Starting phenix.real_space_refine on Wed Jun 25 21:31:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w99_32362/06_2025/7w99_32362.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w99_32362/06_2025/7w99_32362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w99_32362/06_2025/7w99_32362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w99_32362/06_2025/7w99_32362.map" model { file = "/net/cci-nas-00/data/ceres_data/7w99_32362/06_2025/7w99_32362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w99_32362/06_2025/7w99_32362.cif" } resolution = 3.4 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= 0.007 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 18970 2.51 5 N 4982 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29737 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "A" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "B" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "D" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Time building chain proxies: 17.09, per 1000 atoms: 0.57 Number of scatterers: 29737 At special positions: 0 Unit cell: (159.578, 172.694, 240.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 5642 8.00 N 4982 7.00 C 18970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.04 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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: 6.11 Conformation dependent library (CDL) restraints added in 3.4 seconds 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7076 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 51 sheets defined 30.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.785A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.673A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.514A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.537A pdb=" N VAL C 772 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.763A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.503A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.980A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.952A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.806A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.638A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1147 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.071A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.697A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.672A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.541A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.669A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.567A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.696A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.822A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.587A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.019A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.631A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 53 removed outlier: 3.825A pdb=" N ALA B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 3.556A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.636A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.628A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.616A pdb=" N ILE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 172 through 194 Proline residue: B 178 - end of helix removed outlier: 3.606A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 252 removed outlier: 3.756A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.742A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.565A pdb=" N TYR B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 removed outlier: 3.621A pdb=" N VAL B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.744A pdb=" N PHE B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.677A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.617A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 397 through 414 removed outlier: 3.855A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.632A pdb=" N LEU B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 removed outlier: 3.895A pdb=" N ASN B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 512 through 533 removed outlier: 4.057A pdb=" N TYR B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.808A pdb=" N GLY B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 removed outlier: 3.587A pdb=" N ALA B 569 " --> pdb=" O PRO B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.743A pdb=" N THR B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.096A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.815A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.518A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.734A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.577A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.513A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.931A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.556A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN D 764 " --> pdb=" O CYS D 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 773 " --> pdb=" O GLY D 769 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.517A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.529A pdb=" N TYR D 873 " --> pdb=" O MET D 869 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR D 883 " --> pdb=" O ALA D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 891 removed outlier: 4.177A pdb=" N GLY D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.873A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.742A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.593A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.781A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.681A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1147 