final: 0.5876 (mmp) REVERT: B 400 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 849 ARG cc_start: 0.5387 (mtt180) cc_final: 0.4891 (ptm160) REVERT: B 851 ARG cc_start: 0.4920 (mtt180) cc_final: 0.4601 (mtp85) REVERT: B 937 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8774 (mp) REVERT: B 948 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8767 (pp) REVERT: B 1141 ASP cc_start: 0.8838 (t0) cc_final: 0.8293 (t0) REVERT: A 252 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 400 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 849 ARG cc_start: 0.5378 (mtt180) cc_final: 0.4880 (ptm160) REVERT: A 851 ARG cc_start: 0.4911 (mtt180) cc_final: 0.4598 (mtp85) REVERT: A 937 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 948 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8745 (pp) REVERT: A 1141 ASP cc_start: 0.8620 (t0) cc_final: 0.8065 (t0) REVERT: C 252 LEU cc_start: 0.8154 (tp) cc_final: 0.7660 (mp) REVERT: C 400 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8562 (mp) REVERT: C 411 GLN cc_start: 0.8034 (tp40) cc_final: 0.7821 (tm-30) REVERT: C 415 PHE cc_start: 0.7007 (m-80) cc_final: 0.6621 (m-80) REVERT: C 849 ARG cc_start: 0.5502 (mtt180) cc_final: 0.4906 (ptm160) REVERT: C 851 ARG cc_start: 0.4934 (mtt180) cc_final: 0.4604 (mtp85) REVERT: C 937 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8773 (mp) REVERT: C 948 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8535 (pp) REVERT: C 1141 ASP cc_start: 0.8639 (t0) cc_final: 0.8079 (t0) REVERT: D 252 LEU cc_start: 0.8158 (tp) cc_final: 0.7676 (mp) REVERT: D 400 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8556 (mp) REVERT: D 849 ARG cc_start: 0.5480 (mtt180) cc_final: 0.4895 (ptm160) REVERT: D 851 ARG cc_start: 0.4913 (mtt180) cc_final: 0.4594 (mtp85) REVERT: D 937 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8775 (mp) REVERT: D 948 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8762 (pp) REVERT: D 1141 ASP cc_start: 0.8586 (t0) cc_final: 0.8115 (t0) outliers start: 82 outliers final: 55 residues processed: 334 average time/residue: 0.4440 time to fit residues: 233.1419 Evaluate side-chains 321 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 253 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 THR 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 407 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE 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 948 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 102 THR Chi-restraints excluded: chain A residue 149 SER 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 407 VAL Chi-restraints excluded: chain A residue 437 ASP 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 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 1077 ILE 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 407 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 690 ILE 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 D residue 102 THR Chi-restraints excluded: chain D residue 149 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 407 VAL Chi-restraints excluded: chain D residue 473 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 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 65 optimal weight: 5.9990 chunk 331 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 279 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 97 optimal weight: 0.0570 overall best weight: 1.9502 ------------------------------------------------------------------------------- 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 480 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN C 480 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3991 r_free = 0.3991 target = 0.168494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134161 restraints weight = 40594.307| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.49 r_work: 0.3085 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30532 Z= 0.138 Angle : 0.534 9.362 41380 Z= 0.276 Chirality : 0.038 0.191 4676 Planarity : 0.004 0.042 5208 Dihedral : 3.996 18.887 4092 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.41 % Allowed : 9.