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.601A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.565A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.592A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.592A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.421A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 327 Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.554A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.642A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 565 through 566 removed outlier: 7.202A pdb=" N PHE C 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.179A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.574A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 788 through 789 removed outlier: 7.041A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.813A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.771A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.753A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 141 through 143 removed outlier: 6.342A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 259 " --> pdb=" O HIS A 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.510A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.694A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.261A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.261A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.103A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.840A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.947A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AD9, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.319A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 347 through 352 removed outlier: 5.884A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 28 through 31 removed outlier: 8.359A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 268 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.641A pdb=" N VAL D 47 " --> pdb=" O TYR D 279 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.829A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 311 through 319 removed outlier: 6.994A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 324 through 327 removed outlier: 4.044A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.874A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.126A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.806A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 718 through 722 Processing sheet with id=AF4, first strand: chain 'D' and resid 718 through 722 removed outlier: 7.062A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D1047 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'D' and resid 1121 through 1122 1129 hydrogen bonds defined for protein. 3141 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: 13.30 Time building geometry restraints manager: 7.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9659 1.35 - 1.48: 7968 1.48 - 1.61: 12623 1.61 - 1.74: 0 1.74 - 1.87: 194 Bond restraints: 30444 Sorted by residual: bond pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.17e-02 7.31e+03 7.36e+00 bond pdb=" C VAL A 860 " pdb=" N LEU A 861 " ideal model delta sigma weight residual 1.331 1.303 0.028 1.48e-02 4.57e+03 3.57e+00 bond pdb=" CB CYS D 525 " pdb=" SG CYS D 525 " ideal model delta sigma weight residual 1.808 1.868 -0.060 3.30e-02 9.18e+02 3.33e+00 bond pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.16e-02 7.43e+03 2.97e+00 bond pdb=" N SER B 19 " pdb=" CA SER B 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 30439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 39987 1.33 - 2.67: 1151 2.67 - 4.00: 127 4.00 - 5.33: 121 5.33 - 6.66: 10 Bond angle restraints: 41396 Sorted by residual: angle pdb=" N SER A 151 " pdb=" CA SER A 151 " pdb=" CB SER A 151 " ideal model delta sigma weight residual 114.17 109.87 4.30 1.14e+00 7.69e-01 1.42e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 120.79 125.91 -5.12 1.39e+00 5.18e-01 1.36e+01 angle pdb=" C ARG A 214 " pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 121.19 126.98 -5.79 1.59e+00 3.96e-01 1.33e+01 angle pdb=" C LYS A 147 " pdb=" CA LYS A 147 " pdb=" CB LYS A 147 " ideal model delta sigma weight residual 110.96 115.65 -4.69 1.54e+00 4.22e-01 9.27e+00 angle pdb=" N LYS A 147 " pdb=" CA LYS A 147 " pdb=" C LYS A 147 " ideal model delta sigma weight residual 110.97 107.91 3.06 1.09e+00 8.42e-01 7.90e+00 ... (remaining 41391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16896 17.99 - 35.99: 1012 35.99 - 53.98: 151 53.98 - 71.97: 43 71.97 - 89.97: 34 Dihedral angle restraints: 18136 sinusoidal: 7139 harmonic: 10997 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 34.20 58.80 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA ARG A 214 " pdb=" C ARG A 214 " pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta harmonic sigma weight residual -180.00 -147.96 -32.04 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual 93.00 44.66 48.34 1 1.00e+01 1.00e-02 3.22e+01 ... (remaining 18133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3039 0.033 - 0.066: 1099 0.066 - 0.099: 234 0.099 - 0.132: 226 0.132 - 0.165: 18 Chirality restraints: 4616 Sorted by residual: chirality pdb=" CA ILE A 896 " pdb=" N ILE A 896 " pdb=" C ILE A 896 " pdb=" CB ILE A 896 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA ILE A 714 " pdb=" N ILE A 714 " pdb=" C ILE A 714 " pdb=" CB ILE A 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 4613 not shown) Planarity restraints: 5375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 599 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO C 600 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 600 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 600 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 130 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C VAL C 130 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL C 130 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS C 131 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 283 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 284 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.018 5.00e-02 4.00e+02 ... (remaining 5372 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 323 2.64 - 3.21: 26511 3.21 - 3.77: 43677 3.77 - 4.34: 62475 4.34 - 4.90: 103405 Nonbonded interactions: 236391 Sorted by model distance: nonbonded pdb=" O GLN C 755 " pdb=" OG SER A 968 " model vdw 2.076 3.040 nonbonded pdb=" O GLN A 755 " pdb=" OG SER D 968 " model vdw 2.079 3.040 nonbonded pdb=" OG SER D 708 " pdb=" OG SER D 711 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR A 883 " pdb=" OH TYR D 707 " model vdw 2.186 3.040 nonbonded pdb=" O VAL C1040 " pdb=" OG SER D1030 " model vdw 2.202 3.040 ... (remaining 236386 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' 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: 3.310 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: 0.060 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 65.020 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.004 0.060 30486 Z= 0.172 Angle : 0.595 6.664 41480 Z= 0.335 Chirality : 0.042 0.165 4616 Planarity : 0.003 0.036 5375 Dihedral : 12.548 89.967 10934 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.12 % Allowed : 1.61 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.42 (0.11), residues: 3733 helix: -2.51 (0.11), residues: 998 sheet: -2.18 (0.17), residues: 684 loop : -2.16 (0.12), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 203 HIS 0.003 0.001 HIS A 655 PHE 0.018 0.001 PHE A 906 TYR 0.012 0.001 TYR A 707 ARG 0.003 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.26843 ( 1122) hydrogen bonds : angle 9.18060 ( 3141) SS BOND : bond 0.00444 ( 42) SS BOND : angle 1.05241 ( 84) covalent geometry : bond 0.00374 (30444) covalent geometry : angle 0.59355 (41396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 694 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 SER cc_start: 0.8302 (m) cc_final: 0.7983 (p) REVERT: C 133 PHE cc_start: 0.6678 (m-80) cc_final: 0.6477 (m-10) REVERT: C 140 PHE cc_start: 0.4865 (p90) cc_final: 0.3872 (p90) REVERT: C 141 LEU cc_start: 0.6148 (mt) cc_final: 0.5920 (mt) REVERT: C 166 CYS cc_start: 0.6476 (OUTLIER) cc_final: 0.6012 (t) REVERT: C 236 THR cc_start: 0.8867 (p) cc_final: 0.8566 (t) REVERT: C 258 TRP cc_start: 0.4894 (m-10) cc_final: 0.4361 (m-10) REVERT: C 357 ARG cc_start: 0.5471 (ttt180) cc_final: 0.5057 (mpt-90) REVERT: C 369 TYR cc_start: 0.6019 (t80) cc_final: 0.5606 (p90) REVERT: C 541 PHE cc_start: 0.5919 (m-80) cc_final: 0.5166 (m-80) REVERT: C 557 LYS cc_start: 0.7190 (mttt) cc_final: 0.6759 (mtpp) REVERT: C 585 LEU cc_start: 0.7657 (mt) cc_final: 0.7320 (mt) REVERT: C 673 SER cc_start: 0.8509 (p) cc_final: 0.8043 (m) REVERT: C 747 THR cc_start: 0.8908 (m) cc_final: 0.8680 (p) REVERT: C 748 GLU cc_start: 0.7534 (mp0) cc_final: 0.7221 (mp0) REVERT: C 941 THR cc_start: 0.7683 (m) cc_final: 0.7372 (p) REVERT: C 1047 TYR cc_start: 0.8595 (m-80) cc_final: 0.7938 (m-80) REVERT: A 118 LEU cc_start: 0.7871 (mt) cc_final: 0.7628 (mt) REVERT: A 129 LYS cc_start: 0.7067 (mttm) cc_final: 0.6838 (tptp) REVERT: A 170 TYR cc_start: 0.8254 (t80) cc_final: 0.7591 (t80) REVERT: A 287 ASP cc_start: 0.8335 (t0) cc_final: 0.8000 (m-30) REVERT: A 368 LEU cc_start: 0.6810 (tp) cc_final: 0.6384 (tp) REVERT: A 436 TRP cc_start: 0.5393 (t60) cc_final: 0.4938 (t60) REVERT: A 508 TYR cc_start: 0.6982 (m-80) cc_final: 0.6406 (m-80) REVERT: A 869 MET cc_start: 0.8614 (mtt) cc_final: 0.8405 (mtt) REVERT: A 896 ILE cc_start: 0.6835 (mt) cc_final: 0.6543 (mt) REVERT: A 941 THR cc_start: 0.6803 (m) cc_final: 0.6226 (p) REVERT: B 114 LYS cc_start: 0.6179 (mttt) cc_final: 0.5933 (tttt) REVERT: B 131 LYS cc_start: 0.3236 (pttt) cc_final: 0.3032 (pttm) REVERT: B 177 ARG cc_start: 0.3721 (ttp80) cc_final: 0.3124 (ttt90) REVERT: B 215 TYR cc_start: 0.2183 (m-80) cc_final: 0.1960 (m-80) REVERT: B 323 MET cc_start: 0.5935 (mmt) cc_final: 0.5610 (mmt) REVERT: B 474 MET cc_start: 0.0337 (tpp) cc_final: -0.0379 (tpp) REVERT: B 555 PHE cc_start: 0.4120 (t80) cc_final: 0.3729 (t80) REVERT: D 48 LEU cc_start: 0.8239 (tp) cc_final: 0.8012 (mt) REVERT: D 170 TYR cc_start: 0.7122 (t80) cc_final: 0.6595 (t80) REVERT: D 216 LEU cc_start: 0.7607 (tp) cc_final: 0.7393 (tp) REVERT: D 274 THR cc_start: 0.8846 (m) cc_final: 0.8576 (m) REVERT: D 390 LEU cc_start: 0.6877 (mp) cc_final: 0.6299 (tp) REVERT: D 532 ASN cc_start: 0.8429 (p0) cc_final: 0.8089 (t0) REVERT: D 751 ASN cc_start: 0.8493 (m-40) cc_final: 0.8226 (m-40) outliers start: 4 outliers final: 1 residues processed: 697 average time/residue: 0.4265 time to fit residues: 463.7783 Evaluate side-chains 366 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 364 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain D residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 0.9980 chunk 285 optimal weight: 10.0000 chunk 158 optimal weight: 0.0030 chunk 97 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 295 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 342 optimal weight: 3.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS C 519 HIS C 564 GLN C 655 HIS ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 188 ASN A 655 HIS A 919 ASN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 49 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 159 ASN B 241 HIS B 472 GLN B 535 HIS B 572 ASN D 137 ASN D 334 ASN D 895 GLN D 935 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.161251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.132232 restraints weight = 82506.394| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.78 r_work: 0.3876 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30486 Z= 0.160 Angle : 0.595 7.935 41480 Z= 0.309 Chirality : 0.046 0.228 4616 Planarity : 0.004 0.049 5375 Dihedral : 4.194 47.219 4052 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.64 % Allowed : 8.39 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 3733 helix: -0.24 (0.15), residues: 1027 sheet: -1.15 (0.17), residues: 697 loop : -1.53 (0.12), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 328 HIS 0.006 0.001 HIS A 49 PHE 0.023 0.002 PHE D 497 TYR 0.029 0.002 TYR D 495 ARG 0.017 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 1122) hydrogen bonds : angle 5.60714 ( 3141) SS BOND : bond 0.00417 ( 42) SS BOND : angle 1.73259 ( 84) covalent geometry : bond 0.00366 (30444) covalent geometry : angle 0.59067 (41396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 453 time to evaluate : 5.