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3672 helix: 1.88 (0.11), residues: 2380 sheet: -1.10 (0.31), residues: 236 loop : -2.27 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1123 HIS 0.004 0.001 HIS B 166 PHE 0.023 0.001 PHE A 113 TYR 0.012 0.001 TYR C 339 ARG 0.008 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04771 ( 1698) hydrogen bonds : angle 3.51749 ( 5034) SS BOND : bond 0.00042 ( 4) SS BOND : angle 0.40043 ( 8) covalent geometry : bond 0.00320 (30528) covalent geometry : angle 0.53442 (41372) *********************** 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 359 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 282 time to evaluate : 3.485 Fit side-chains REVERT: B 94 LEU cc_start: 0.8356 (mt) cc_final: 0.8060 (pt) REVERT: B 241 TYR cc_start: 0.6863 (m-80) cc_final: 0.6566 (m-80) REVERT: B 285 MET cc_start: 0.6329 (mmm) cc_final: 0.5963 (mmp) REVERT: B 400 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8481 (mp) REVERT: B 849 ARG cc_start: 0.5499 (mtt180) cc_final: 0.4943 (ptm160) REVERT: B 851 ARG cc_start: 0.4861 (mtt180) cc_final: 0.4553 (mtp-110) REVERT: B 937 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8732 (mp) REVERT: B 948 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8690 (pp) REVERT: B 1141 ASP cc_start: 0.8790 (t0) cc_final: 0.8289 (t0) REVERT: A 165 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6089 (mtp-110) REVERT: A 400 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 411 GLN cc_start: 0.7991 (tp40) cc_final: 0.7703 (tm-30) REVERT: A 415 PHE cc_start: 0.6869 (m-80) cc_final: 0.6550 (m-80) REVERT: A 849 ARG cc_start: 0.5482 (mtt180) cc_final: 0.4903 (ptm160) REVERT: A 851 ARG cc_start: 0.4893 (mtt180) cc_final: 0.4590 (mtp-110) REVERT: A 937 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8733 (mp) REVERT: A 948 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8682 (pp) REVERT: A 1141 ASP cc_start: 0.8538 (t0) cc_final: 0.8069 (t0) REVERT: C 252 LEU cc_start: 0.8119 (tp) cc_final: 0.7644 (mp) REVERT: C 400 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8556 (mp) REVERT: C 411 GLN cc_start: 0.8016 (tp40) cc_final: 0.7747 (tm-30) REVERT: C 415 PHE cc_start: 0.7129 (m-80) cc_final: 0.6662 (m-80) REVERT: C 849 ARG cc_start: 0.5527 (mtt180) cc_final: 0.4945 (ptm160) REVERT: C 851 ARG cc_start: 0.4880 (mtt180) cc_final: 0.4557 (mtp-110) REVERT: C 937 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8703 (mp) REVERT: C 948 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8383 (pp) REVERT: C 1141 ASP cc_start: 0.8546 (t0) cc_final: 0.8079 (t0) REVERT: D 94 LEU cc_start: 0.8360 (mt) cc_final: 0.8069 (pt) REVERT: D 241 TYR cc_start: 0.6855 (m-80) cc_final: 0.6573 (m-80) REVERT: D 252 LEU cc_start: 0.8139 (tp) cc_final: 0.7688 (mp) REVERT: D 400 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8513 (mp) REVERT: D 849 ARG cc_start: 0.5484 (mtt180) cc_final: 0.4900 (ptm160) REVERT: D 851 ARG cc_start: 0.4859 (mtt180) cc_final: 0.4547 (mtp-110) REVERT: D 937 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8735 (mp) REVERT: D 948 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8694 (pp) REVERT: D 1141 ASP cc_start: 0.8455 (t0) cc_final: 0.7949 (t0) outliers start: 77 outliers final: 48 residues processed: 338 average time/residue: 0.4390 time to fit residues: 231.3480 Evaluate side-chains 326 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 265 time to evaluate : 2.988 ------------------------------------------------------------------------------- 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 407 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE 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 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 165 ARG 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 