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 PHE cc_start: 0.4774 (p90) cc_final: 0.4095 (p90) REVERT: C 166 CYS cc_start: 0.5977 (OUTLIER) cc_final: 0.5492 (p) REVERT: C 236 THR cc_start: 0.8446 (p) cc_final: 0.8191 (t) REVERT: C 258 TRP cc_start: 0.5376 (m-10) cc_final: 0.4555 (m-10) REVERT: C 357 ARG cc_start: 0.5871 (ttt180) cc_final: 0.5525 (mpt-90) REVERT: C 557 LYS cc_start: 0.7261 (mttt) cc_final: 0.7013 (mtmt) REVERT: C 577 ARG cc_start: 0.7299 (ttp80) cc_final: 0.7019 (ttp80) REVERT: C 1047 TYR cc_start: 0.8727 (m-80) cc_final: 0.8061 (m-80) REVERT: C 1111 GLU cc_start: 0.7087 (pt0) cc_final: 0.6689 (pt0) REVERT: A 287 ASP cc_start: 0.8333 (t0) cc_final: 0.8015 (m-30) REVERT: A 508 TYR cc_start: 0.7310 (m-80) cc_final: 0.7044 (m-80) REVERT: A 750 SER cc_start: 0.8722 (m) cc_final: 0.8293 (t) REVERT: A 751 ASN cc_start: 0.8746 (m-40) cc_final: 0.8516 (m-40) REVERT: A 1040 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8517 (p) REVERT: A 1045 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8177 (mmtm) REVERT: A 1091 ARG cc_start: 0.8635 (ptp-110) cc_final: 0.8266 (ttm-80) REVERT: B 114 LYS cc_start: 0.6342 (mttt) cc_final: 0.6071 (tttt) REVERT: B 152 MET cc_start: -0.2362 (mmm) cc_final: -0.2719 (mmm) REVERT: B 177 ARG cc_start: 0.3348 (ttp80) cc_final: 0.3093 (ttm-80) REVERT: B 323 MET cc_start: 0.5509 (mmt) cc_final: 0.5002 (mmm) REVERT: B 453 THR cc_start: 0.4016 (m) cc_final: 0.3497 (p) REVERT: B 455 MET cc_start: 0.5832 (tmm) cc_final: 0.5575 (ppp) REVERT: B 474 MET cc_start: 0.0102 (tpp) cc_final: -0.0284 (tpp) REVERT: B 555 PHE cc_start: 0.3828 (t80) cc_final: 0.3625 (t80) REVERT: D 128 ILE cc_start: 0.8517 (mp) cc_final: 0.8201 (pt) REVERT: D 140 PHE cc_start: 0.5907 (p90) cc_final: 0.5236 (p90) REVERT: D 495 TYR cc_start: 0.3811 (m-80) cc_final: 0.2913 (m-80) REVERT: D 532 ASN cc_start: 0.8682 (p0) cc_final: 0.8293 (t0) REVERT: D 703 ASN cc_start: 0.8603 (t0) cc_final: 0.8321 (t0) REVERT: D 1041 ASP cc_start: 0.7852 (t0) cc_final: 0.7509 (t0) outliers start: 54 outliers final: 31 residues processed: 488 average time/residue: 0.4458 time to fit residues: 347.5554 Evaluate side-chains 363 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 330 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 316 optimal weight: 0.6980 chunk 370 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 356 optimal weight: 0.7980 chunk 105 optimal weight: 0.0970 chunk 273 optimal weight: 0.6980 chunk 202 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 895 GLN C1054 GLN A 49 HIS A 239 GLN A 919 ASN A 965 GLN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 334 ASN D 655 HIS ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.160691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.130949 restraints weight = 81963.431| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.98 r_work: 0.3857 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30486 Z= 0.112 Angle : 0.527 9.204 41480 Z= 0.271 Chirality : 0.043 0.195 4616 Planarity : 0.004 0.044 5375 Dihedral : 3.878 31.235 4052 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.54 % Allowed : 11.39 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.84 (0.13), residues: 3733 helix: 0.67 (0.16), residues: 1011 sheet: -0.62 (0.18), residues: 730 loop : -1.16 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 436 HIS 0.020 0.001 HIS C 519 PHE 0.020 0.001 PHE D 338 TYR 0.022 0.001 TYR D 495 ARG 0.009 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 1122) hydrogen bonds : angle 5.08383 ( 3141) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.53312 ( 84) covalent geometry : bond 0.00251 (30444) covalent geometry : angle 0.52287 (41396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 368 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.6627 (tt0) cc_final: 0.5368 (tp30) REVERT: C 236 THR cc_start: 0.8529 (p) cc_final: 0.8271 (t) REVERT: C 357 ARG cc_start: 0.5847 (ttt180) cc_final: 0.5453 (mpt-90) REVERT: C 439 ASN cc_start: 0.5557 (p0) cc_final: 0.4715 (t0) REVERT: C 1047 TYR cc_start: 0.8749 (m-80) cc_final: 0.8049 (m-80) REVERT: A 508 TYR cc_start: 0.7402 (m-80) cc_final: 0.7077 (m-80) REVERT: A 750 SER cc_start: 0.8689 (m) cc_final: 0.8329 (t) REVERT: A 751 ASN cc_start: 0.8685 (m-40) cc_final: 0.8447 (m-40) REVERT: A 979 ASP cc_start: 0.8040 (t0) cc_final: 0.7829 (t0) REVERT: A 988 GLU cc_start: 0.8513 (mp0) cc_final: 0.7987 (pm20) REVERT: A 1040 VAL cc_start: 0.9012 (m) cc_final: 0.8650 (p) REVERT: A 1073 LYS cc_start: 0.8882 (tptt) cc_final: 0.8468 (mptt) REVERT: A 1091 ARG cc_start: 0.8619 (ptp-110) cc_final: 0.8335 (ttm-80) REVERT: B 114 LYS cc_start: 0.6144 (mttt) cc_final: 0.5919 (tttt) REVERT: B 177 ARG cc_start: 0.3216 (ttp80) cc_final: 0.2969 (ttm-80) REVERT: B 323 MET cc_start: 0.5760 (mmt) cc_final: 0.5178 (mmm) REVERT: B 453 THR cc_start: 0.3360 (m) cc_final: 0.3023 (p) REVERT: B 455 MET cc_start: 0.5809 (tmm) cc_final: 0.5451 (ppp) REVERT: B 462 MET cc_start: 0.4942 (mtt) cc_final: 0.4310 (mmm) REVERT: B 474 MET cc_start: 0.0145 (tpp) cc_final: -0.0267 (tpp) REVERT: B 509 ASP cc_start: 0.1372 (OUTLIER) cc_final: -0.0060 (t0) REVERT: D 453 TYR cc_start: 0.4634 (p90) cc_final: 0.4262 (p90) REVERT: D 464 PHE cc_start: 0.6617 (m-80) cc_final: 0.6363 (m-80) REVERT: D 532 ASN cc_start: 0.8667 (p0) cc_final: 0.8315 (t0) REVERT: D 