407 VAL Chi-restraints excluded: chain A residue 437 ASP 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 C residue 102 THR 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 407 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 690 ILE 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 D residue 102 THR 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 407 VAL 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 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1077 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 265 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 299 optimal weight: 0.1980 chunk 342 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 D1013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136174 restraints weight = 40405.590| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.48 r_work: 0.3140 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 30532 Z= 0.110 Angle : 0.501 8.667 41380 Z= 0.260 Chirality : 0.037 0.176 4676 Planarity : 0.004 0.040 5208 Dihedral : 3.826 18.556 4092 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.03 % Allowed : 10.47 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 3672 helix: 2.06 (0.11), residues: 2384 sheet: -1.07 (0.31), residues: 236 loop : -2.18 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 691 HIS 0.004 0.001 HIS A 166 PHE 0.022 0.001 PHE A 113 TYR 0.010 0.001 TYR D 964 ARG 0.008 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1698) hydrogen bonds : angle 3.40425 ( 5034) SS BOND : bond 0.00036 ( 4) SS BOND : angle 0.33665 ( 8) covalent geometry : bond 0.00242 (30528) covalent geometry : angle 0.50148 (41372) *********************** 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 364 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 299 time to evaluate : 3.395 Fit side-chains revert: symmetry clash REVERT: B 94 LEU cc_start: 0.8338 (mt) cc_final: 0.8068 (pt) REVERT: B 241 TYR cc_start: 0.6792 (m-80) cc_final: 0.6542 (m-80) REVERT: B 285 MET cc_start: 0.6325 (mmm) cc_final: 0.6004 (mmp) REVERT: B 400 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 454 HIS cc_start: 0.7897 (t70) cc_final: 0.7413 (t-90) REVERT: B 574 MET cc_start: 0.9140 (mtt) cc_final: 0.8935 (mtt) REVERT: B 849 ARG cc_start: 0.5510 (mtt180) cc_final: 0.4973 (ptm160) REVERT: B 851 ARG cc_start: 0.4941 (mtt180) cc_final: 0.4613 (mtp-110) REVERT: B 948 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8601 (pp) REVERT: B 1141 ASP cc_start: 0.8796 (t0) cc_final: 0.8240 (t0) REVERT: A 94 LEU cc_start: 0.8332 (mt) cc_final: 0.8067 (pt) REVERT: A 165 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6173 (mtp-110) REVERT: A 400 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 411 GLN cc_start: 0.8045 (tp40) cc_final: 0.7738 (tm-30) REVERT: A 415 PHE cc_start: 0.6848 (m-80) cc_final: 0.6479 (m-80) REVERT: A 849 ARG cc_start: 0.5459 (mtt180) cc_final: 0.4912 (ptm160) REVERT: A 851 ARG cc_start: 0.4938 (mtt180) cc_final: 0.4605 (mtp-110) REVERT: A 1141 ASP cc_start: 0.8541 (t0) cc_final: 0.7949 (t0) REVERT: C 241 TYR cc_start: 0.6747 (m-80) cc_final: 0.6485 (m-80) REVERT: C 252 LEU cc_start: 0.8084 (tp) cc_final: 0.7634 (mp) REVERT: C 400 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8505 (mp) REVERT: C 454 HIS cc_start: 0.7882 (t70) cc_final: 0.7409 (t-90) REVERT: C 849 ARG cc_start: 0.5443 (mtt180) cc_final: 0.4886 (ptm160) REVERT: C 851 ARG cc_start: 0.4947 (mtt180) cc_final: 0.4608 (mtp-110) REVERT: C 948 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8297 (pp) REVERT: C 988 ASN cc_start: 0.7679 (t0) cc_final: 0.7318 (t0) REVERT: D 94 LEU cc_start: 0.8343 (mt) cc_final: 0.8078 (pt) REVERT: D 145 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7535 (ptt90) REVERT: D 241 TYR cc_start: 0.6798 (m-80) cc_final: 0.6564 (m-80) REVERT: D 252 LEU cc_start: 0.8136 (tp) cc_final: 0.7688 (mp) REVERT: D 400 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8502 (mp) REVERT: D 454 HIS cc_start: 