703 ASN cc_start: 0.8738 (t0) cc_final: 0.8369 (t0) REVERT: D 1041 ASP cc_start: 0.7819 (t0) cc_final: 0.7585 (t0) outliers start: 51 outliers final: 29 residues processed: 401 average time/residue: 0.3970 time to fit residues: 259.4750 Evaluate side-chains 349 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 319 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 373 optimal weight: 0.7980 chunk 278 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN B 277 ASN D 14 GLN D 165 ASN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.152647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.122529 restraints weight = 83499.531| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.10 r_work: 0.3717 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 30486 Z= 0.263 Angle : 0.690 10.481 41480 Z= 0.363 Chirality : 0.048 0.184 4616 Planarity : 0.005 0.053 5375 Dihedral : 4.792 27.175 4051 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.48 % Allowed : 12.81 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.95 (0.13), residues: 3733 helix: 0.54 (0.16), residues: 996 sheet: -0.47 (0.18), residues: 712 loop : -1.30 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 258 HIS 0.005 0.001 HIS C 245 PHE 0.032 0.002 PHE D 497 TYR 0.037 0.002 TYR D 495 ARG 0.017 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 1122) hydrogen bonds : angle 5.42513 ( 3141) SS BOND : bond 0.00541 ( 42) SS BOND : angle 2.14807 ( 84) covalent geometry : bond 0.00600 (30444) covalent geometry : angle 0.68436 (41396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 341 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 PHE cc_start: 0.6124 (p90) cc_final: 0.5756 (p90) REVERT: C 153 MET cc_start: 0.0997 (tpt) cc_final: 0.0775 (tpt) REVERT: C 258 TRP cc_start: 0.5945 (m-10) cc_final: 0.4619 (m-10) REVERT: C 304 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8696 (tmmt) REVERT: C 357 ARG cc_start: 0.5888 (ttt180) cc_final: 0.5380 (mpt-90) REVERT: C 1139 ASP cc_start: 0.8579 (t0) cc_final: 0.8174 (t0) REVERT: A 697 MET cc_start: 0.8694 (ptm) cc_final: 0.8467 (ptm) REVERT: A 750 SER cc_start: 0.8677 (m) cc_final: 0.8352 (t) REVERT: A 779 GLN cc_start: 0.9040 (tp40) cc_final: 0.8827 (tm-30) REVERT: A 1040 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8763 (p) REVERT: B 35 GLU cc_start: 0.6561 (mt-10) cc_final: 0.5930 (tp30) REVERT: B 50 TYR cc_start: 0.7895 (t80) cc_final: 0.7614 (t80) REVERT: B 323 MET cc_start: 0.5656 (mmt) cc_final: 0.5036 (mmm) REVERT: B 453 THR cc_start: 0.3521 (m) cc_final: 0.3216 (p) REVERT: B 474 MET cc_start: -0.0019 (tpp) cc_final: -0.0458 (mmp) REVERT: B 475 LYS cc_start: 0.7644 (mttm) cc_final: 0.7238 (mttm) REVERT: D 379 CYS cc_start: 0.1929 (OUTLIER) cc_final: 0.1524 (p) REVERT: D 390 LEU cc_start: 0.6564 (mp) cc_final: 0.6019 (mt) REVERT: D 532 ASN cc_start: 0.8808 (p0) cc_final: 0.8587 (t0) outliers start: 82 outliers final: 55 residues processed: 395 average time/residue: 0.4278 time to fit residues: 273.4608 Evaluate side-chains 338 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 281 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 379 CYS Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 36 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 362 optimal weight: 0.9990 chunk 296 optimal weight: 0.0020 chunk 272 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 47 optimal weight: 0.0870 overall best weight: 0.5566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C1119 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN D 914 ASN D1010 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.156576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.126493 restraints weight = 82075.316| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.95 r_work: 0.3785 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 30486 Z= 0.108 Angle : 0.529 8.541 41480 Z= 0.275 Chirality : 0.043 0.190 4616 Planarity : 0.004 0.055 5375 Dihedral : 4.125 26.222 4050 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.79 % Allowed : 14.14 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.60 (0.13), residues: 3733 helix: 0.98 (0.17), residues: 1007 sheet: -0.34 (0.18), residues: 737 loop : -1.15 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.003 0.000 HIS C 69 PHE 0.028 0.001 PHE D 392 TYR 0.031 0.001 TYR D 495 ARG 0.010 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 1122) hydrogen bonds : angle 4.89003 ( 3141) SS BOND : bond 0.00325 ( 42) SS BOND : angle 1.98931 ( 84) covalent geometry : bond 0.00241 (30444) covalent geometry : angle 0.52227 (41396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 341 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 THR cc_start: 0.8454 (p) cc_final: 0.8248 (t) REVERT: C 304 LYS cc_start: 0.9097 (tmtt) cc_final: 0.8659 (tmmt) REVERT: C 357 ARG cc_start: 0.5875 (ttt180) cc_final: 0.5427 (mpt-90) REVERT: C 787 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: C 1047 TYR cc_start: 0.8834 (m-80) cc_final: 0.8092 (m-80) REVERT: A 392 PHE cc_start: 0.5466 (OUTLIER) cc_final: 0.4005 (m-80) REVERT: A 750 SER cc_start: 0.8546 (m) cc_final: 0.8299 (t) REVERT: A 774 GLN cc_start: 0.8880 (mp10) cc_final: 0.8653 (mm110) REVERT: A 858 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9079 (mt) REVERT: A 981 LEU cc_start: 0.8126 (mt) cc_final: 0.7852 (pp) REVERT: A 1040 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8871 (p) REVERT: B 35 GLU cc_start: 0.6350 (mt-10) cc_final: 0.5914 (tp30) REVERT: B 50 TYR cc_start: 0.7800 (t80) cc_final: 0.7567 (t80) REVERT: B 323 MET cc_start: 0.5690 (mmt) cc_final: 0.5189 (mmm) REVERT: B 474 MET cc_start: 0.0089 (tpp) cc_final: -0.0196 (tpp) REVERT: B 475 LYS cc_start: 0.7636 (mttm) cc_final: 0.7295 (mttm) REVERT: D 177 MET cc_start: -0.3784 (mmt) cc_final: -0.4194 (mmm) REVERT: D 317 ASN cc_start: 0.8384 (t0) cc_final: 0.7929 (t0) REVERT: D 390 LEU cc_start: 0.6466 (mp) cc_final: 0.5973 (mt) REVERT: D 1039 ARG cc_start: 0.9001 (mtp85) cc_final: 0.8728 (mtp85) REVERT: D 1041 ASP cc_start: 0.7774 (t0) cc_final: 0.7559 (t0) outliers start: 59 outliers final: 36 residues processed: 375 average time/residue: 0.3857 time to fit residues: 240.5306 Evaluate side-chains 339 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 311 optimal weight: 8.9990 chunk 350 optimal weight: 6.9990 chunk 366 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 275 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 954 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN B 472 GLN D 245 HIS D 334 ASN D 460 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN D1010 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.148169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.118650 restraints weight = 83495.119| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.78 r_work: 0.3685 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 30486 Z= 0.321 Angle : 0.780 10.903 41480 Z= 0.407 Chirality : 0.051 0.243 4616 Planarity : 0.005 0.056 5375 Dihedral : 5.325 29.631 4050 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.09 % Allowed : 14.81 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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 (0.13), residues: 3733 helix: 0.45 (0.16), residues: 975 sheet: -0.44 (0.19), residues: 708 loop : -1.45 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 258 HIS 0.007 0.001 HIS C 245 PHE 0.046 0.003 PHE D 497 TYR 0.041 0.003 TYR B 41 ARG 0.015 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.05292 ( 1122) hydrogen bonds : angle 5.68051 ( 3141) SS BOND : bond 0.00522 ( 42) SS BOND : angle 2.52782 ( 84) covalent geometry : bond 0.00754 (30444) covalent geometry : angle 0.77218 (41396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 321 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 242 LEU cc_start: 0.6557 (mp) cc_final: 0.6330 (mt) REVERT: C 357 ARG cc_start: 0.6111 (ttt180) cc_final: 0.5511 (mpt-90) REVERT: C 787 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: A 170 TYR cc_start: 0.8097 (t80) cc_final: 0.7807 (t80) REVERT: A 244 LEU cc_start: 0.5353 (mp) cc_final: 0.4888 (mp) REVERT: A 392 PHE cc_start: 0.5332 (OUTLIER) cc_final: 0.4010 (m-80) REVERT: A 571 ASP cc_start: 0.6864 (m-30) cc_final: 0.6521 (t0) REVERT: A 697 MET cc_start: 0.8740 (ptm) cc_final: 0.8522 (ptm) REVERT: A 750 SER cc_start: 0.8642 (m) cc_final: 0.8322 (t) REVERT: A 858 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8993 (mt) REVERT: A 900 MET cc_start: 0.8958 (mtm) cc_final: 0.8539 (mtp) REVERT: A 904 TYR cc_start: 0.7421 (t80) cc_final: 0.6653 (t80) REVERT: A 1040 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8801 (p) REVERT: B 35 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6131 (tp30) REVERT: B 37 GLU cc_start: 0.7003 (pt0) cc_final: 0.6776 (pt0) REVERT: B 50 TYR cc_start: 0.8001 (t80) cc_final: 0.7671 (t80) REVERT: B 323 MET cc_start: 0.5705 (mmt) cc_final: 0.5255 (mtm) REVERT: B 474 MET cc_start: 0.0075 (tpp) cc_final: -0.0172 (mmp) REVERT: B 475 LYS cc_start: 0.7582 (mttm) cc_final: 0.7199 (mttm) REVERT: B 480 MET cc_start: 0.2277 (mmt) cc_final: 0.1920 (mmm) REVERT: B 482 ARG cc_start: 0.5610 (mtm180) cc_final: 0.5236 (mtm180) REVERT: D 164 ASN cc_start: 0.5647 (p0) cc_final: 0.5058 (p0) REVERT: D 390 LEU cc_start: 0.6439 (mp) cc_final: 0.6002 (mm) REVERT: D 808 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7676 (p0) REVERT: D 1041 ASP cc_start: 0.7998 (t0) cc_final: 0.7777 (t0) outliers start: 102 outliers final: 68 residues processed: 394 average time/residue: 0.3766 time to fit residues: 245.9377 Evaluate side-chains 355 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 282 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 808 ASP Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 129 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 954 GLN A 544 ASN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.153103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.123318 restraints weight = 82088.879| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.92 r_work: 0.3741 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30486 Z= 0.125 Angle : 0.564 11.091 41480 Z= 0.292 Chirality : 0.044 0.243 4616 Planarity : 0.004 0.057 5375 Dihedral : 4.479 28.181 4050 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.00 % Allowed : 16.41 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.76 (0.13), residues: 3733 helix: 0.83 (0.17), residues: 999 sheet: -0.28 (0.19), residues: 745 loop : -1.31 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 353 HIS 0.004 0.001 HIS B 228 PHE 0.027 0.001 PHE D 392 TYR 0.026 0.001 TYR D 495 ARG 0.010 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 1122) hydrogen bonds : angle 5.05963 ( 3141) SS BOND : bond 0.00532 ( 42) SS BOND : angle 2.04022 ( 84) covalent geometry : bond 0.00286 (30444) covalent geometry : angle 0.55696 (41396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 357 ARG cc_start: 0.5851 (ttt180) cc_final: 0.5345 (mpt-90) REVERT: C 495 TYR cc_start: 0.0402 (m-80) cc_final: -0.0093 (m-80) REVERT: C 1047 TYR cc_start: 0.8831 (m-80) cc_final: 0.7973 (m-80) REVERT: A 41 LYS cc_start: 0.8406 (mptt) cc_final: 0.8061 (mmmm) REVERT: A 170 TYR cc_start: 0.7987 (t80) cc_final: 0.7741 (t80) REVERT: A 392 PHE cc_start: 0.5409 (OUTLIER) cc_final: 0.3932 (m-80) REVERT: A 571 ASP cc_start: 0.7004 (m-30) cc_final: 0.6655 (t0) REVERT: A 858 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8965 (mt) REVERT: A 979 ASP cc_start: 0.7927 (t0) cc_final: 0.7610 (t0) REVERT: B 35 GLU cc_start: 0.6383 (mt-10) cc_final: 0.6002 (tp30) REVERT: B 41 TYR cc_start: 0.6149 (m-10) cc_final: 0.5877 (m-10) REVERT: B 82 MET cc_start: 0.8074 (mmm) cc_final: 0.5804 (ptt) REVERT: B 323 MET cc_start: 0.5849 (mmt) cc_final: 0.5549 (mtm) REVERT: B 475 LYS cc_start: 0.7645 (mttm) cc_final: 0.7323 (mttm) REVERT: B 482 ARG cc_start: 0.5419 (mtm180) cc_final: 0.4984 (mtm110) REVERT: D 22 THR cc_start: 0.5983 (OUTLIER) cc_final: 0.5488 (p) REVERT: D 164 ASN cc_start: 0.5649 (p0) cc_final: 0.5086 (p0) REVERT: D 390 LEU cc_start: 0.6380 (mp) cc_final: 0.6085 (mt) REVERT: D 541 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5631 (m-80) REVERT: D 964 LYS cc_start: 0.8818 (tttp) cc_final: 0.8549 (ttmm) outliers start: 66 outliers final: 40 residues processed: 361 average time/residue: 0.3818 time to fit residues: 227.0121 Evaluate side-chains 329 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 285 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 151 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 335 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.150644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.120899 restraints weight = 81870.925| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.76 r_work: 0.3710 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 30486 Z= 0.173 Angle : 0.606 12.682 41480 Z= 0.313 Chirality : 0.045 0.267 4616 Planarity : 0.004 0.069 5375 Dihedral : 4.559 27.315 4050 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.21 % Allowed : 16.84 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.77 (0.13), residues: 3733 helix: 0.83 (0.17), residues: 999 sheet: -0.25 (0.19), residues: 743 loop : -1.33 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 353 HIS 0.004 0.001 HIS D 146 PHE 0.024 0.002 PHE C 823 TYR 0.019 0.002 TYR D 495 ARG 0.012 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1122) hydrogen bonds : angle 5.09083 ( 3141) SS BOND : bond 0.00514 ( 42) SS BOND : angle 2.17995 ( 84) covalent geometry : bond 0.00405 (30444) covalent geometry : angle 0.59895 (41396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 298 time to evaluate : 4.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.5331 (p90) REVERT: C 357 ARG cc_start: 0.6005 (ttt180) cc_final: 0.5457 (mpt-90) REVERT: C 572 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.7978 (p) REVERT: C 1047 TYR cc_start: 0.8870 (m-80) cc_final: 0.8036 (m-80) REVERT: A 159 VAL cc_start: 0.7727 (t) cc_final: 0.7439 (t) REVERT: A 170 TYR cc_start: 0.8038 (t80) cc_final: 0.7807 (t80) REVERT: A 392 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.4102 (m-80) REVERT: A 571 ASP cc_start: 0.7083 (m-30) cc_final: 0.6603 (t0) REVERT: A 858 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8976 (mt) REVERT: A 900 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8334 (mtm) REVERT: A 979 ASP cc_start: 0.8031 (t0) cc_final: 0.7664 (t0) REVERT: A 983 ARG cc_start: 0.7262 (mtp180) cc_final: 0.6868 (mtp180) REVERT: B 35 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6025 (tp30) REVERT: B 41 TYR cc_start: 0.5791 (m-10) cc_final: 0.5511 (m-10) REVERT: B 50 TYR cc_start: 0.7808 (t80) cc_final: 0.7536 (t80) REVERT: B 82 MET cc_start: 0.8160 (mmm) cc_final: 0.6040 (ptt) REVERT: B 475 LYS cc_start: 0.7436 (mttm) cc_final: 0.7105 (mttm) REVERT: B 482 ARG cc_start: 0.5454 (mtm180) cc_final: 0.5077 (mtm110) REVERT: D 22 THR cc_start: 0.6134 (OUTLIER) cc_final: 0.5910 (p) REVERT: D 164 ASN cc_start: 0.5757 (p0) cc_final: 0.5141 (p0) REVERT: D 541 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5834 (m-80) REVERT: D 739 THR cc_start: 0.8615 (m) cc_final: 0.8356 (t) REVERT: D 964 LYS cc_start: 0.8833 (tttp) cc_final: 0.8567 (ttmm) outliers start: 73 outliers final: 54 residues processed: 347 average time/residue: 0.4620 time to fit residues: 265.6125 Evaluate side-chains 342 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 281 time to evaluate : 5.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 77 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 337 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 151 optimal weight: 0.0570 chunk 85 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN ** D 563 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 = 0.4308 r_free = 0.4308 target = 0.152922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.123219 restraints weight = 81973.606| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.86 r_work: 0.3740 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30486 Z= 0.128 Angle : 0.561 12.742 41480 Z= 0.290 Chirality : 0.044 0.287 4616 Planarity : 0.004 0.064 5375 Dihedral : 4.300 29.167 4050 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.94 % Allowed : 17.23 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.58 (0.14), residues: 3733 helix: 1.03 (0.17), residues: 993 sheet: -0.10 (0.19), residues: 724 loop : -1.25 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 353 HIS 0.003 0.001 HIS B 228 PHE 0.027 0.001 PHE C 823 TYR 0.018 0.001 TYR D 495 ARG 0.009 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 1122) hydrogen bonds : angle 4.88175 ( 3141) SS BOND : bond 0.00480 ( 42) SS BOND : angle 2.01838 ( 84) covalent geometry : bond 0.00295 (30444) covalent geometry : angle 0.55401 (41396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 313 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 ILE cc_start: 0.7634 (mt) cc_final: 0.7423 (mm) REVERT: C 242 LEU cc_start: 0.7306 (mm) cc_final: 0.6894 (mm) REVERT: C 357 ARG cc_start: 0.5854 (ttt180) cc_final: 0.5491 (mpt-90) REVERT: C 547 THR cc_start: 0.7985 (p) cc_final: 0.7775 (t) REVERT: C 1047 TYR cc_start: 0.8852 (m-80) cc_final: 0.8007 (m-80) REVERT: A 159 VAL cc_start: 0.7347 (t) cc_final: 0.7005 (t) REVERT: A 170 TYR cc_start: 0.8038 (t80) cc_final: 0.7811 (t80) REVERT: A 392 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.4032 (m-80) REVERT: A 452 ARG cc_start: 0.6783 (mmm-85) cc_final: 0.6416 (mtp85) REVERT: A 571 ASP cc_start: 0.7135 (m-30) cc_final: 0.6818 (t0) REVERT: A 858 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8967 (mt) REVERT: A 900 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8316 (mtm) REVERT: A 979 ASP cc_start: 0.7959 (t0) cc_final: 0.7585 (t0) REVERT: A 983 ARG cc_start: 0.7428 (mtp180) cc_final: 0.7077 (mtp180) REVERT: B 35 GLU cc_start: 0.6324 (mt-10) cc_final: 0.5982 (tp30) REVERT: B 41 TYR cc_start: 0.5685 (m-10) cc_final: 0.5480 (m-10) REVERT: B 50 TYR cc_start: 0.7807 (t80) cc_final: 0.7586 (t80) REVERT: B 82 MET cc_start: 0.7937 (mmm) cc_final: 0.6017 (ptt) REVERT: B 398 GLU cc_start: 0.3834 (mp0) cc_final: 0.3096 (pm20) REVERT: B 482 ARG cc_start: 0.5313 (mtm180) cc_final: 0.5002 (mtm110) REVERT: D 164 ASN cc_start: 0.5584 (p0) cc_final: 0.5032 (p0) REVERT: D 541 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.5820 (m-80) REVERT: D 964 LYS cc_start: 0.8828 (tttp) cc_final: 0.8564 (ttmm) REVERT: D 1119 ASN cc_start: 0.8224 (m110) cc_final: 0.7997 (p0) outliers start: 64 outliers final: 49 residues processed: 355 average time/residue: 0.4246 time to fit residues: 251.7685 Evaluate side-chains 345 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 266 optimal weight: 0.0470 chunk 287 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 370 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 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 = 0.4300 r_free = 0.4300 target = 0.152074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.122342 restraints weight = 82089.948| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.85 r_work: 0.3728 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30486 Z= 0.139 Angle : 0.575 12.163 41480 Z= 0.297 Chirality : 0.044 0.293 4616 Planarity : 0.004 0.058 5375 Dihedral : 4.297 29.127 4050 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.09 % Allowed : 17.32 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.58 (0.14), residues: 3733 helix: 0.98 (0.17), residues: 1007 sheet: -0.08 (0.19), residues: 745 loop : -1.25 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 353 HIS 0.003 0.001 HIS B 228 PHE 0.027 0.001 PHE C 823 TYR 0.017 0.001 TYR A1138 ARG 0.010 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 1122) hydrogen bonds : angle 4.87876 ( 3141) SS BOND : bond 0.00469 ( 42) SS BOND : angle 1.99088 ( 84) covalent geometry : bond 0.00323 (30444) covalent geometry : angle 0.56818 (41396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 299 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 ILE cc_start: 0.7714 (mt) cc_final: 0.7479 (mm) REVERT: C 238 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.5158 (p90) REVERT: C 357 ARG cc_start: 0.5916 (ttt180) cc_final: 0.5495 (mpt-90) REVERT: C 572 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.7962 (p) REVERT: C 740 MET cc_start: 0.8398 (mmm) cc_final: 0.7691 (mtt) REVERT: C 1047 TYR cc_start: 0.8851 (m-80) cc_final: 0.7998 (m-80) REVERT: A 159 VAL cc_start: 0.7413 (t) cc_final: 0.7072 (t) REVERT: A 170 TYR cc_start: 0.8066 (t80) cc_final: 0.7839 (t80) REVERT: A 214 ARG cc_start: 0.6020 (mmm160) cc_final: 0.5738 (mmm160) REVERT: A 392 PHE cc_start: 0.5588 (OUTLIER) cc_final: 0.4282 (m-80) REVERT: A 571 ASP cc_start: 0.7310 (m-30) cc_final: 0.7109 (t0) REVERT: A 858 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8960 (mt) REVERT: A 900 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8320 (mtm) REVERT: A 979 ASP cc_start: 0.7932 (t0) cc_final: 0.7550 (t0) REVERT: A 983 ARG cc_start: 0.7453 (mtp180) cc_final: 0.7105 (mtp180) REVERT: B 35 GLU cc_start: 0.6400 (mt-10) cc_final: 0.6023 (tp30) REVERT: B 41 TYR cc_start: 0.5692 (m-10) cc_final: 0.5453 (m-10) REVERT: B 50 TYR cc_start: 0.7814 (t80) cc_final: 0.7443 (t80) REVERT: B 82 MET cc_start: 0.7871 (mmm) cc_final: 0.6051 (ptt) REVERT: B 482 ARG cc_start: 0.5361 (mtm180) cc_final: 0.5033 (mtm110) REVERT: D 164 ASN cc_start: 0.5699 (p0) cc_final: 0.5126 (p0) REVERT: D 186 PHE cc_start: 0.6332 (m-80) cc_final: 0.6085 (m-10) REVERT: D 541 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5936 (m-80) REVERT: D 774 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8208 (mm-40) REVERT: D 776 LYS cc_start: 0.8350 (tttp) cc_final: 0.8071 (tttp) REVERT: D 964 LYS cc_start: 0.8850 (tttp) cc_final: 0.8591 (ttmm) REVERT: D 1019 ARG cc_start: 0.8166 (tpt170) cc_final: 0.7825 (tpt170) outliers start: 69 outliers final: 58 residues processed: 342 average time/residue: 0.3936 time to fit residues: 224.9626 Evaluate side-chains 357 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 293 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 366 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 342 optimal weight: 4.9990 chunk 170 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 354 optimal weight: 1.9990 chunk 376 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 350 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 544 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 HIS D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.154655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.124556 restraints weight = 83710.691| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.83 r_work: 0.3755 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 30486 Z= 0.108 Angle : 0.542 11.728 41480 Z= 0.278 Chirality : 0.043 0.293 4616 Planarity : 0.004 0.056 5375 Dihedral : 4.054 26.863 4050 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.64 % Allowed : 17.87 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.44 (0.14), residues: 3733 helix: 1.11 (0.17), residues: 1010 sheet: 0.08 (0.19), residues: 739 loop : -1.20 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 353 HIS 0.005 0.001 HIS D1048 PHE 0.027 0.001 PHE C 823 TYR 0.016 0.001 TYR B 516 ARG 0.007 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 1122) hydrogen bonds : angle 4.68660 ( 3141) SS BOND : bond 0.00419 ( 42) SS BOND : angle 1.73688 ( 84) covalent geometry : bond 0.00248 (30444) covalent geometry : angle 0.53669 (41396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17153.92 seconds wall clock time: 301 minutes 33.08 seconds (18093.08 seconds total)