0.7893 (t70) cc_final: 0.7411 (t-90) REVERT: D 849 ARG cc_start: 0.5427 (mtt180) cc_final: 0.4881 (ptm160) REVERT: D 851 ARG cc_start: 0.4946 (mtt180) cc_final: 0.4602 (mtp-110) REVERT: D 948 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8604 (pp) REVERT: D 1141 ASP cc_start: 0.8374 (t0) cc_final: 0.7849 (t0) outliers start: 65 outliers final: 43 residues processed: 348 average time/residue: 0.4456 time to fit residues: 242.6320 Evaluate side-chains 328 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 3.093 ------------------------------------------------------------------------------- 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 407 VAL 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 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 165 ARG 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 407 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 908 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 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 407 VAL 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 145 ARG 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 407 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1077 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 255 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 305 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 217 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 286 optimal weight: 20.0000 chunk 158 optimal weight: 0.0470 overall best weight: 1.5282 ------------------------------------------------------------------------------- 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** A 862 GLN A1013 ASN C 411 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4003 r_free = 0.4003 target = 0.169556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135801 restraints weight = 40450.040| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.52 r_work: 0.3149 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30532 Z= 0.122 Angle : 0.518 9.282 41380 Z= 0.267 Chirality : 0.038 0.178 4676 Planarity : 0.004 0.041 5208 Dihedral : 3.801 18.627 4092 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.72 % Allowed : 10.53 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3672 helix: 2.10 (0.11), residues: 2380 sheet: -0.62 (0.32), residues: 216 loop : -2.26 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1123 HIS 0.003 0.001 HIS B 166 PHE 0.010 0.001 PHE C 627 TYR 0.010 0.001 TYR B 339 ARG 0.009 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 1698) hydrogen bonds : angle 3.41489 ( 5034) SS BOND : bond 0.00049 ( 4) SS BOND : angle 0.33643 ( 8) covalent geometry : bond 0.00276 (30528) covalent geometry : angle 0.51844 (41372) ********************** 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 338 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 283 time to evaluate : 3.458 Fit side-chains revert: symmetry clash REVERT: B 94 LEU cc_start: 0.8337 (mt) cc_final: 0.8122 (pt) REVERT: B 241 TYR cc_start: 0.6770 (m-80) cc_final: 0.6568 (m-80) REVERT: B 285 MET cc_start: 0.6419 (mmm) cc_final: 0.6076 (mmp) REVERT: B 400 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8551 (mp) REVERT: B 454 HIS cc_start: 0.7896 (t70) cc_final: 0.7439 (t-90) REVERT: B 849 ARG cc_start: 0.5567 (mtt180) cc_final: 0.5061 (ptm160) REVERT: B 851 ARG cc_start: 0.5035 (mtt180) cc_final: 0.4764 (mtp-110) REVERT: B 1141 ASP cc_start: 0.8824 (t0) cc_final: 0.8282 (t0) REVERT: A 94 LEU cc_start: 0.8329 (mt) cc_final: 0.8116 (pt) REVERT: A 165 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6209 (mtp-110) REVERT: A 241 TYR cc_start: 0.6706 (m-80) cc_final: 0.6434 (m-80) REVERT: A 400 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 411 GLN cc_start: 0.8092 (tp40) cc_final: 0.7773 (tm-30) REVERT: A 415 PHE cc_start: 0.6791 (m-80) cc_final: 0.6457 (m-80) REVERT: A 454 HIS cc_start: 0.7912 (t70) cc_final: 0.7469 (t-90) REVERT: A 849 ARG cc_start: 0.5389 (mtt180) cc_final: 0.4973 (ptm160) REVERT: A 851 ARG cc_start: 0.5011 (mtt180) cc_final: 0.4757 (mtp-110) REVERT: A 948 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8592 (pp) REVERT: C 241 TYR cc_start: 0.6746 (m-80) cc_final: 0.6521 (m-80) REVERT: C 252 LEU cc_start: 0.8162 (tp) cc_final: 0.7727 (mp) REVERT: C 400 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8560 (mp) REVERT: C 411 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: C 415 PHE cc_start: 0.7111 (m-80) cc_final: 0.6892 (m-80) REVERT: C 454 HIS cc_start: 0.7835 (t70) cc_final: 0.7400 (t-90) REVERT: C 849 ARG cc_start: 0.5547 (mtt180) cc_final: 0.5023 (ptm160) REVERT: C 851 ARG cc_start: 0.5026 (mtt180) cc_final: 0.4754 (mtp-110) REVERT: C 948 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8375 (pp) REVERT: C 988 ASN cc_start: 0.7657 (t0) cc_final: 0.7296 (t0) REVERT: D 94 LEU cc_start: 0.8336 (mt) cc_final: 0.8135 (pt) REVERT: D 145 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7542 (ptt90) REVERT: D 252 LEU cc_start: 0.8201 (tp) cc_final: 0.7772 (mp) REVERT: D 400 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8548 (mp) REVERT: D 454 HIS cc_start: 0.7846 (t70) cc_final: 0.7404 (t-90) REVERT: D 849 ARG cc_start: 0.5522 (mtt180) cc_final: 0.5014 (ptm160) REVERT: D 851 ARG cc_start: 0.5016 (mtt180) cc_final: 0.4745 (mtp-110) REVERT: D 1141 ASP cc_start: 0.8442 (t0) cc_final: 0.7917 (t0) outliers start: 55 outliers final: 41 residues processed: 325 average time/residue: 0.4395 time to fit residues: 223.4358 Evaluate side-chains 335 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 285 time to evaluate : 3.242 ------------------------------------------------------------------------------- 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 407 VAL 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 A residue 165 ARG 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 407 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL 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 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 411 GLN 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 D residue 145 ARG Chi-restraints excluded: chain D residue 149 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 407 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL 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 1077 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8522 > 50: distance: 27 - 31: 35.594 distance: 31 - 32: 48.143 distance: 31 - 137: 33.241 distance: 32 - 33: 14.062 distance: 32 - 35: 48.803 distance: 33 - 34: 39.355 distance: 33 - 39: 39.762 distance: 34 - 145: 35.460 distance: 35 - 36: 39.406 distance: 36 - 38: 41.265 distance: 39 - 40: 48.963 distance: 40 - 41: 18.749 distance: 40 - 43: 19.574 distance: 41 - 45: 58.347 distance: 45 - 46: 47.067 distance: 46 - 47: 38.783 distance: 46 - 49: 45.848 distance: 49 - 50: 22.442 distance: 50 - 52: 39.180 distance: 54 - 55: 56.423 distance: 54 - 57: 26.143 distance: 55 - 64: 40.631 distance: 57 - 58: 14.028 distance: 59 - 60: 32.677 distance: 60 - 61: 39.232 distance: 61 - 62: 6.478 distance: 61 - 63: 6.252 distance: 64 - 65: 40.347 distance: 65 - 66: 39.705 distance: 66 - 71: 40.683 distance: 68 - 69: 13.976 distance: 68 - 70: 50.440 distance: 72 - 75: 47.338 distance: 73 - 74: 40.844 distance: 75 - 76: 14.567 distance: 76 - 78: 40.653 distance: 79 - 80: 33.719 distance: 80 - 81: 23.440 distance: 80 - 83: 5.776 distance: 81 - 82: 16.893 distance: 81 - 86: 40.935 distance: 82 - 105: 30.473 distance: 83 - 84: 31.565 distance: 84 - 85: 50.838 distance: 86 - 87: 37.923 distance: 87 - 88: 34.207 distance: 87 - 90: 13.905 distance: 88 - 89: 34.818 distance: 88 - 91: 35.953 distance: 89 - 111: 35.067 distance: 93 - 98: 40.711 distance: 94 - 117: 35.955 distance: 95 - 96: 37.639 distance: 95 - 97: 56.252 distance: 99 - 100: 39.063 distance: 99 - 102: 38.897 distance: 100 - 101: 66.754 distance: 100 - 105: 34.219 distance: 101 - 123: 33.031 distance: 102 - 104: 38.638